Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001448.1 Hibiscus syriacus cultivar Beakdansim tig00002799_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: 1849635
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 9
Found at i:1477999 original size:10 final size:10
Alignment explanation
Indices: 1477984--1478283 Score: 111
Period size: 10 Copynumber: 29.4 Consensus size: 10
1477974 ATAATTACAC
*
1477984 TTTATATATT
1 TTTATATATA
1477994 TTTATATATA
1 TTTATATATA
*
1478004 TATATATATA
1 TTTATATATA
*
1478014 TATATAATATA
1 TTTAT-ATATA
* *
1478025 CTTATACTTTA
1 TTTATA-TATA
*
1478036 TATATATATA
1 TTTATATATA
* **
1478046 TGTATAT-GC
1 TTTATATATA
*
1478055 TTTATAGTAAA
1 TTTATA-TATA
1478066 CTTTATATATA
1 -TTTATATATA
*
1478077 --TATA-CT-
1 TTTATATATA
*
1478083 TTTACTTTATA
1 TTTA-TATATA
1478094 GTTTATATA-A
1 -TTTATATATA
*
1478104 -TTATACATA
1 TTTATATATA
*
1478113 CTTACGT-TATA
1 TTTA--TATATA
*
1478124 TGTATATATA
1 TTTATATATA
1478134 CTTTATAT-TA
1 -TTTATATATA
*
1478144 TATACTTATATA
1 TTTA--TATATA
* *
1478156 TTT-TA-GTC
1 TTTATATATA
*
1478164 TTTATAATTAGA
1 TTTAT-A-TATA
1478176 GTTTATATATA
1 -TTTATATATA
*
1478187 TATATATATA
1 TTTATATATA
*
1478197 TATATATATA
1 TTTATATATA
*
1478207 TATATATATA
1 TTTATATATA
*
1478217 TATAT-TACTA
1 TTTATATA-TA
* *
1478227 CTTATATTTA
1 TTTATATATA
1478237 TATTATATATA
1 T-TTATATATA
*
1478248 TGTATATATA
1 TTTATATATA
1478258 GTTTATATATA
1 -TTTATATATA
*
1478269 TATATATATAA
1 TTTATATAT-A
1478280 TTTA
1 TTTA
1478284 AAGTTTATAT
Statistics
Matches: 218, Mismatches: 42, Indels: 59
0.68 0.13 0.18
Matches are distributed among these distances:
7 1 0.00
8 16 0.07
9 16 0.07
10 103 0.47
11 61 0.28
12 16 0.07
13 5 0.02
ACGTcount: A:0.39, C:0.05, G:0.04, T:0.53
Consensus pattern (10 bp):
TTTATATATA
Found at i:1478001 original size:2 final size:2
Alignment explanation
Indices: 1477986--1478052 Score: 66
Period size: 2 Copynumber: 33.5 Consensus size: 2
1477976 AATTACACTT
* *
1477986 TA TA TA TT TT TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA CT-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
* *
1478027 TA TA CTT TA TA TA TA TA TA TG TA TA T
1 TA TA -TA TA TA TA TA TA TA TA TA TA T
1478053 GCTTTATAGT
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
1 2 0.04
2 51 0.93
3 2 0.04
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (2 bp):
TA
Found at i:1478038 original size:133 final size:131
Alignment explanation
Indices: 1477789--1478045 Score: 331
Period size: 133 Copynumber: 1.9 Consensus size: 131
1477779 ACTAAAACTT
*
1477789 TTTATATATATACACGTACTTATACTTTATATGTATATATACTTTAGTCTTTATAATTACACCTT
1 TTTATATATATACAC-TACTTATACTTTATATATATATATACTTTAGTCTTTATAATTACACCTT
* * *
1477854 TTATTATTATATATGTATATATGCTTTATAGTAAAACTTTATATATATATATATACATACTTTAT
65 TTATTATTATATATATATATATGATATATAGTAAAACTTTATATATATATATATACATACTTTAT
1477919 AG
130 AG
* *
1477921 TTTATATATATACA-TACTTATACTTTATATTATACTTATATACTTTTGTCTTTATAATTACACT
1 TTTATATATATACACTACTTATACTTTATA-TATA--TATATACTTTAGTCTTTATAATTACACC
* *
1477985 TTATATATTTTTATATATATATATAT-ATATATA-TAATATACTTATACTTTATATATATATA
63 TT-T-TATTATTATATATATATATATGATATATAGTAA-A-ACTT-TA-TATATATATATATA
1478046 TGTATATGCT
Statistics
Matches: 108, Mismatches: 8, Indels: 13
0.84 0.06 0.10
Matches are distributed among these distances:
130 15 0.14
131 3 0.03
132 14 0.13
133 31 0.29
134 7 0.06
135 23 0.21
136 2 0.02
137 13 0.12
ACGTcount: A:0.37, C:0.09, G:0.03, T:0.51
Consensus pattern (131 bp):
