Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000002.1 Hibiscus syriacus cultivar Beakdansim tig00000003_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: 2131600
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 10
Found at i:1911439 original size:15 final size:16
Alignment explanation
Indices: 1911419--1911448 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1911409 TACTTATCTT
1911419 ATTTTATT-TTTTTTC
1 ATTTTATTATTTTTTC
1911434 ATTTTATTATTTTTT
1 ATTTTATTATTTTTT
1911449 GTTTTGAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (16 bp):
ATTTTATTATTTTTTC
Found at i:1912750 original size:24 final size:24
Alignment explanation
Indices: 1912706--1912760 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
1912696 ACGAGTCCAT
*
1912706 TAAAAATATTTTTTAAATTAAACA
1 TAAAAATATTTTATAAATTAAACA
* *
1912730 TAAAAATGA-TTTATAATTTAAAGA
1 TAAAAAT-ATTTTATAAATTAAACA
*
1912754 AAAAAAT
1 TAAAAAT
1912761 TAGGGCGAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 25 0.96
25 1 0.04
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (24 bp):
TAAAAATATTTTATAAATTAAACA
Found at i:1916185 original size:20 final size:21
Alignment explanation
Indices: 1916148--1916187 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1916138 AAATTAAGTT
1916148 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
1916169 AAATG-ATTTTACA-ATTTTA
1 AAATGAATTTTA-AGATTTTA
1916188 TATTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
AAATGAATTTTAAGATTTTAC
Found at i:1916473 original size:65 final size:64
Alignment explanation
Indices: 1916357--1916565 Score: 217
Period size: 65 Copynumber: 3.2 Consensus size: 64
1916347 ATTTGAGGTG
* * * *
1916357 ATGCACCGATGCATCAA-CCATGCATCGATGCA-TTAGCGAAT-TAATTGAAACATCGAATGCAT
1 ATGCATCGATGCA-CAAGCCATGCATCGATGCACTCA--GAATAT-TTTCAAACATCGAATGCAT
*
1916419 TCC
62 TTC
* **** * *
1916422 ATGCACCGATGCATTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTTG
1 ATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTC-AAACATCGAATGCATTTC
** *
1916487 ATGCATCGATGCACAAGCCATGCATCGATGCACTCAGGCTATTTTCAAACATCGAATGTATTTC
1 ATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAAACATCGAATGCATTTC
1916551 ATGCATCGATGCACA
1 ATGCATCGATGCACA
1916566 CTTGGTGCAT
Statistics
Matches: 121, Mismatches: 19, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
64 37 0.31
65 83 0.69
66 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (64 bp):
ATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAAACATCGAATGCATTTC
Found at i:1916575 original size:64 final size:65
Alignment explanation
Indices: 1916404--1916582 Score: 225
Period size: 65 Copynumber: 2.8 Consensus size: 65
1916394 GAATTAATTG
* * ** *
1916404 AAACATCGAATGCATTCCATGCACCGATGCATTCTCCATGCATCGATGCACTCTGAATATTTTCA
1 AAACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCA
* ** **
1916469 AAACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCACTCAGGCTATTTTC-
1 AAACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCA
* ***
1916533 AAACATCGAATGTATTTCATGCATCGATGCACACTTGGTGCATCGATGCA
1 AAACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCA
1916583 TCAAGTGTTC
Statistics
Matches: 97, Mismatches: 17, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
64 43 0.44
65 54 0.56
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (65 bp):
AAACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCA
Found at i:1922400 original size:44 final size:42
Alignment explanation
Indices: 1922344--1922467 Score: 131
Period size: 44 Copynumber: 2.8 Consensus size: 42
1922334 TTTGTGCTTC
* * *
1922344 ATGCACCGATGCATTTAACAATGCATCGATGCATCCCTTTGAAT
1 ATGCATCGATGCA-TAAACAATGCACCGATGCATCCC-TTGAAT
* * * *
1922388 ATGTATCGATGCATCACCATGATGCACCGATGCATGCCTTGAAT
1 ATGCATCGATGCATAAACA--ATGCACCGATGCATCCCTTGAAT
*
1922432 ATGCATCGATGCATAAGACCATGCACCGATGCATCC
1 ATGCATCGATGCATAA-ACAATGCACCGATGCATCC
1922468 GTCGGGTTTT
Statistics
Matches: 66, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
43 19 0.29
44 31 0.47
45 16 0.24
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.26
Consensus pattern (42 bp):
ATGCATCGATGCATAAACAATGCACCGATGCATCCCTTGAAT
Found at i:1923739 original size:20 final size:21
Alignment explanation
Indices: 1923702--1923741 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1923692 AAATTAAGTT
1923702 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
1923723 AAATG-ATTTTACA-ATTTTA
1 AAATGAATTTTA-AGATTTTA
1923742 TATTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
AAATGAATTTTAAGATTTTAC
Found at i:1923950 original size:18 final size:18
Alignment explanation
Indices: 1923911--1923963 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
1923901 ATTTGAGGTG
* *
1923911 ATGCACCGATGCATCAACC
1 ATGCATCGATGCAT-TACC
1923930 ATGCATCGATGCATTACC
1 ATGCATCGATGCATTACC
1923948 ATGCATCGATGCATTA
1 ATGCATCGATGCATTA
1923964 GTGAATTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
18 19 0.59
19 13 0.41
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (18 bp):
ATGCATCGATGCATTACC
Found at i:1924046 original size:65 final size:63
Alignment explanation
Indices: 1923928--1924135 Score: 229
Period size: 65 Copynumber: 3.2 Consensus size: 63
1923918 GATGCATCAA
* * * *
1923928 CCATGCATCGATGCATTACCATGCATCGATGCATTAGTGAAT-TAATTGAAACATCGAATGCATT
1 CCATGCATCGATGCATTACCATGCATCGATGCACT-CTGAATAT-TTTCAAACATCGAATGCATT
* *
1923992 CCATGCACCGATGCATTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATT
1 CCATGCATCGATGCATT-ACCATGCATCGATGCACTCTGAATATTTTC-AAACATCGAATGCATT
** ** * * **
1924057 TGATGCATCGATGCACAAGCCATGCATCGATACACTCAGGCTATTTTCAAACATCGAATGCATT
1 CCATGCATCGATGCATTA-CCATGCATCGATGCACTCTGAATATTTTCAAACATCGAATGCATT
*
1924121 TCATGCATCGATGCA
1 CCATGCATCGATGCA
1924136 CACTTGGTGC
Statistics
Matches: 123, Mismatches: 17, Indels: 8
0.83 0.11 0.05
Matches are distributed among these distances:
64 53 0.43
65 70 0.57
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (63 bp):
CCATGCATCGATGCATTACCATGCATCGATGCACTCTGAATATTTTCAAACATCGAATGCATT
Found at i:1930538 original size:22 final size:22
Alignment explanation
Indices: 1930493--1930569 Score: 138
Period size: 22 Copynumber: 3.5 Consensus size: 22
1930483 GAATTCATGA
*
1930493 GGGGGAATCGGTACTCCCTT-G
1 GGGGGAATCGGTACCCCCTTGG
1930514 GGGGGAATCGGTACCCCCTTGG
1 GGGGGAATCGGTACCCCCTTGG
1930536 GGGGGAATCGGTACCCCCTTGG
1 GGGGGAATCGGTACCCCCTTGG
1930558 GGGGGAATCGGT
1 GGGGGAATCGGT
1930570 TCCCTCTGAG
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
21 19 0.35
22 35 0.65
ACGTcount: A:0.14, C:0.23, G:0.43, T:0.19
Consensus pattern (22 bp):
GGGGGAATCGGTACCCCCTTGG
Found at i:1939083 original size:24 final size:24
Alignment explanation
Indices: 1939039--1939085 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1939029 ATAAAGAACC
*
1939039 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
1939063 AAAATAAAGTTTAAACA-ACCATT
1 AAAATAAA-CTTAAACATACCATT
1939086 CAACCAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:1942268 original size:20 final size:19
Alignment explanation
Indices: 1942239--1942276 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1942229 AAAGGTAAAG
1942239 TTAAAATGAAAGAGAAAAA
1 TTAAAATGAAAGAGAAAAA
*
1942258 TTAATAATGAAAGATAAAA
1 TTAA-AATGAAAGAGAAAA
1942277 GAAAAAGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.66, C:0.00, G:0.13, T:0.21
Consensus pattern (19 bp):
TTAAAATGAAAGAGAAAAA
Found at i:1949160 original size:24 final size:24
Alignment explanation
Indices: 1949116--1949162 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1949106 ATAAAGAACC
*
1949116 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
1949140 AAAATAAAGTTTAAACA-ACCATT
1 AAAATAAA-CTTAAACATACCATT
1949163 CAACCAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:1951292 original size:56 final size:53
Alignment explanation
Indices: 1951193--1951304 Score: 161
Period size: 56 Copynumber: 2.1 Consensus size: 53
1951183 ACCCACGTAG
*
1951193 TGAGTTTTTGTTCTTTGTTTAATTATTATGTTTATAGTACTTGTCTGTGTTCT
1 TGAGTTTTTGTTCTTTGTTTAATTATTATGCTTATAGTACTTGTCTGTGTTCT
* * *
1951246 TGAGTTTTTGTTCTTTGTTTGTTAATTGTTATGCTTATAGTGCTTGTGTGTGTTCT
1 TGAGTTTTTGTTCTTTG--T-TTAATTATTATGCTTATAGTACTTGTCTGTGTTCT
1951302 TGA
1 TGA
1951305 TATTTTTATA
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
53 17 0.33
55 1 0.02
56 34 0.65
ACGTcount: A:0.13, C:0.07, G:0.21, T:0.59
Consensus pattern (53 bp):
TGAGTTTTTGTTCTTTGTTTAATTATTATGCTTATAGTACTTGTCTGTGTTCT
Found at i:1954117 original size:19 final size:20
Alignment explanation
Indices: 1954093--1954138 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
1954083 TGCTATCTCA
1954093 TTCCTT-AAAATTTTTAAAT
1 TTCCTTGAAAATTTTTAAAT
* *
1954112 TTCCTTGTATATTTTTAAAT
1 TTCCTTGAAAATTTTTAAAT
1954132 TTCCTTG
1 TTCCTTG
1954139 TATTTTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.26, C:0.13, G:0.04, T:0.57
Consensus pattern (20 bp):
TTCCTTGAAAATTTTTAAAT
Found at i:1954127 original size:20 final size:20
Alignment explanation
Indices: 1954102--1954141 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1954092 ATTCCTTAAA
1954102 ATTTTTAAATTTCCTTGTAT
1 ATTTTTAAATTTCCTTGTAT
1954122 ATTTTTAAATTTCCTTGTAT
1 ATTTTTAAATTTCCTTGTAT
1954142 TTTAAATATT
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:0.25, C:0.10, G:0.05, T:0.60
Consensus pattern (20 bp):
ATTTTTAAATTTCCTTGTAT
Found at i:1957169 original size:42 final size:42
Alignment explanation
Indices: 1957101--1957185 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 42
1957091 ATATCAAACT
* * *
1957101 ATTTAAATATATTTATGCACTTAATATTCTCTAATTGATGAG
1 ATTTAAATATATTTATACACTAAATATTATCTAATTGATGAG
* *
1957143 ATTTAAATATATTTATACAGTAAATATTATCTAATTTATGAG
1 ATTTAAATATATTTATACACTAAATATTATCTAATTGATGAG
1957185 A
1 A
1957186 ATAAGAAGTG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.45
Consensus pattern (42 bp):
ATTTAAATATATTTATACACTAAATATTATCTAATTGATGAG
Found at i:1969188 original size:32 final size:32
Alignment explanation
Indices: 1969121--1969190 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
1969111 GTGACATTGG
* * *
1969121 CTCTATTGTGCATTATCTTAATGACATGCTAA
1 CTCTGTTGTGCATTATCTGAATGACATACTAA
*
1969153 CTCTGTTGTGCATTATCTGAATG-CAATACTGA
1 CTCTGTTGTGCATTATCTGAATGAC-ATACTAA
1969185 CTCTGT
1 CTCTGT
1969191 AGTGACTCGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 1 0.03
32 32 0.97
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (32 bp):
CTCTGTTGTGCATTATCTGAATGACATACTAA
Found at i:1970371 original size:20 final size:20
Alignment explanation
Indices: 1970346--1970396 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
1970336 GAAGGGGCAA
1970346 TATCGATACTCCTTTAGAAG
1 TATCGATACTCCTTTAGAAG
1970366 TATCGATACTCCTTTAGAAG
1 TATCGATACTCCTTTAGAAG
1970386 TATCGATACTC
1 TATCGATACTC
1970397 TCTGCCCAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (20 bp):
TATCGATACTCCTTTAGAAG
Found at i:1976005 original size:20 final size:21
Alignment explanation
Indices: 1975972--1976011 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
1975962 AGACTAAAGG
*
1975972 GGCAGTATTAATACT-TCTTT
1 GGCAGTATCAATACTCTCTTT
*
1975992 GGCAGTATCGATACTCTCTT
1 GGCAGTATCAATACTCTCTT
1976012 CCTATAAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40
Consensus pattern (21 bp):
GGCAGTATCAATACTCTCTTT
Found at i:1979142 original size:83 final size:83
Alignment explanation
Indices: 1979003--1979168 Score: 332
Period size: 83 Copynumber: 2.0 Consensus size: 83
1978993 AACCCATATC
1979003 CCTTAACACATCAAAACAACAATAACAATACTATTAGCATCCACCTAAACTAGGGGGGATAAGTA
1 CCTTAACACATCAAAACAACAATAACAATACTATTAGCATCCACCTAAACTAGGGGGGATAAGTA
1979068 GATCATGGATTAGTGCAT
66 GATCATGGATTAGTGCAT
1979086 CCTTAACACATCAAAACAACAATAACAATACTATTAGCATCCACCTAAACTAGGGGGGATAAGTA
1 CCTTAACACATCAAAACAACAATAACAATACTATTAGCATCCACCTAAACTAGGGGGGATAAGTA
1979151 GATCATGGATTAGTGCAT
66 GATCATGGATTAGTGCAT
1979169 AGGACCATAA
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 83 1.00
ACGTcount: A:0.41, C:0.20, G:0.16, T:0.23
Consensus pattern (83 bp):
CCTTAACACATCAAAACAACAATAACAATACTATTAGCATCCACCTAAACTAGGGGGGATAAGTA
GATCATGGATTAGTGCAT
Found at i:1979481 original size:152 final size:153
Alignment explanation
Indices: 1979141--1979493 Score: 417
Period size: 154 Copynumber: 2.3 Consensus size: 153
1979131 TAAACTAGGG
* * *
1979141 GGGATAAGTAGATCATGGATTAGTGCATAGGACCATAACCCAACAAGCCAAGAAAAAATCATCAT
1 GGGATAAGTAG--CATAGATTAGTGCATACGACCATAACCTAACAAGCCAAGAAAAAATCATCAT
* * *
1979206 ATCAAAGAGATGATATTATTAAGATTCGAATGTAAATTTCACATACGATTATATATTCAAATGTA
64 ATCAAAGAGATGATATTATTAAGATTCGAATGTAAATTTCAAATACGAATATATATTCAAATATA
*
1979271 ATGTTTTATATACATATGAAAAAATA
129 A-GTTTTATATACATATAAAAAAATA
* * * * *
1979297 GGGATAAGTAGCACAGATTAATGCATACGACCATAACCTAACAAGCCAAGAAAAATTTATCATGT
1 GGGATAAGTAGCATAGATTAGTGCATACGACCATAACCTAACAAGCCAAGAAAAAATCATCATAT
* * * ** * * * **
1979362 TAAA-AGGTTATATTATTCGGATTTGAATGTATATTTTAAATATTAATATGA-ATTCAAATATAA
66 CAAAGAGATGATATTATTAAGATTCGAATGTAAATTTCAAATACGAATAT-ATATTCAAATATAA
1979425 -TTTTATATACATAATAAAAAAACTA
130 GTTTTATATACAT-ATAAAAAAA-TA
*
1979450 -GGATAAGTAGCATAGATTAGTGCATATGACCATAACCTAACAAG
1 GGGATAAGTAGCATAGATTAGTGCATACGACCATAACCTAACAAG
1979494 GTAGGGAAAG
Statistics
Matches: 169, Mismatches: 25, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
151 12 0.07
152 49 0.29
153 47 0.28
154 50 0.30
156 11 0.07
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.30
Consensus pattern (153 bp):
GGGATAAGTAGCATAGATTAGTGCATACGACCATAACCTAACAAGCCAAGAAAAAATCATCATAT
CAAAGAGATGATATTATTAAGATTCGAATGTAAATTTCAAATACGAATATATATTCAAATATAAG
TTTTATATACATATAAAAAAATA
Found at i:1983110 original size:31 final size:32
Alignment explanation
Indices: 1983070--1983130 Score: 83
Period size: 31 Copynumber: 1.9 Consensus size: 32
1983060 AGGTAAAATA
1983070 TATACTTTTAATA-ACTAAACTATTA-ATTTTAT
1 TATACTTTTAATATA-TAAACT-TTAGATTTTAT
1983102 TATA-TTTTAATATATAAACTTTAGATTTT
1 TATACTTTTAATATATAAACTTTAGATTTT
1983131 TTTAAACTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
30 3 0.11
31 19 0.70
32 5 0.19
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (32 bp):
TATACTTTTAATATATAAACTTTAGATTTTAT
Found at i:1983429 original size:13 final size:13
Alignment explanation
Indices: 1983406--1983431 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1983396 CTAAAATAAT
1983406 AAAATTAAATTTA
1 AAAATTAAATTTA
1983419 AAAATTAAATTTA
1 AAAATTAAATTTA
1983432 TACTCAAACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AAAATTAAATTTA
Found at i:1987919 original size:21 final size:21
Alignment explanation
Indices: 1987889--1987928 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1987879 TAAAATAAAA
* *
1987889 TTTAACTTAATATATTATATT
1 TTTAACTTAAAAAATTATATT
*
1987910 TTTAATTTAAAAAATTATA
1 TTTAACTTAAAAAATTATA
1987929 CAATTGATAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (21 bp):
TTTAACTTAAAAAATTATATT
Found at i:1988341 original size:2 final size:2
Alignment explanation
Indices: 1988324--1988364 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
1988314 TTTGAGCACC
* *
1988324 AT AT AT AC AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1988365 AGCATTATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:1988567 original size:21 final size:21
Alignment explanation
Indices: 1988543--1988583 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1988533 ATAACTGTCA
1988543 ATTTTTTAACATTAAATATTT
1 ATTTTTTAACATTAAATATTT
1988564 ATTTTTTAACATTAAATATT
1 ATTTTTTAACATTAAATATT
1988584 CACAATCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTTTTTAACATTAAATATTT
Found at i:1988805 original size:3 final size:3
Alignment explanation
Indices: 1988797--1988883 Score: 146
Period size: 3 Copynumber: 30.3 Consensus size: 3
1988787 TATGATTTTG
1988797 ATA ATA ATA ATA AT- ATA ATA AT- ATA ATA ATA AT- ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1988842 ATA ATA ATA ATA ATA ATA A-A ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1988884 CAACAACAAC
Statistics
Matches: 80, Mismatches: 0, Indels: 8
0.91 0.00 0.09
Matches are distributed among these distances:
2 8 0.10
3 72 0.90
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1989863 original size:23 final size:22
Alignment explanation
Indices: 1989821--1989866 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
1989811 CTACCCTTTA
*
1989821 TTTTAATAATTTACTTTTAATT
1 TTTTAATAATTTACTATTAATT
1989843 TTTTAACTAATTTA-TAATTAATT
1 TTTTAA-TAATTTACT-ATTAATT
1989866 T
1 T
1989867 ATAATTATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (22 bp):
TTTTAATAATTTACTATTAATT
Found at i:1993144 original size:20 final size:19
Alignment explanation
Indices: 1993095--1993146 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 19
1993085 ATAAATTACA
*
1993095 AGGCAACAACAGGCAGCAAC
1 AGGC-ACAACATGCAGCAAC
*
1993115 AGGCAC--CATGCGGCAAC
1 AGGCACAACATGCAGCAAC
1993132 AGGCAGCAACATGCA
1 AGGCA-CAACATGCA
1993147 ACATTTATGC
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
17 14 0.54
18 1 0.04
19 2 0.08
20 9 0.35
ACGTcount: A:0.38, C:0.31, G:0.27, T:0.04
Consensus pattern (19 bp):
AGGCACAACATGCAGCAAC
Found at i:1996057 original size:18 final size:18
Alignment explanation
Indices: 1996036--1996074 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1996026 TTAAGTTTAA
* * *
1996036 GTTCATGTTTGGGTTTGG
1 GTTCAGGTTCGGGTTCGG
1996054 GTTCAGGTTCGGGTTCGG
1 GTTCAGGTTCGGGTTCGG
1996072 GTT
1 GTT
1996075 TATATTTAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.05, C:0.10, G:0.41, T:0.44
Consensus pattern (18 bp):
GTTCAGGTTCGGGTTCGG
Found at i:1996834 original size:12 final size:12
Alignment explanation
Indices: 1996795--1996863 Score: 58
Period size: 12 Copynumber: 6.0 Consensus size: 12
1996785 TTCATCCCTA
*
1996795 TATAATTTATAT
1 TATAATTAATAT
*
1996807 TATAA--ACTATT
1 TATAATTAATA-T
1996818 TATAATTAATAT
1 TATAATTAATAT
1996830 TATAATTAATAT
1 TATAATTAATAT
*
1996842 TA-ATATTAA-CT
1 TATA-ATTAATAT
1996853 TAT-ATTAATAT
1 TATAATTAATAT
1996864 AATATAGTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
10 7 0.15
11 11 0.24
12 25 0.54
13 3 0.07
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (12 bp):
TATAATTAATAT
Found at i:1996839 original size:16 final size:16
Alignment explanation