TTTATATATATACACTACTTATACTTTATATATATATATACTTTAGTCTTTATAATTACACCTTT
TATTATTATATATATATATATGATATATAGTAAAACTTTATATATATATATATACATACTTTATA
G
Found at i:1478186 original size:2 final size:2
Alignment explanation
Indices: 1478179--1478516 Score: 131
Period size: 2 Copynumber: 171.0 Consensus size: 2
1478169 AATTAGAGTT
1478179 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
1478221 T- TA CTA CT- TA TA TT TA TA T- TA TA TA TA TG TA TA TA TA GTT
1 TA TA -TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
* * *
1478261 TA TA TA TA TA TA TA TA TA -A TT TA AA GTT TA TA TA TA TA CT- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA
* * * * *
1478303 TA TA CTT TA TA TT TA AA CTA TA TA -A TG TA TA -A T- TA TA CA TA
1 TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
* ** * *
1478344 -A TA TA TA AA TA TA -A GG TGA -A TA TA TT TA AA TA TA -A T- TCA
1 TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA T-A
* * * * *
1478383 TA TA TA -A TT TA TA TA TA AA CTA TA TA GTT TA TA CA TGG TA TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA T-A TA TA
* * * * *
1478425 TA TA -A TT TA TA CA TA -A TA TA TA TA TA GTT TG TA GA TA GTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA
* * *
1478467 TA -A TA -A TA TA AA TA TA AA CTA TA TA GTT TA TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA
1478508 TA TA T- TA TA
1 TA TA TA TA TA
1478517 ATTGTTTGAA
Statistics
Matches: 245, Mismatches: 56, Indels: 70
0.66 0.15 0.19
Matches are distributed among these distances:
1 20 0.08
2 208 0.85
3 17 0.07
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1478435 original size:11 final size:11
Alignment explanation
Indices: 1478421--1478518 Score: 67
Period size: 11 Copynumber: 8.9 Consensus size: 11
1478411 TTATACATGG
*
1478421 TATATATAATT
1 TATATATAATA
*
1478432 TATACATAATA
1 TATATATAATA
* *
1478443 TATATATAGTT
1 TATATATAATA
* * *
1478454 TGTAGATAGTA
1 TATATATAATA
1478465 TATA-ATAATA
1 TATATATAATA
*
1478475 TAAATATAA-A
1 TATATATAATA
*
1478485 CTATATAGT-TTA
1 -TATATA-TAATA
1478497 TATATATAATA
1 TATATATAATA
1478508 TATATTATAAT
1 TATA-TATAAT
1478519 TGTTTGAATT
Statistics
Matches: 67, Mismatches: 14, Indels: 11
0.73 0.15 0.12
Matches are distributed among these distances:
10 10 0.15
11 49 0.73
12 8 0.12
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (11 bp):
TATATATAATA
Found at i:1484812 original size:6 final size:6
Alignment explanation
Indices: 1484803--1484854 Score: 54
Period size: 6 Copynumber: 9.0 Consensus size: 6
1484793 TGTTATTTTG
* * *
1484803 TTATTT TTATTT TTA-TT TTATTA TTATTA TTATTT TT-TTT TTCTTT
1 TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT
*
1484849 TCATTT
1 TTATTT
1484855 ATTTAGCATT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
5 10 0.25
6 30 0.75
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.79
Consensus pattern (6 bp):
TTATTT
Found at i:1484947 original size:19 final size:19
Alignment explanation
Indices: 1484925--1484962 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1484915 AATTAATTCG
1484925 AATTGAATTTTTAAATTTT
1 AATTGAATTTTTAAATTTT
* *
1484944 AATTTAATTTTTTAATTTT
1 AATTGAATTTTTAAATTTT
1484963 TGCGATTAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (19 bp):
AATTGAATTTTTAAATTTT
Found at i:1485942 original size:19 final size:19
Alignment explanation
Indices: 1485918--1485954 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
1485908 ACCTTACTAA
1485918 CTCT-TTTTATTTT-TTTC
1 CTCTCTTTTATTTTATTTC