Indices: 1996817--1996863 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 16
1996807 TATAAACTAT
1996817 TTATAATTAATATTATAA
1 TTAT-ATTAATATTA-AA
*
1996835 TTAATATTAATATTAAC
1 TT-ATATTAATATTAAA
1996852 TTATATTAATAT
1 TTATATTAATAT
1996864 AATATAGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 10 0.37
17 3 0.11
18 12 0.44
19 2 0.07
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (16 bp):
TTATATTAATATTAAA
Found at i:1997036 original size:15 final size:15
Alignment explanation
Indices: 1997018--1997068 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
1997008 AACTATATGC
1997018 TATATTAATATAAAT
1 TATATTAATATAAAT
*
1997033 TATAGTTAAGAT-AAT
1 TATA-TTAATATAAAT
* *
1997048 TAACATTAATATAAAC
1 T-ATATTAATATAAAT
1997064 TATAT
1 TATAT
1997069 AGCACATTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
15 17 0.61
16 11 0.39
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (15 bp):
TATATTAATATAAAT
Found at i:1997116 original size:21 final size:21
Alignment explanation
Indices: 1997092--1997131 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1997082 AAATTGTAGT
* *
1997092 TTATAAATTATATACTATAGG
1 TTATAAAGTATAAACTATAGG
1997113 TTATAAAGTATAAACTATA
1 TTATAAAGTATAAACTATA
1997132 TAGTACACTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.40
Consensus pattern (21 bp):
TTATAAAGTATAAACTATAGG
Found at i:1997316 original size:19 final size:19
Alignment explanation
Indices: 1997292--1997328 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1997282 ATGACCAACA
*
1997292 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
1997311 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
1997329 CAGTATCGCA
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:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:1997701 original size:21 final size:22
Alignment explanation
Indices: 1997655--1997704 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
1997645 CTACGGTGAC
1997655 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
*
1997677 ATCCGTCCCCATCTCCGGC-AA
1 ATCCGTCCCCATCTCCGACGAA
1997698 ATCCGTC
1 ATCCGTC
1997705 TATCTCCATC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 9 0.33
22 18 0.67
ACGTcount: A:0.20, C:0.46, G:0.14, T:0.20
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:1998153 original size:20 final size:20
Alignment explanation
Indices: 1998104--1998177 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 20
1998094 GCGATTTTAG
*
1998104 TTTCGCGTTGCGATAGTCAA
1 TTTCGCGTTGCGATAGTCAT
* *
1998124 ATTAGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
* **
1998144 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATAGTCAT
*
1998164 TTTCGTGTTGCGAT
1 TTTCGCGTTGCGAT
1998178 TTTAAGTTTC
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.16, C:0.16, G:0.24, T:0.43
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:1998187 original size:20 final size:20
Alignment explanation
Indices: 1998144--1998187 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1998134 CGATAGTCAT
* *
1998144 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
1998164 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
1998184 TTTC
1 TTTC
1998188 AGAAACTATT
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:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:2000107 original size:20 final size:20
Alignment explanation
Indices: 2000080--2000148 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 20
2000070 GAAACTTAAA
2000080 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
2000100 ATCACAACGCGGAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
2000120 ATCGCAACACGAATTTGACT
1 ATCGCAACGCGAAAATGACT
2000140 ATCGCAACG
1 ATCGCAACG
2000149 AGATAATCGC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.38, C:0.26, G:0.19, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:2000179 original size:33 final size:34
Alignment explanation
Indices: 2000140--2000214 Score: 116
Period size: 33 Copynumber: 2.2 Consensus size: 34
2000130 GAATTTGACT
*
2000140 ATCGCAACGAGATAATCGCAATGCG-AAATAAAA
1 ATCGCAACGAGAAAATCGCAATGCGAAAATAAAA
* *
2000173 ATCGCAATGTGAAAATCGCAATGCGAAAATAAAA
1 ATCGCAACGAGAAAATCGCAATGCGAAAATAAAA
2000207 ATCGCAAC
1 ATCGCAAC
2000215 ACAAATTTAG
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 22 0.59
34 15 0.41
ACGTcount: A:0.48, C:0.19, G:0.17, T:0.16
Consensus pattern (34 bp):
ATCGCAACGAGAAAATCGCAATGCGAAAATAAAA
Found at i:2000189 original size:14 final size:14
Alignment explanation
Indices: 2000170--2000202 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
2000160 ATGCGAAATA
*
2000170 AAAATCGCAATGTG
1 AAAATCGCAATGCG
2000184 AAAATCGCAATGCG
1 AAAATCGCAATGCG
2000198 AAAAT
1 AAAAT
2000203 AAAAATCGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.48, C:0.15, G:0.18, T:0.18
Consensus pattern (14 bp):
AAAATCGCAATGCG
Found at i:2000255 original size:20 final size:20
Alignment explanation
Indices: 2000230--2000278 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
2000220 TTTAGTTTCG
2000230 CGTTGCGATAGTCATTTCCA
1 CGTTGCGATAGTCATTTCCA
* *
2000250 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTCCA
2000270 CGTTGCGAT
1 CGTTGCGAT
2000279 TTTAAGTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCA
Found at i:2000288 original size:20 final size:20
Alignment explanation
Indices: 2000265--2000308 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
2000255 CGATAGTCAT
2000265 TTTCGCGTTGCGATTTTAAG
1 TTTCGCGTTGCGATTTTAAG
*
2000285 TTTCGTGTTGCGATTTTAAG
1 TTTCGCGTTGCGATTTTAAG
2000305 TTTC
1 TTTC
2000309 AGAAACTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.14, C:0.14, G:0.23, T:0.50
Consensus pattern (20 bp):
TTTCGCGTTGCGATTTTAAG
Found at i:2000860 original size:42 final size:43
Alignment explanation
Indices: 2000814--2000906 Score: 120
Period size: 42 Copynumber: 2.2 Consensus size: 43
2000804 CTCTCCTATC
2000814 GTTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCCTCCCA-CA
1 GTTCAAGAGGCCCCTATCATCCCTCAAGAGGT-CCCTCCCACCA
* ** *
2000856 GTTCAAGAGGCCCCTGTCATCGTTGAAGAGGTCCCTCCCACCA
1 GTTCAAGAGGCCCCTATCATCCCTCAAGAGGTCCCTCCCACCA
2000899 -TTCAAGAG
1 GTTCAAGAG
2000907 CCCGATTCAC
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
42 41 0.91
43 4 0.09
ACGTcount: A:0.24, C:0.37, G:0.19, T:0.20
Consensus pattern (43 bp):
GTTCAAGAGGCCCCTATCATCCCTCAAGAGGTCCCTCCCACCA
Found at i:2000884 original size:21 final size:21
Alignment explanation
Indices: 2000784--2000891 Score: 85
Period size: 21 Copynumber: 5.1 Consensus size: 21
2000774 GCCCGACTCA
*
2000784 CCTGTCATCGTTCAAGAGACC
1 CCTGTCATCGTTCAAGAGGCC
* *
2000805 TCT-CCTATCGTTCAAGAGGCC
1 CCTGTC-ATCGTTCAAGAGGCC
* ** *
2000826 CCTATCATCCCTCAAGAGTCC
1 CCTGTCATCGTTCAAGAGGCC
**
2000847 CCTCCCA-CAGTTCAAGAGGCC
1 CCTGTCATC-GTTCAAGAGGCC
* *
2000868 CCTGTCATCGTTGAAGAGGTC
1 CCTGTCATCGTTCAAGAGGCC
2000889 CCT
1 CCT
2000892 CCCACCATTC
Statistics
Matches: 66, Mismatches: 17, Indels: 8
0.73 0.19 0.09
Matches are distributed among these distances:
20 2 0.03
21 62 0.94
22 2 0.03
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (21 bp):
CCTGTCATCGTTCAAGAGGCC
Found at i:2000905 original size:21 final size:20
Alignment explanation
Indices: 2000837--2000906 Score: 52
Period size: 21 Copynumber: 3.4 Consensus size: 20
2000827 CTATCATCCC
2000837 TCAAGA-GTCCCCTCCCACAGT
1 TCAAGAGGT-CCCTCCCACA-T
* ** *
2000858 TCAAGAGGCCCCTGTCATCGT
1 TCAAGAGGTCCCTCCCA-CAT
*
2000879 TGAAGAGGTCCCTCCCACCAT
1 TCAAGAGGTCCCTCCCA-CAT
2000900 TCAAGAG
1 TCAAGAG
2000907 CCCGATTCAC
Statistics
Matches: 36, Mismatches: 11, Indels: 4
0.71 0.22 0.08
Matches are distributed among these distances:
21 34 0.94
22 2 0.06
ACGTcount: A:0.24, C:0.36, G:0.20, T:0.20
Consensus pattern (20 bp):
TCAAGAGGTCCCTCCCACAT
Found at i:2002308 original size:14 final size:14
Alignment explanation
Indices: 2002289--2002325 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
2002279 GCTTGTTTAA
2002289 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
2002303 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
2002317 TTGATTTGT
1 TTGATTTGT
2002326 TTAATTGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:2002484 original size:20 final size:20
Alignment explanation
Indices: 2002459--2002522 Score: 110
Period size: 20 Copynumber: 3.2 Consensus size: 20
2002449 AACGCTAAAC
2002459 TCAAAATCGCAATGCGAAAG
1 TCAAAATCGCAATGCGAAAG
2002479 TCAAAATCGCAATGCGAAAG
1 TCAAAATCGCAATGCGAAAG
* *
2002499 CCAAAATCGCAACGCGAAAG
1 TCAAAATCGCAATGCGAAAG
2002519 TCAA
1 TCAA
2002523 TTCACGTTGC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.45, C:0.23, G:0.19, T:0.12
Consensus pattern (20 bp):
TCAAAATCGCAATGCGAAAG
Found at i:2002586 original size:20 final size:20
Alignment explanation
Indices: 2002561--2002691 Score: 157
Period size: 20 Copynumber: 6.8 Consensus size: 20
2002551 GCGATTTTCT
*
2002561 CGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCG
* *
2002581 CGTTGCGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCG
2002601 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
2002621 CGTTTCGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
*
2002635 CGTTGCGATAGTCAAATTAG
1 CGTTGCGATAGTCAAATTCG
2002655 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
2002675 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
2002692 GAATGTGTAA
Statistics
Matches: 95, Mismatches: 10, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
14 11 0.12
16 1 0.01
18 1 0.01
20 82 0.86
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:2002587 original size:34 final size:34
Alignment explanation
Indices: 2002527--2002663 Score: 141
Period size: 34 Copynumber: 3.9 Consensus size: 34
2002517 AGTCAATTCA
* * *
2002527 CGTTGCGATAGTCTAATACGCTTTGCGATTTTCT
1 CGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT
* *
2002561 CGTTGCGATAGTCAAATTCCCGTTGCGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCGCGTTGCGAT--T----TTCT
*
2002601 CGTTGCGATAGTCAAATTCGCGTTTCGATTTT-T
1 CGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT
*
2002634 GCGTTGCGATAGTCAAATTAGCGTTGCGAT
1 -CGTTGCGATAGTCAAATTCGCGTTGCGAT
2002664 AGTCAAATTC
Statistics
Matches: 86, Mismatches: 10, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
34 54 0.63
36 1 0.01
38 1 0.01
40 30 0.35
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.36
Consensus pattern (34 bp):
CGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT
Found at i:2002610 original size:74 final size:74
Alignment explanation
Indices: 2002521--2002691 Score: 247
Period size: 74 Copynumber: 2.3 Consensus size: 74
2002511 CGCGAAAGTC
* *
2002521 AATTCACGTTGCGATAGTCTAATACGC-TTTGCGATTTTCT-CGTTGCGATAGTCAAATTCCCGT
1 AATTCACGTTGCGATAGTCAAATACGCGTTT-CGATTTT-TGCGTTGCGATAGTCAAATTACCGT
2002584 TGCGATAATCA
64 TGCGATAATCA
* *
2002595 AATTCACGTTGCGATAGTCAAATTCGCGTTTCGATTTTTGCGTTGCGATAGTCAAATTAGCGTTG
1 AATTCACGTTGCGATAGTCAAATACGCGTTTCGATTTTTGCGTTGCGATAGTCAAATTACCGTTG
*
2002660 CGATAGTCA
66 CGATAATCA
* *
2002669 AATTCGCGTTGCGATATTCAAAT
1 AATTCACGTTGCGATAGTCAAAT
2002692 GAATGTGTAA
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
73 1 0.01
74 84 0.95
75 3 0.03
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.35
Consensus pattern (74 bp):
AATTCACGTTGCGATAGTCAAATACGCGTTTCGATTTTTGCGTTGCGATAGTCAAATTACCGTTG
CGATAATCA
Found at i:2002639 original size:54 final size:54
Alignment explanation
Indices: 2002581--2002683 Score: 172
Period size: 54 Copynumber: 1.9 Consensus size: 54
2002571 GTCAAATTCC
*
2002581 CGTTGCGATAATCAAATTCA-CGTTGCGATAGTCAAATTCGCGTTTCGATTTTTG
1 CGTTGCGATAATCAAATT-AGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTG
*
2002635 CGTTGCGATAGTCAAATTAGCGTTGCGATAGTCAAATTCGCGTTGCGAT
1 CGTTGCGATAATCAAATTAGCGTTGCGATAGTCAAATTCGCGTTGCGAT
2002684 ATTCAAATGA
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
53 1 0.02
54 45 0.98
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.34
Consensus pattern (54 bp):
CGTTGCGATAATCAAATTAGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTG
Found at i:2002844 original size:140 final size:140
Alignment explanation
Indices: 2002662--2002944 Score: 512
Period size: 140 Copynumber: 2.0 Consensus size: 140
2002652 TAGCGTTGCG
* * *
2002662 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGCGATAGCAACTGAACATATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATAAATGTGTAATAAGCGATAACAACTGAACAAATCA
*
2002727 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGCTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
2002792 AATACACATA
131 AATACACATA
*
2002802 ATAGTCAAATTCGCGTTGCGATATTCAAATAAATGTGTAATAAGTGATAACAACTGAACAAATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATAAATGTGTAATAAGCGATAACAACTGAACAAATCA
*
2002867 TAGCAATGCTCGAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGCTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
2002932 AATACACATA
131 AATACACATA
2002942 ATA
1 ATA
2002945 CAACGTTTGC
Statistics
Matches: 137, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
140 137 1.00
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.28
Consensus pattern (140 bp):
ATAGTCAAATTCGCGTTGCGATATTCAAATAAATGTGTAATAAGCGATAACAACTGAACAAATCA
TAGCAATGCTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:2003022 original size:18 final size:18
Alignment explanation
Indices: 2002999--2003036 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
2002989 GTGAAGCCGG
*
2002999 TTTTGATTGGGATTTTGA
1 TTTTGATTGCGATTTTGA
2003017 TTTTGATTGCGATTTTGA
1 TTTTGATTGCGATTTTGA
2003035 TT
1 TT
2003037 GCCTTTTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.03, G:0.24, T:0.58
Consensus pattern (18 bp):
TTTTGATTGCGATTTTGA
Found at i:2005087 original size:14 final size:14
Alignment explanation
Indices: 2005068--2005104 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2005058 TCCCGTGGCA
2005068 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
*
2005082 TTTTCTTCGGGGAT
1 TTTTCTTCGGGGAC
2005096 TTCTTCTTC
1 TT-TTCTTC
2005105 TTATTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.05, C:0.22, G:0.22, T:0.51
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:2005328 original size:24 final size:24
Alignment explanation
Indices: 2005294--2005347 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2005284 CTGAAACATC
2005294 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
2005318 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
2005342 ATCAAA
1 ATCAAA
2005348 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:2005361 original size:24 final size:24
Alignment explanation
Indices: 2005294--2005361 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
2005284 CTGAAACATC
* * *
2005294 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
2005318 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
2005342 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
2005362 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:2006243 original size:20 final size:20
Alignment explanation
Indices: 2006218--2006265 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
2006208 GCGATTTTCT
2006218 AAAATCGCAACGCGATAGTC
1 AAAATCGCAACGCGATAGTC
2006238 AAAATCGCAACGCGATAGTC
1 AAAATCGCAACGCGATAGTC
2006258 AAAATCGC
1 AAAATCGC
2006266 GTTGTGAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.42, C:0.25, G:0.19, T:0.15
Consensus pattern (20 bp):
AAAATCGCAACGCGATAGTC
Found at i:2006322 original size:19 final size:19
Alignment explanation
Indices: 2006287--2006334 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
2006277 GGAAACTGAT
* *
2006287 TTGCGATATTGGAGATCGCG
1 TTGCGAT-TTAGAGATCGCA
2006307 TTGCGATTTAGAGATCGCA
1 TTGCGATTTAGAGATCGCA
2006326 TTGCGATTT
1 TTGCGATTT
2006335 TGTTGGTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 19 0.73
20 7 0.27
ACGTcount: A:0.21, C:0.15, G:0.29, T:0.35
Consensus pattern (19 bp):
TTGCGATTTAGAGATCGCA
Found at i:2007759 original size:24 final size:24
Alignment explanation
Indices: 2007727--2007782 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
2007717 GTTTTAATAC
2007727 CGAAATTATATGGCTAAGAAATTA
1 CGAAATTATATGGCTAAGAAATTA
*
2007751 CGAAATTATATGTCTAAGAAATTA
1 CGAAATTATATGGCTAAGAAATTA
*
2007775 TGAAATTA
1 CGAAATTA
2007783 CCCTTGAGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.46, C:0.07, G:0.14, T:0.32
Consensus pattern (24 bp):
CGAAATTATATGGCTAAGAAATTA
Found at i:2010050 original size:24 final size:24
Alignment explanation
Indices: 2009942--2010050 Score: 85
Period size: 24 Copynumber: 4.5 Consensus size: 24
2009932 ATGTTTTATC
* * *
2009942 TGATTTCCGATTTGCATTCTGTTT
1 TGATTTCTGATATGAATTCTGTTT
** * *
2009966 TGATACCTGACT-TGGATTTTGTTT
1 TGATTTCTGA-TATGAATTCTGTTT
* *
2009990 TGATTTCTGATATGGATTCTGTTC
1 TGATTTCTGATATGAATTCTGTTT
* * *
2010014 TAATATCTTATATGAATTCTGTTT
1 TGATTTCTGATATGAATTCTGTTT
*
2010038 TGATTTATGATAT
1 TGATTTCTGATAT
2010051 CTCCGTTTAC
Statistics
Matches: 65, Mismatches: 18, Indels: 4
0.75 0.21 0.05
Matches are distributed among these distances:
23 1 0.02
24 63 0.97
25 1 0.02
ACGTcount: A:0.20, C:0.11, G:0.17, T:0.52
Consensus pattern (24 bp):
TGATTTCTGATATGAATTCTGTTT
Found at i:2012154 original size:20 final size:20
Alignment explanation
Indices: 2012126--2012170 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
2012116 TTGAAATGGG
*
2012126 TTGACCCGACCCGACCCGAT
1 TTGACCCGACCCGACCCGAC
*
2012146 TTGATCCGACCCGACCCGAC
1 TTGACCCGACCCGACCCGAC
2012166 TTGAC
1 TTGAC
2012171 TTGACCAGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.20, C:0.42, G:0.20, T:0.18
Consensus pattern (20 bp):
TTGACCCGACCCGACCCGAC
Found at i:2012174 original size:25 final size:25
Alignment explanation
Indices: 2012128--2012188 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
2012118 GAAATGGGTT
*
2012128 GACCCGACCCGACCCGATTTGATCC-
1 GACCCGACCCGACCCGACTTGA-CCA
**
2012153 GACCCGACCCGACTTGACTTGACCA
1 GACCCGACCCGACCCGACTTGACCA
*
2012178 GATCCGACCCG
1 GACCCGACCCG
2012189 TTGACCGTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 2 0.06
25 29 0.94
ACGTcount: A:0.21, C:0.43, G:0.21, T:0.15
Consensus pattern (25 bp):
GACCCGACCCGACCCGACTTGACCA
Found at i:2014157 original size:48 final size:48
Alignment explanation
Indices: 2014105--2014198 Score: 125
Period size: 48 Copynumber: 2.0 Consensus size: 48
2014095 TTCGATTTGC
* * * *
2014105 ATTCTGTTCTGATACCTGACCTGGATTCTGTTATGATTTCTGATATGG
1 ATTCTGTTATGATACCTGACCTGAATTCTATTATGATTTATGATATGG
* * *
2014153 ATTCTGTTATGATATCTGATCTGAATTCTATTTTGATTTATGATAT
1 ATTCTGTTATGATACCTGACCTGAATTCTATTATGATTTATGATAT
2014199 CTCCATTTAC
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.22, C:0.13, G:0.17, T:0.48
Consensus pattern (48 bp):
ATTCTGTTATGATACCTGACCTGAATTCTATTATGATTTATGATATGG
Found at i:2014189 original size:24 final size:24
Alignment explanation
Indices: 2014105--2014181 Score: 100
Period size: 24 Copynumber: 3.2 Consensus size: 24
2014095 TTCGATTTGC
* * *
2014105 ATTCTGTTCTGATACCTGACCTGG
1 ATTCTGTTATGATATCTGATCTGG
* *
2014129 ATTCTGTTATGATTTCTGATATGG
1 ATTCTGTTATGATATCTGATCTGG
*
2014153 ATTCTGTTATGATATCTGATCTGA
1 ATTCTGTTATGATATCTGATCTGG
2014177 ATTCT
1 ATTCT
2014182 ATTTTGATTT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.21, C:0.16, G:0.18, T:0.45
Consensus pattern (24 bp):
ATTCTGTTATGATATCTGATCTGG
Found at i:2014997 original size:20 final size:19
Alignment explanation
Indices: 2014961--2015029 Score: 59
Period size: 22 Copynumber: 3.4 Consensus size: 19
2014951 TCTGAGGGGG
*
2014961 TTATATTACATAT-ATAGT
1 TTATATAACATATAATAGT
2014979 TTATATAACATATAAATAGAT
1 TTATATAACATAT-AATAG-T
*
2015000 TGTATATATACATATACTATAGG
1 T-TATATA-ACATATA--ATAGT
2015023 TTATATA
1 TTATATA
2015030 TATAGTTTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
18 12 0.29
20 4 0.10
21 2 0.05
22 13 0.31
23 7 0.17
24 4 0.10
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.43
Consensus pattern (19 bp):
TTATATAACATATAATAGT
Found at i:2015009 original size:24 final size:25
Alignment explanation
Indices: 2014980--2015033 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
2014970 ATATATAGTT
*
2014980 TATATAACATATA-AATAGATTGTA
1 TATATAACATATACAATAGATTATA
* *
2015004 TATAT-ACATATACTATAGGTTATA
1 TATATAACATATACAATAGATTATA
2015028 TATATA
1 TATATA
2015034 GTTTATATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.41
Consensus pattern (25 bp):
TATATAACATATACAATAGATTATA
Found at i:2015033 original size:13 final size:13
Alignment explanation
Indices: 2015011--2015044 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
2015001 GTATATATAC
2015011 ATATACTATAGGTT
1 ATATA-TATAGGTT
*
2015025 ATATATATAGTTT
1 ATATATATAGGTT
2015038 ATATATA
1 ATATATA
2015045 CTATACATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.47
Consensus pattern (13 bp):
ATATATATAGGTT
Found at i:2015049 original size:20 final size:20
Alignment explanation
Indices: 2014961--2015065 Score: 69
Period size: 20 Copynumber: 5.5 Consensus size: 20
2014951 TCTGAGGGGG
2014961 TTATAT-TAC-ATATATAGT
1 TTATATATACTATATATAGT
* *
2014979 TTATATA-ACATATAAATAGA
1 TTATATATAC-TATATATAGT
* * *
2014999 TTGTATATA-TACATATACT
1 TTATATATACTATATATAGT
* **
2015018 ATAGGT-TA-TATATATAGT
1 TTATATATACTATATATAGT
*
2015036 TTATATATACTATACATAGT
1 TTATATATACTATATATAGT
*
2015056 TTATAAATAC
1 TTATATATAC
2015066 ATGTACTATA
Statistics
Matches: 63, Mismatches: 18, Indels: 10
0.69 0.20 0.11
Matches are distributed among these distances:
18 21 0.33
19 10 0.16
20 31 0.49
21 1 0.02
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.44
Consensus pattern (20 bp):
TTATATATACTATATATAGT
Found at i:2015073 original size:55 final size:57
Alignment explanation
Indices: 2014966--2015103 Score: 185
Period size: 55 Copynumber: 2.5 Consensus size: 57
2014956 GGGGGTTATA
* *
2014966 TTACATATATAGTTTATATA-ACATATAAATAGATTGTATATATACATATACTATAGG
1 TTACATATATAGTTTATATATAC-TATAAATAGATTGTATAAATACATATACTATAAG
* * *
2015023 TTATATATATAGTTTATATATACTATACATAG-TT-TATAAATACATGTACTATAAG
1 TTACATATATAGTTTATATATACTATAAATAGATTGTATAAATACATATACTATAAG
*
2015078 TTACATATATAGTTTACATATA-TATA
1 TTACATATATAGTTTATATATACTATA
2015104 TATATACTAT
Statistics
Matches: 73, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
54 4 0.05
55 38 0.52
56 2 0.03
57 27 0.37
58 2 0.03
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (57 bp):
TTACATATATAGTTTATATATACTATAAATAGATTGTATAAATACATATACTATAAG
Found at i:2015235 original size:28 final size:28
Alignment explanation
Indices: 2015148--2015249 Score: 109
Period size: 28 Copynumber: 3.6 Consensus size: 28
2015138 TATGTATAGT
* *
2015148 GTTTAGGGTTTAAGGTTTA-GTGTTTGAG
1 GTTTAGGGTTTAGGGTTTATGT-TTTAAG
* * * * *
2015176 ATTTTTGGATTTAGGATTT-TGGTTTAAG
1 -GTTTAGGGTTTAGGGTTTATGTTTTAAG
2015204 GTTTAGGGTTTAGGGTTTATGTTTTAAG
1 GTTTAGGGTTTAGGGTTTATGTTTTAAG
2015232 GTTTAGGGTTTAGGGTTT
1 GTTTAGGGTTTAGGGTTT
2015250 TATAAACTAT
Statistics
Matches: 59, Mismatches: 12, Indels: 5
0.78 0.16 0.07
Matches are distributed among these distances:
27 14 0.24
28 31 0.53
29 14 0.24
ACGTcount: A:0.18, C:0.00, G:0.32, T:0.50
Consensus pattern (28 bp):
GTTTAGGGTTTAGGGTTTATGTTTTAAG
Found at i:2015246 original size:7 final size:7
Alignment explanation
Indices: 2015148--2015249 Score: 80
Period size: 7 Copynumber: 14.6 Consensus size: 7
2015138 TATGTATAGT
2015148 GTTTAGG
1 GTTTAGG
*
2015155 GTTTAAG
1 GTTTAGG
*
2015162 GTTTAGT
1 GTTTAGG
*
2015169 GTTTGAGA
1 GTTT-AGG
* *
2015177 TTTTTGG
1 GTTTAGG
*
2015184 ATTTAGG
1 GTTTAGG
* *
2015191 ATTT-TG
1 GTTTAGG
*
2015197 GTTTAAG
1 GTTTAGG
2015204 GTTTAGG
1 GTTTAGG
2015211 GTTTAGG
1 GTTTAGG
*
2015218 GTTTATG
1 GTTTAGG
* *
2015225 TTTTAAG
1 GTTTAGG
2015232 GTTTAGG
1 GTTTAGG
2015239 GTTTAGG
1 GTTTAGG
2015246 GTTT
1 GTTT
2015250 TATAAACTAT
Statistics
Matches: 75, Mismatches: 18, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
6 4 0.05
7 66 0.88
8 5 0.07
ACGTcount: A:0.18, C:0.00, G:0.32, T:0.50
Consensus pattern (7 bp):
GTTTAGG
Found at i:2015333 original size:49 final size:47
Alignment explanation
Indices: 2015242--2015334 Score: 132
Period size: 48 Copynumber: 1.9 Consensus size: 47
2015232 GTTTAGGGTT
** *
2015242 TAGGGTTTTATAAACTATATACTTTATTACTTTATATAGTTTATGTA
1 TAGGGTTTTATAAACTATATAAGTAATTACTTTATATAGTTTATGTA
*
2015289 TAGGGTTTTTATAAACTATATAAGTAATTTACTTTATATGGTTTAT
1 TAGGG-TTTTATAAACTATATAAGTAA-TTACTTTATATAGTTTAT
2015335 ATTTATAGGT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
47 5 0.12
48 18 0.45
49 17 0.43
ACGTcount: A:0.32, C:0.05, G:0.12, T:0.51
Consensus pattern (47 bp):
TAGGGTTTTATAAACTATATAAGTAATTACTTTATATAGTTTATGTA
Found at i:2015341 original size:15 final size:16
Alignment explanation
Indices: 2015321--2015357 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
2015311 AGTAATTTAC
2015321 TTTATATGGTT-TATA
1 TTTATATGGTTATATA
2015336 TTTATA-GGTTATATA
1 TTTATATGGTTATATA
*
2015351 TATATAT
1 TTTATAT
2015358 ATATATAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (16 bp):
TTTATATGGTTATATA
Found at i:2015364 original size:23 final size:24
Alignment explanation
Indices: 2015332--2015380 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
2015322 TTATATGGTT
*
2015332 TATATTTATAGGTTATATATA-TA
1 TATATATATAGGTTATATATACTA
*
2015355 TATATATATAGTTTATATATACTA
1 TATATATATAGGTTATATATACTA
2015379 TA
1 TA
2015381 CATAGTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51
Consensus pattern (24 bp):
TATATATATAGGTTATATATACTA
Found at i:2015385 original size:20 final size:19
Alignment explanation
Indices: 2015349--2015391 Score: 68
Period size: 20 Copynumber: 2.2 Consensus size: 19
2015339 ATAGGTTATA
*
2015349 TATATATATATATATAGTT
1 TATATATATATACATAGTT
2015368 TATATATACTATACATAGTT
1 TATATATA-TATACATAGTT
2015388 TATA
1 TATA
2015392 CATGCATGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.49
Consensus pattern (19 bp):
TATATATATATACATAGTT
Found at i:2015735 original size:15 final size:15
Alignment explanation
Indices: 2015700--2015830 Score: 58
Period size: 13 Copynumber: 9.6 Consensus size: 15
2015690 CTATATATTT
*
2015700 TATATAGTTTTTACA
1 TATATAGTTTATACA
*
2015715 TATATAGTTTATATA
1 TATATAGTTTATACA
* *
2015730 TGTATA-TATATAC-
1 TATATAGTTTATACA
*
2015743 TATATTAG--TATAAA
1 TATA-TAGTTTATACA
* *
2015757 T-TATATTTTATAAA
1 TATATAGTTTATACA
*
2015771 CTATATACTTT-T---
1 -TATATAGTTTATACA
2015783 TATA-A-TTTATACA
1 TATATAGTTTATACA
2015796 TATATAGTTTAT--A
1 TATATAGTTTATACA
*
2015809 TACATAGTTTAT--A
1 TATATAGTTTATACA
2015822 TATATAGTT
1 TATATAGTT
2015831 CATATAAACA
Statistics
Matches: 92, Mismatches: 11, Indels: 28
0.70 0.08 0.21
Matches are distributed among these distances:
9 3 0.03
10 2 0.02
11 4 0.04
12 2 0.02
13 34 0.37
14 15 0.16
15 25 0.27
16 7 0.08
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.51
Consensus pattern (15 bp):
TATATAGTTTATACA
Found at i:2015762 original size:65 final size:65
Alignment explanation
Indices: 2015633--2015768 Score: 154
Period size: 65 Copynumber: 2.1 Consensus size: 65
2015623 ACTTTATTAC
* * *
2015633 TTTATATAGTTTATGCATAATGTTTCTATATAAATATATATAATTATAATTTATAAACTATATAT
1 TTTATATAGTTTATACATAATGTTTATATATAAATATATATAACTATAATTTATAAACTATATAT
* **
2015698 TTTATATAGTTTTTACATATATAGTTTATATATGTATATATAT-ACTAT-ATTAGTATAAA-T-T
1 TTTATATAGTTTATACATA-AT-GTTTATATATAAATATATATAACTATAATT--TATAAACTAT
2015759 ATAT
62 ATAT
2015763 TTTATA
1 TTTATA
2015769 AACTATATAC
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
65 31 0.51
66 7 0.11
67 23 0.38
ACGTcount: A:0.40, C:0.04, G:0.05, T:0.51
Consensus pattern (65 bp):
TTTATATAGTTTATACATAATGTTTATATATAAATATATATAACTATAATTTATAAACTATATAT
Found at i:2015820 original size:28 final size:28
Alignment explanation
Indices: 2015784--2015855 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 28
2015774 TATACTTTTT
*
2015784 ATAATTTATACATATATAGTT-TATATAC
1 ATAATTTATA-ATATATAGTTATATAAAC
*
2015812 ATAGTTTAT-ATATATAGTTCATATAAAC
1 ATAATTTATAATATATAGTT-ATATAAAC
2015840 ATAATTTAT-ATATATA
1 ATAATTTATAATATATA
2015856 ACTTATAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
26 10 0.26
28 29 0.74
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (28 bp):
ATAATTTATAATATATAGTTATATAAAC
Found at i:2015848 original size:81 final size:81
Alignment explanation
Indices: 2015669--2015849 Score: 217
Period size: 81 Copynumber: 2.2 Consensus size: 81
2015659 TATATAAATA
* * * **
2015669 TATATAATTATAATTTATAAACTATATATTTTATATAGTTTTTACATATATAGTTTATATATGTA
1 TATA-AATCATAATTTATAAACTATATATTTTATATAATTTATACATATATAGTTTATATACATA
2015734 TATATATACTATATTAG
65 TATATATACTATATTAG
* *
2015751 TATAAATTATATTTTATAAACTATATACTTTT-TATAATTTATACATATATAGTTTATATACATA
1 TATAAATCATAATTTATAAACTATATA-TTTTATATAATTTATACATATATAGTTTATATACATA
*
2015815 GTTTATATA-TATAGTTCA-
65 -TATATATACTATA-TT-AG
2015833 TATAAA-CATAATTTATA
1 TATAAATCATAATTTATA
2015850 TATATAACTT
Statistics
Matches: 87, Mismatches: 8, Indels: 9
0.84 0.08 0.09
Matches are distributed among these distances:
81 63 0.72
82 23 0.26
83 1 0.01
ACGTcount: A:0.41, C:0.05, G:0.04, T:0.50
Consensus pattern (81 bp):
TATAAATCATAATTTATAAACTATATATTTTATATAATTTATACATATATAGTTTATATACATAT
ATATATACTATATTAG
Found at i:2015856 original size:13 final size:13
Alignment explanation
Indices: 2015783--2015930 Score: 62
Period size: 13 Copynumber: 11.6 Consensus size: 13
2015773 ATATACTTTT
2015783 TATAATTTATACATA
1 TATAATTTAT--ATA
*
2015798 TATAGTTTATATA
1 TATAATTTATATA
* *
2015811 CATAGTTTATATA
1 TATAATTTATATA
* *
2015824 TATAGTTCATATAAA
1 TATAATT--TATATA
*
2015839 CATAATTTATATA
1 TATAATTTATATA
*
2015852 TATAA-CT-TATA
1 TATAATTTATATA
*
2015863 -ATAATTATATAGTT
1 TATAATT-TATA-TA
*
2015877 TATAA--TATAAA
1 TATAATTTATATA
*
2015888 TATAGTTTATATA
1 TATAATTTATATA
* *
2015901 TA-CACTTATAT-
1 TATAATTTATATA
*
2015912 TAT-ATATATAT-
1 TATAATTTATATA
2015923 TATAATTT
1 TATAATTT
2015931 TTTTTCAATT
Statistics
Matches: 101, Mismatches: 21, Indels: 25
0.69 0.14 0.17
Matches are distributed among these distances:
10 4 0.04
11 19 0.19
12 15 0.15
13 39 0.39
14 1 0.01
15 23 0.23
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (13 bp):
TATAATTTATATA
Found at i:2015890 original size:18 final size:17
Alignment explanation
Indices: 2015869--2015902 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
2015859 TATAATAATT
2015869 ATATAGTTTATAATATAA
1 ATATAGTTTAT-ATATAA
2015887 ATATAGTTTATATATA
1 ATATAGTTTATATATA
2015903 CACTTATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (17 bp):
ATATAGTTTATATATAA
Found at i:2016949 original size:30 final size:30
Alignment explanation
Indices: 2016908--2016966 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
2016898 GAGTTGGTGC
2016908 TTGGATTACTTAAATCATTAAACTATACTA
1 TTGGATTACTTAAATCATTAAACTATACTA
*
2016938 TTGGGTTACTTAAATCATTAAACTATACT
1 TTGGATTACTTAAATCATTAAACTATACT
2016967 CTAAATTTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.37, C:0.14, G:0.08, T:0.41
Consensus pattern (30 bp):
TTGGATTACTTAAATCATTAAACTATACTA
Found at i:2018069 original size:32 final size:32
Alignment explanation
Indices: 2018033--2018093 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
2018023 ATCTTTGGTG
*
2018033 TTGAAGCAATAAAAGATAGAAAAATTGACACA
1 TTGAAACAATAAAAGATAGAAAAATTGACACA
* *
2018065 TTGAAATAATAAAAGATAGGAAAATTGAC
1 TTGAAACAATAAAAGATAGAAAAATTGAC
2018094 TCAAAAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.56, C:0.07, G:0.16, T:0.21
Consensus pattern (32 bp):
TTGAAACAATAAAAGATAGAAAAATTGACACA
Found at i:2018707 original size:20 final size:20
Alignment explanation
Indices: 2018679--2018730 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
2018669 AGGCAAGGGA
* **
2018679 GTTTAAAAACCAGTTAGAGG
1 GTTTCAAAACCAGCAAGAGG
*
2018699 GTTTCAAAACCAGCAAGGGG
1 GTTTCAAAACCAGCAAGAGG
*
2018719 GTTTCGAAACCA
1 GTTTCAAAACCA
2018731 TAAGAACATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.37, C:0.17, G:0.25, T:0.21
Consensus pattern (20 bp):
GTTTCAAAACCAGCAAGAGG
Found at i:2019273 original size:3 final size:3
Alignment explanation
Indices: 2019265--2019314 Score: 59
Period size: 3 Copynumber: 16.7 Consensus size: 3
2019255 TTTGTCTGGG
*
2019265 TTA TTA TTA TT- TATA TTA -TA TTA TTA TTA ATA TTTA TTA TTA TTA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
2019310 TTA TT
1 TTA TT
2019315 TAATATTTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
2 3 0.07
3 35 0.85
4 3 0.07
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:2019298 original size:23 final size:24
Alignment explanation
Indices: 2019265--2019324 Score: 81
Period size: 23 Copynumber: 2.6 Consensus size: 24
2019255 TTTGTCTGGG
*
2019265 TTATTATTATTTATATTA-TATTA
1 TTATTAATATTTATATTATTATTA
2019288 TTATTAATA-TT-TATTATTATTA
1 TTATTAATATTTATATTATTATTA
2019310 TTATTTAATATTTAT
1 TTA-TTAATATTTAT
2019325 GTTAATTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
21 5 0.16
22 10 0.31
23 14 0.44
24 2 0.06
25 1 0.03
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (24 bp):
TTATTAATATTTATATTATTATTA
Found at i:2019304 original size:16 final size:16
Alignment explanation
Indices: 2019265--2019321 Score: 78
Period size: 16 Copynumber: 3.5 Consensus size: 16
2019255 TTTGTCTGGG
*
2019265 TTATTATTATTTATAT
1 TTATTATTATTAATAT
2019281 TATATTATTATTAATAT
1 T-TATTATTATTAATAT
*
2019298 TTATTATTATTATTAT
1 TTATTATTATTAATAT
*
2019314 TTAATATT
1 TTATTATT
2019322 TATGTTAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
16 22 0.59
17 15 0.41
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTATTATTATTAATAT
Found at i:2022173 original size:31 final size:30
Alignment explanation
Indices: 2022110--2022205 Score: 174
Period size: 30 Copynumber: 3.2 Consensus size: 30
2022100 TAACGACTAA
*
2022110 ACACTTAAATGATAATGGAGAAAATGTTAG
1 ACACTTAAATGATAATGGAGAAAACGTTAG
2022140 ACACTTAAATGATAATGGAGAAAAACGTTAG
1 ACACTTAAATGATAATGGAG-AAAACGTTAG
2022171 ACACTTAAATGATAATGGAGAAAACGTTAG
1 ACACTTAAATGATAATGGAGAAAACGTTAG
2022201 ACACT
1 ACACT
2022206 ACAAAAAAAT
Statistics
Matches: 64, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
30 35 0.55
31 29 0.45
ACGTcount: A:0.47, C:0.10, G:0.19, T:0.24
Consensus pattern (30 bp):
ACACTTAAATGATAATGGAGAAAACGTTAG
Found at i:2025973 original size:23 final size:21
Alignment explanation
Indices: 2025935--2025976 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
2025925 TTATTAATAT
*
2025935 AAATTATATAGTTTATATAAA
1 AAATTATATAGATTATATAAA
2025956 AAATTATATATGAATTATATA
1 AAATTATATA-G-ATTATATA
2025977 TAAACTATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 1 0.06
23 7 0.39
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (21 bp):
AAATTATATAGATTATATAAA
Found at i:2026057 original size:33 final size:33
Alignment explanation
Indices: 2026020--2026085 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
2026010 TAATTATAAA
* * *
2026020 TAATATATACTATGTATAAAGTATATAGTTTAT
1 TAATATAAACTATATATAAACTATATAGTTTAT
*
2026053 TAATATAAACTATATATGAACTATATAGTTTAT
1 TAATATAAACTATATATAAACTATATAGTTTAT
2026086 ATTTATATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.44
Consensus pattern (33 bp):
TAATATAAACTATATATAAACTATATAGTTTAT
Found at i:2026248 original size:29 final size:29
Alignment explanation
Indices: 2026213--2026275 Score: 108
Period size: 29 Copynumber: 2.2 Consensus size: 29
2026203 ATATGTAAAT
* *
2026213 TATATATATTATATAGTTTACATTTGAAC
1 TATATATACTATATAGTTTACATATGAAC
2026242 TATATATACTATATAGTTTACATATGAAC
1 TATATATACTATATAGTTTACATATGAAC
2026271 TATAT
1 TATAT
2026276 GTATAAACTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.46
Consensus pattern (29 bp):
TATATATACTATATAGTTTACATATGAAC
Found at i:2026365 original size:24 final size:24
Alignment explanation
Indices: 2026336--2026394 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
2026326 ATATATAAAC
2026336 TATATAATTTACGT-ATGAACTATA
1 TATATAATTTA-GTAATGAACTATA
* *
2026360 TATATAGTTTATTAATGAACTATA
1 TATATAATTTAGTAATGAACTATA
* *
2026384 TAAATTATTTA
1 TATATAATTTA
2026395 TATAGTATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
23 1 0.03
24 28 0.97
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.46
Consensus pattern (24 bp):
TATATAATTTAGTAATGAACTATA
Found at i:2026423 original size:9 final size:9
Alignment explanation
Indices: 2026411--2026491 Score: 51
Period size: 9 Copynumber: 8.8 Consensus size: 9
2026401 ATATACTACA
2026411 TATATAAAC
1 TATATAAAC
**
2026420 TATATTTAC
1 TATATAAAC
2026429 TATATAATTTAC
1 TATATAA---AC
*
2026441 -ATATGAAC
1 TATATAAAC
2026449 TATATATATA-
1 TATATA-A-AC
*
2026459 TATATATA-
1 TATATAAAC
*
2026467 TATATAAAT
1 TATATAAAC
2026476 TATATAAAC
1 TATATAAAC
2026485 TATATAA
1 TATATAA
2026492 TATAGTTGAT
Statistics
Matches: 56, Mismatches: 9, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
8 10 0.18
9 31 0.55
10 7 0.12
11 6 0.11
12 2 0.04
ACGTcount: A:0.49, C:0.06, G:0.01, T:0.43
Consensus pattern (9 bp):
TATATAAAC
Found at i:2026456 original size:2 final size:2
Alignment explanation
Indices: 2026449--2026715 Score: 92
Period size: 2 Copynumber: 127.0 Consensus size: 2
2026439 ACATATGAAC
* *
2026449 TA TA TA TA TA TA TA TA TA TA TA TA AA T- TA TA TA AA CTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* *
2026491 -A TA TA GT- TGA TA TT TA TA TA CTA TA TA -A TA TA TA TA GTT TA
1 TA TA TA -TA T-A TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA
* * * *
2026532 CA T- TA T- TG CA TA TGA -A CTA TA TA TA TA GTT TA T- TA -A TGA
1 TA TA TA TA TA TA TA T-A TA -TA TA TA TA TA -TA TA TA TA TA T-A
* * * *
2026571 -A CTA TA TA AA CA -A TT TA TA TA GTA TA TA GTA TA TA TA TA AA
1 TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA
*
2026612 CTA TA GT- TGA TA TT TA TA TA T- TA TA TA CTA TA TA CTA TA TA CTA
1 -TA TA -TA T-A TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA -TA
2026656 TA TA CTA TA TA CTA TA TA CTA TA TA CTA TA TA CTA TA TA CTA TA
1 TA TA -TA TA TA -TA TA TA -TA TA TA -TA TA TA -TA TA TA -TA TA
2026700 TA CTA TA TA TA CTA TA
1 TA -TA TA TA TA -TA TA
2026716 CAATATAGTT
Statistics
Matches: 203, Mismatches: 23, Indels: 78
0.67 0.08 0.26
Matches are distributed among these distances:
1 13 0.06
2 150 0.74
3 40 0.20
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (2 bp):
TA
Found at i:2026509 original size:56 final size:58
Alignment explanation
Indices: 2026389--2026526 Score: 151
Period size: 56 Copynumber: 2.4 Consensus size: 58
2026379 CTATATAAAT
* * * ** *
2026389 TATTTATATAGTATATACTACATATATAAACTATATTTACTATATAATTTACATATGA
1 TATTTATATACTATATAATATATATATAAACTATATAAACTATATAATATACATATGA
* * *
2026447 -A-CTATATA-TATATATATATATATATAAATTATATAAACTATATAATATA-GT-TGA
1 TATTTATATACTATATA-ATATATATATAAACTATATAAACTATATAATATACATATGA
2026501 TATTTATATACTATATAATATATATA
1 TATTTATATACTATATAATATATATA
2026527 GTTTACATTA
Statistics
Matches: 67, Mismatches: 9, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
54 3 0.04
55 8 0.12
56 49 0.73
57 7 0.10
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (58 bp):
TATTTATATACTATATAATATATATATAAACTATATAAACTATATAATATACATATGA
Found at i:2026517 original size:9 final size:8
Alignment explanation
Indices: 2026449--2026715 Score: 92
Period size: 9 Copynumber: 31.8 Consensus size: 8
2026439 ACATATGAAC
2026449 TATATATA
1 TATATATA
2026457 TATATATA
1 TATATATA
2026465 TATATATA
1 TATATATA
*
2026473 AAT-TATA
1 TATATATA
*
2026480 TAAACTATA
1 TATA-TATA
2026489 TA-ATATA
1 TATATATA
*
2026496 GT-TGATATT
1 -TAT-ATATA
2026505 TATATACTA
1 TATATA-TA
2026514 TATA-ATA
1 TATATATA
*
2026521 TATATAGTT
1 TATATA-TA
*
2026530 TACAT-TA
1 TATATATA
**
2026537 T-TGCATA
1 TATATATA
2026544 TGA-ACTATA
1 T-ATA-TATA
*
2026553 TATATAGTT
1 TATATA-TA
2026562 TAT-TA-A
1 TATATATA
2026568 TGA-ACTATA
1 T-ATA-TATA
* *
2026577 TAAACA-A
1 TATATATA
*
2026584 TTTATATA
1 TATATATA
2026592 GTATATAGTA
1 -TATATA-TA
2026602 TATATATA
1 TATATATA
*
2026610 AACTATAGT-
1 TA-TATA-TA
*
2026619 TGATATTTA
1 T-ATATATA
2026628 TATAT-TA
1 TATATATA
2026635 TATACTATA
1 TATA-TATA
2026644 TACTATATA
1 TA-TATATA
2026653 CTATATACTA
1 -TATATA-TA
2026663 TATACTATA
1 TATA-TATA
2026672 TACTATATA
1 TA-TATATA
2026681 CTATATACTA
1 -TATATA-TA
2026691 TATACTATA
1 TATA-TATA
2026700 TACTATATA
1 TA-TATATA
2026709 TACTATA
1 TA-TATA
2026716 CAATATAGTT
Statistics
Matches: 198, Mismatches: 23, Indels: 75
0.67 0.08 0.25
Matches are distributed among these distances:
6 1 0.01
7 31 0.16
8 45 0.23
9 99 0.50
10 22 0.11
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (8 bp):
TATATATA
Found at i:2026635 original size:7 final size:7
Alignment explanation
Indices: 2026626--2026722 Score: 160
Period size: 7 Copynumber: 13.9 Consensus size: 7
2026616 AGTTGATATT
*
2026626 TATATAT
1 TATATAC
2026633 TATATAC
1 TATATAC
2026640 TATATAC
1 TATATAC
2026647 TATATAC
1 TATATAC
2026654 TATATAC
1 TATATAC
2026661 TATATAC
1 TATATAC
2026668 TATATAC
1 TATATAC
2026675 TATATAC
1 TATATAC
2026682 TATATAC
1 TATATAC
2026689 TATATAC
1 TATATAC
2026696 TATATAC
1 TATATAC
2026703 TATATA-
1 TATATAC
2026709 TACTATAC
1 TA-TATAC
*
2026717 AATATA
1 TATATA
2026723 GTTTACATAT
Statistics
Matches: 86, Mismatches: 2, Indels: 4
0.93 0.02 0.04
Matches are distributed among these distances:
6 2 0.02
7 83 0.97
8 1 0.01
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.43
Consensus pattern (7 bp):
TATATAC
Found at i:2026834 original size:34 final size:34
Alignment explanation
Indices: 2026795--2026864 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 34
2026785 TAAACTATAA
* * *
2026795 AATATAGTTGATATTTATATACTATATACAATAT
1 AATATAATTGATACTTATATAATATATACAATAT
* * *
2026829 AATATAATTTATACTTATATAATTTATACTATAT
1 AATATAATTGATACTTATATAATATATACAATAT
2026863 AA
1 AA
2026865 ATTCAAAGTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.46
Consensus pattern (34 bp):
AATATAATTGATACTTATATAATATATACAATAT
Found at i:2026850 original size:15 final size:14
Alignment explanation
Indices: 2026830--2026864 Score: 61
Period size: 15 Copynumber: 2.4 Consensus size: 14
2026820 ATACAATATA
2026830 ATATAATTTATACTT
1 ATATAATTTATAC-T
2026845 ATATAATTTATACT
1 ATATAATTTATACT
2026859 ATATAA
1 ATATAA
2026865 ATTCAAAGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.49
Consensus pattern (14 bp):
ATATAATTTATACT
Found at i:2027027 original size:31 final size:33
Alignment explanation
Indices: 2026985--2027068 Score: 100
Period size: 33 Copynumber: 2.6 Consensus size: 33
2026975 ATATGAACTA
* *
2026985 TATATAAAAACTATAT-TTATAAAGTATA-TGG
1 TATATATAAACTATATATTATAAAGTATATTAG
* *
2027016 TATATATAAACTATATATTATATAGTTTATTAG
1 TATATATAAACTATATATTATAAAGTATATTAG
* *
2027049 AATATATAACCTATATATTA
1 TATATATAAACTATATATTA
2027069 ATTTATTAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
31 15 0.33
32 10 0.22
33 20 0.44
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.43
Consensus pattern (33 bp):
TATATATAAACTATATATTATAAAGTATATTAG
Found at i:2027037 original size:18 final size:18
Alignment explanation
Indices: 2026928--2027039 Score: 50
Period size: 18 Copynumber: 6.7 Consensus size: 18
2026918 ATAAACTATT
*
2026928 TATATAGTATATAGTACA-
1 TATATAGTATATA-TAAAC
*
2026946 TATATAGTTTATAT-AAC
1 TATATAGTATATATAAAC
* *
2026963 TATGTAGTTTATATATGAAC
1 TATATAG--TATATATAAAC
2026983 --TATA-TATA-A-AAAC
1 TATATAGTATATATAAAC
*
2026996 --TATA-T-T-TATAAAG
1 TATATAGTATATATAAAC
*
2027009 TATATGGTATATATAAAC
1 TATATAGTATATATAAAC
*
2027027 TATATATTATATA
1 TATATAGTATATA
2027040 GTTTATTAGA
Statistics
Matches: 72, Mismatches: 11, Indels: 22
0.69 0.10 0.21
Matches are distributed among these distances:
12 2 0.03
13 11 0.15
14 1 0.01
15 7 0.10
16 2 0.03
17 8 0.11
18 32 0.44
19 6 0.08
20 3 0.04
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (18 bp):
TATATAGTATATATAAAC
Found at i:2027082 original size:25 final size:25
Alignment explanation
Indices: 2027052--2027122 Score: 115
Period size: 25 Copynumber: 2.8 Consensus size: 25
2027042 TTATTAGAAT
2027052 ATATAACCTATATATTAATTTATTA
1 ATATAACCTATATATTAATTTATTA
*
2027077 ATATAAACTATATATTAATTTATTA
1 ATATAACCTATATATTAATTTATTA
*
2027102 ATATAAGCATATATATTAATT
1 ATATAA-CCTATATATTAATT
2027123 GAAAGAATTG
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
25 30 0.71
26 12 0.29
ACGTcount: A:0.46, C:0.06, G:0.01, T:0.46
Consensus pattern (25 bp):
ATATAACCTATATATTAATTTATTA
Found at i:2027626 original size:103 final size:104
Alignment explanation
Indices: 2027401--2027626 Score: 355
Period size: 104 Copynumber: 2.2 Consensus size: 104
2027391 TTCATTTTTT
* * *
2027401 TTCATCCGTGTTCATCCCAAAAACCCTCATTTGATCTTCACAAACACCAAAACCCAAACCATTTT
1 TTCATTCGTGTTCATCTCAAAAACCCTCATTTGATCTTCACAAACACCAAAACCCAAACCATTTA
* *
2027466 GTGTTTTTTTCGATCAAACACCCAAAAAATCAACCCTTA
66 GTGATTTTTTCGACCAAACACCCAAAAAATCAACCCTTA
* * *
2027505 TTCATTCATTTTCATCTCAAAAACCCTCATTTGATCTTCACAAACACCAAAACCCAAACTATTTA
1 TTCATTCGTGTTCATCTCAAAAACCCTCATTTGATCTTCACAAACACCAAAACCCAAACCATTTA
* *
2027570 GT-ATTTTTTCGACCAAACACCCAAAAATTCAACCCTTG
66 GTGATTTTTTCGACCAAACACCCAAAAAATCAACCCTTA
2027608 TTCATTCGTGTTCATCTCA
1 TTCATTCGTGTTCATCTCA
2027627 GTTCTTCCCC
Statistics
Matches: 110, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
103 49 0.45
104 61 0.55
ACGTcount: A:0.34, C:0.30, G:0.05, T:0.31
Consensus pattern (104 bp):
TTCATTCGTGTTCATCTCAAAAACCCTCATTTGATCTTCACAAACACCAAAACCCAAACCATTTA
GTGATTTTTTCGACCAAACACCCAAAAAATCAACCCTTA
Found at i:2027746 original size:106 final size:109
Alignment explanation
Indices: 2027533--2027746 Score: 240
Period size: 106 Copynumber: 2.0 Consensus size: 109
2027523 AAAAACCCTC
**
2027533 ATTTGATCTTCACAAACACCAAAACCCAAACTATTTAGTATTTTTTCGACCAAACACCCAAAAAT
1 ATTTGATCTTCACAAACACCAAAACCCAAAC--TCCAGTATTTTTTCGACCAAACACCCAAAAAT
* * *** *
2027598 TCAACCCTTGTTCATTCGTGTTCATCTCAGTTCTTCCCCAAACCATT
64 TAAACCCTTGTTCATTCGTGTTCATCCCAACCCTT-CACAAACCATT
* *
2027645 ATTTGATCTTCACAAACACCAAAACCTAAAC-CCA-T-TTTTTTC-ATCAAACACCCAAAAATTA
1 ATTTGATCTTCACAAACACCAAAACCCAAACTCCAGTATTTTTTCGACCAAACACCCAAAAATTA
* *
2027706 AACCCTTGTTCATTTGTGTTCTTCCCCAAACCCTT-ACAAAC
66 AACCCTTGTTCATTCGTGTTCAT-CCC-AACCCTTCACAAAC
2027747 ACCCAAAACT
Statistics
Matches: 88, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
106 43 0.49
107 9 0.10
108 5 0.06
109 1 0.01
112 30 0.34
ACGTcount: A:0.34, C:0.30, G:0.05, T:0.31
Consensus pattern (109 bp):
ATTTGATCTTCACAAACACCAAAACCCAAACTCCAGTATTTTTTCGACCAAACACCCAAAAATTA
AACCCTTGTTCATTCGTGTTCATCCCAACCCTTCACAAACCATT
Found at i:2027955 original size:24 final size:24
Alignment explanation
Indices: 2027934--2028050 Score: 101
Period size: 24 Copynumber: 4.9 Consensus size: 24
2027924 CCCAAACCCA
* *
2027934 AACCCAAACCCGAACCCGAACCCGG
1 AACCCAAACCCAAACCCGAACTC-G
* *
2027959 AA-CCAAACCCAAACCCAAACTTG
1 AACCCAAACCCAAACCCGAACTCG
** ** * * *
2027982 AACCTGATTCCAAACTCGATCTCA
1 AACCCAAACCCAAACCCGAACTCG
*
2028006 AACCCAAACCCAAACCCAAACTCG
1 AACCCAAACCCAAACCCGAACTCG
*
2028030 AATCCAAACCCAAACCCGAAC
1 AACCCAAACCCAAACCCGAAC
2028051 CCGTATCCAA
Statistics
Matches: 68, Mismatches: 23, Indels: 3
0.72 0.24 0.03
Matches are distributed among these distances:
23 3 0.04
24 63 0.93
25 2 0.03
ACGTcount: A:0.42, C:0.42, G:0.08, T:0.09
Consensus pattern (24 bp):
AACCCAAACCCAAACCCGAACTCG
Found at i:2028025 original size:30 final size:30
Alignment explanation
Indices: 2027991--2028052 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
2027981 GAACCTGATT
2027991 CCAAACTCG-ATCTCAAACCCAAACCCAAAC
1 CCAAACTCGAATC-CAAACCCAAACCCAAAC
*
2028021 CCAAACTCGAATCCAAACCCAAACCCGAAC
1 CCAAACTCGAATCCAAACCCAAACCCAAAC
2028051 CC
1 CC
2028053 GTATCCAAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 27 0.90
31 3 0.10
ACGTcount: A:0.42, C:0.45, G:0.05, T:0.08
Consensus pattern (30 bp):
CCAAACTCGAATCCAAACCCAAACCCAAAC
Found at i:2028036 original size:42 final size:41
Alignment explanation
Indices: 2027924--2028040 Score: 119
Period size: 42 Copynumber: 2.8 Consensus size: 41
2027914 CTAACCAGAG
* *
2027924 CCCAAACCCAAACCCAAACCCGAACCCGAACCCGGAACCAAA
1 CCCAAACCCAAACCCAAA-CCGAATCCAAACCCGGAACCAAA
*** * * *
2027966 CCCAAACCCAAACTTGAACCTGATTCCAAACTC-GATCTCAAA
1 CCCAAACCCAAACCCAAACC-GAATCCAAACCCGGAAC-CAAA
2028008 CCCAAACCCAAACCCAAACTCGAATCCAAACCC
1 CCCAAACCCAAACCCAAAC-CGAATCCAAACCC
2028041 AAACCCGAAC
Statistics
Matches: 59, Mismatches: 13, Indels: 6
0.76 0.17 0.08
Matches are distributed among these distances:
41 5 0.08
42 53 0.90
43 1 0.02
ACGTcount: A:0.41, C:0.44, G:0.07, T:0.09
Consensus pattern (41 bp):
CCCAAACCCAAACCCAAACCGAATCCAAACCCGGAACCAAA
Found at i:2028053 original size:6 final size:6
Alignment explanation
Indices: 2027924--2028052 Score: 80
Period size: 6 Copynumber: 21.5 Consensus size: 6
2027914 CTAACCAGAG
* * *
2027924 CCCAAA CCCAAA CCCAAA CCCGAA CCCGAA CCCGGAA -CCAAA CCCAAA
1 CCCAAA CCCAAA CCCAAA CCCAAA CCCAAA CCC-AAA CCCAAA CCCAAA
*** ** * * * * * *
2027972 CCCAAA CTTGAA CCTGAT TCCAAA CTCGAT CTCAAA CCCAAA CCCAAA
1 CCCAAA CCCAAA CCCAAA CCCAAA CCCAAA CCCAAA CCCAAA CCCAAA
* * * *
2028020 CCCAAA CTCGAA TCCAAA CCCAAA CCCGAA CCC
1 CCCAAA CCCAAA CCCAAA CCCAAA CCCAAA CCC
2028053 GTATCCAAAC
Statistics
Matches: 96, Mismatches: 25, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
5 2 0.02
6 91 0.95
7 3 0.03
ACGTcount: A:0.41, C:0.44, G:0.07, T:0.08
Consensus pattern (6 bp):
CCCAAA
Found at i:2030645 original size:20 final size:20
Alignment explanation
Indices: 2030620--2030687 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
2030610 TAGTTGGTGC
* *
2030620 TTGATATTGCTTGCTTATGT
1 TTGATATTGTTTGCTTCTGT
*
2030640 TTGATATTGTTTACTTCTGT
1 TTGATATTGTTTGCTTCTGT
* *
2030660 TTGATATTGTTTGATTCTGC
1 TTGATATTGTTTGCTTCTGT
2030680 TTGATATT
1 TTGATATT
2030688 TGTAAGGGTT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.16, C:0.09, G:0.18, T:0.57
Consensus pattern (20 bp):
TTGATATTGTTTGCTTCTGT
Found at i:2031455 original size:19 final size:19
Alignment explanation
Indices: 2031413--2031470 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
2031403 TAATTTAATG
2031413 ATTATAAATAAAATATATAAGA
1 ATTATAAAT--AATATA-AAGA
2031435 ATTATAAATAATATAAAGA
1 ATTATAAATAATATAAAGA
** *
2031454 ATTGGAATTAATATAAA
1 ATTATAAATAATATAAA
2031471 AACCAAATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
19 18 0.55
20 6 0.18
22 9 0.27
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (19 bp):
ATTATAAATAATATAAAGA
Found at i:2031627 original size:16 final size:16
Alignment explanation
Indices: 2031606--2031643 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
2031596 TATTACTTAT
2031606 AAGTCAGGTAAATATC
1 AAGTCAGGTAAATATC
2031622 AAGTCAGGTAAATATC
1 AAGTCAGGTAAATATC
*
2031638 TAGTCA
1 AAGTCA
2031644 ATTCAATAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.26
Consensus pattern (16 bp):
AAGTCAGGTAAATATC
Found at i:2034661 original size:2 final size:2
Alignment explanation
Indices: 2034654--2034700 Score: 76
Period size: 2 Copynumber: 23.0 Consensus size: 2
2034644 TGAGGTTAGG
*
2034654 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2034696 GAT AT
1 -AT AT
2034701 TTCCTTTTCA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 40 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2040820 original size:20 final size:20
Alignment explanation
Indices: 2040621--2040810 Score: 274
Period size: 20 Copynumber: 9.5 Consensus size: 20
2040611 ATTTCCCACA
* *
2040621 AATTTGTAAAGCCTCTGGGA
1 AATTTGTAAAGCCTCCGGGT
*
2040641 AATTTGTAAAGCCTCTAGGG-
1 AATTTGTAAAGCCTC-CGGGT
*
2040661 AATTTGTAAAGCCTCCGGAT
1 AATTTGTAAAGCCTCCGGGT
2040681 AATTTGTAAAGCCTCCGGGT
1 AATTTGTAAAGCCTCCGGGT
*
2040701 AATTTTTAAAGCCTCCGGGT
1 AATTTGTAAAGCCTCCGGGT
*
2040721 AATTTGTAAAGGCTCCGGGT
1 AATTTGTAAAGCCTCCGGGT
2040741 AATTTGTAAAGCCTCCGGGT
1 AATTTGTAAAGCCTCCGGGT
*
2040761 AATTTGTAACGCCTCCGGGT
1 AATTTGTAAAGCCTCCGGGT
* * *
2040781 TATTTGTAAAACCTTCGGGT
1 AATTTGTAAAGCCTCCGGGT
2040801 AATTTGTAAA
1 AATTTGTAAA
2040811 TCCTTTGGGT
Statistics
Matches: 154, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
19 2 0.01
20 149 0.97
21 3 0.02
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (20 bp):
AATTTGTAAAGCCTCCGGGT
Found at i:2041159 original size:42 final size:42
Alignment explanation
Indices: 2041105--2041206 Score: 114
Period size: 42 Copynumber: 2.4 Consensus size: 42
2041095 GTATGAAGTC
* * * *
2041105 TCACGGAGGAGTAGTGAAGTATTCCAGTCTCGAATCCAACCT
1 TCACGGAAGAGTAGTGAAGCAATCCAATCTCGAATCCAACCT
* * * ** *
2041147 TCACGGAAGAGTAGTGAAGCAATCCAATTTTGAGTCTGATCT
1 TCACGGAAGAGTAGTGAAGCAATCCAATCTCGAATCCAACCT
2041189 TCACGGAAGAGTAGTGAA
1 TCACGGAAGAGTAGTGAA
2041207 ACAGATTCTG
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (42 bp):
TCACGGAAGAGTAGTGAAGCAATCCAATCTCGAATCCAACCT
Found at i:2041528 original size:11 final size:10
Alignment explanation
Indices: 2041486--2041535 Score: 50
Period size: 11 Copynumber: 4.9 Consensus size: 10
2041476 GTGACATTTT
2041486 TTATAT-TTA
1 TTATATATTA
2041495 TTATATATATA
1 TTATATAT-TA
*
2041506 TAATAATATTA
1 TTAT-ATATTA
2041517 TTATATTATTA
1 TTATA-TATTA
2041528 TTAT-TATT
1 TTATATATT
2041536 TATAAAGCCC
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
9 10 0.29
10 2 0.06
11 19 0.54
12 4 0.11
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
TTATATATTA
Found at i:2044841 original size:13 final size:13
Alignment explanation
Indices: 2044823--2044863 Score: 57
Period size: 13 Copynumber: 3.1 Consensus size: 13
2044813 ATAAAACATT
2044823 AGAAATAAAATAA
1 AGAAATAAAATAA
2044836 AGAAATAAAATAA
1 AGAAATAAAATAA
2044849 A-ATAATAATAATAA
1 AGA-AATAA-AATAA
2044863 A
1 A
2044864 AACAGAAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 1 0.04
13 19 0.73
14 6 0.23
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.20
Consensus pattern (13 bp):
AGAAATAAAATAA
Found at i:2044862 original size:32 final size:31
Alignment explanation
Indices: 2044808--2044877 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 31
2044798 AATTTAATAT
*
2044808 ATAAAATAAAACATTAGAAATAAAATAAAGAA
1 ATAAAATAAAACAATAGAAATAAAA-AAAGAA
* *
2044840 ATAAAATAAAATAATA-ATAATAAAAACAGAA
1 ATAAAATAAAACAATAGA-AATAAAAAAAGAA
2044871 ATGAAAA
1 AT-AAAA
2044878 CGCAAAAGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 8 0.24
32 25 0.76
ACGTcount: A:0.73, C:0.03, G:0.06, T:0.19
Consensus pattern (31 bp):
ATAAAATAAAACAATAGAAATAAAAAAAGAA
Found at i:2046200 original size:18 final size:19
Alignment explanation
Indices: 2046166--2046220 Score: 62
Period size: 18 Copynumber: 3.0 Consensus size: 19
2046156 AATATATGCT
2046166 ATATAATTATAGT--ATATA
1 ATATAA-TATAGTACATATA
*
2046184 ATATAATAT-GTACATATT
1 ATATAATATAGTACATATA
*
2046202 ATGTAATATAGTACATATA
1 ATATAATATAGTACATATA
2046221 CATTATATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 2 0.06
17 3 0.10
18 18 0.58
19 8 0.26
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.42
Consensus pattern (19 bp):
ATATAATATAGTACATATA
Done.