1485935 CTCTCTTTTATTTTATTTC
1 CTCTCTTTTATTTTATTTC
1485954 C
1 C
1485955 ATCATATGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
18 9 0.50
19 5 0.28
ACGTcount: A:0.08, C:0.22, G:0.00, T:0.70
Consensus pattern (19 bp):
CTCTCTTTTATTTTATTTC
Found at i:1488867 original size:106 final size:106
Alignment explanation
Indices: 1488730--1490065 Score: 2161
Period size: 106 Copynumber: 12.6 Consensus size: 106
1488720 AAAAGTTGTC
* * *
1488730 TGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGACATTGGACTCC
1 TGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* *
1488795 AGACAACGCATGTTCAACTTCACGACGAAGGGACCGTTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
* * *
1488836 TGTCAATAAACAATTTCCCAATATCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
1 TGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* *
1488901 AGACAACACATGTTCAACTTCACGACGAAGGGACCGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
* *
1488942 TGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
1 TGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* *
1489007 AGACAACGCATGTTCAACTTCATGACGAAGGGACCGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
* * * **
1489048 TGTCAATAAACAATTTCCCAATATCAGAGCCAATTTCAACTTCACAGTGAAGGATATTGGACTCC
1 TGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* *
1489113 AGACAACGCATGTTCAAATTCACGACGAAGGGACCGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
* * *
1489154 TGTCAACAAATAACTTCTCAATTTCAGAGCCAATTTCAACTTTACAACGAAGGATATTGGACTCC
1 TGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
*
1489219 AGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
*
1489260 TGTAAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
1 TGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
*
1489325 AGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
1489366 TGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
1 TGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
*
1489431 AGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
*
1489472 TGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAATGAAGGATATTGGACTCC
1 TGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
*
1489537 AGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
* * *
1489578 TGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTTAACTTCACAATGAAGGATATTGGACTCC
1 TGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
1489643 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
* * *
1489684 TGTCAATAAACAACTTCCCAATTTCAGAGGCAATTTCAACTTCACAACGAAAGATATTGGACTCC
1 TGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
1489749 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
* * * *
1489790 TGTCAATAAACAACTTCCCAATTTCATAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCT
1 TGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
1489855 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
* * * *
1489896 TGTCAACAAACAACGTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCA
1 TGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* * *
1489961 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
* * * * * * * *
1490002 TGTCAACAAACAA-TTTTCCAGTTCCAGAGTCAATTTCAACTTCACGACGGAGGATATTGAACTC
1 TGTCAATAAACAACTTCT-CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
1490066 GGAACAATGC
Statistics
Matches: 1155, Mismatches: 74, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
105 2 0.00
106 1153 1.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
TGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
Found at i:1490866 original size:26 final size:27
Alignment explanation
Indices: 1490823--1490873 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
1490813 CGAAATAAAC
*
1490823 ATATATATTTATATATTA-TATTATAT
1 ATATATATTTACATATTATTATTATAT
1490849 ATATATATTGTACA-ATTATTATTAT
1 ATATATATT-TACATATTATTATTAT
1490874 TATTAAACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 13 0.59
27 9 0.41
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (27 bp):
ATATATATTTACATATTATTATTATAT
Found at i:1492285 original size:9 final size:9
Alignment explanation
Indices: 1492271--1492372 Score: 75
Period size: 9 Copynumber: 11.3 Consensus size: 9
1492261 TTTCATTTCC
1492271 TTTATTATT
1 TTTATTATT
1492280 TTTATTATT
1 TTTATTATT
1492289 TTT-TTATT
1 TTTATTATT
* *
1492297 TCTGATT-TA
1 T-TTATTATT
* *
1492306 TTTAATGTT
1 TTTATTATT
*
1492315 TTTTTTA-T
1 TTTATTATT
*
1492323 TTTGTTATT
1 TTTATTATT
*
1492332 TTTATTTTT
1 TTTATTATT
1492341 AATTTATTATT
1 --TTTATTATT
*
1492352 ATTATTATT
1 TTTATTATT
*
1492361 ATTATTATT
1 TTTATTATT
1492370 TTT
1 TTT
1492373 CTTTTCTTTT
Statistics
Matches: 73, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
8 16 0.22
9 47 0.64
10 2 0.03
11 8 0.11
ACGTcount: A:0.22, C:0.01, G:0.03, T:0.75
Consensus pattern (9 bp):
TTTATTATT
Found at i:1492323 original size:16 final size:14
Alignment explanation
Indices: 1492311--1492366 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
1492301 ATTTATTTAA
*
1492311 TGTTTTTTTTATTT
1 TGTTATTTTTATTT
1492325 TGTTATTTTTATTT
1 TGTTATTTTTATTT
*
1492339 T-TAATTTATTATTAT
1 TGTTATTT-TTATT-T
* *
1492354 TATTATTATTATT
1 TGTTATTTTTATT
1492367 ATTTTTCTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
13 5 0.14
14 19 0.54
15 7 0.20
16 4 0.11
ACGTcount: A:0.21, C:0.00, G:0.04, T:0.75
Consensus pattern (14 bp):
TGTTATTTTTATTT
Found at i:1492336 original size:6 final size:6
Alignment explanation
Indices: 1492316--1492377 Score: 52
Period size: 6 Copynumber: 9.7 Consensus size: 6
1492306 TTTAATGTTT
* * *
1492316 TTTTTA TTTTGTTA TTTTTA TTTTTAA TTTATTA TTATTA TTATTA TTATTA
1 TTTTTA -TTT-TTA TTTTTA TTTTT-A TTT-TTA TTTTTA TTTTTA TTTTTA
*
1492368 TTTTTC TTTT
1 TTTTTA TTTT
1492378 CTTTTCATTT
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
6 31 0.63
7 13 0.27
8 5 0.10
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTTTA
Found at i:1492352 original size:3 final size:3
Alignment explanation
Indices: 1492344--1492369 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1492334 TATTTTTAAT
1492344 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
1492370 TTTCTTTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1492480 original size:19 final size:19
Alignment explanation
Indices: 1492458--1492495 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1492448 AATTAATTCG
1492458 AATTGAATTTTTAAATTTT
1 AATTGAATTTTTAAATTTT
* *
1492477 AATTTAATTTTTTAATTTT
1 AATTGAATTTTTAAATTTT
1492496 CGCGATTAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (19 bp):
AATTGAATTTTTAAATTTT
Found at i:1499198 original size:22 final size:22
Alignment explanation
Indices: 1499171--1499247 Score: 97
Period size: 22 Copynumber: 3.6 Consensus size: 22
1499161 TGAAAAGAAG
*
1499171 ATCGCAACACGATCTTCCAAGA
1 ATCGCAACGCGATCTTCCAAGA
* *
1499193 ATCGCAATGCGA--TT-CATAAA
1 ATCGCAACGCGATCTTCCA-AGA
1499213 ATCGCAACGCGATCTTCCAAGA
1 ATCGCAACGCGATCTTCCAAGA
1499235 ATCGCAACGCGAT
1 ATCGCAACGCGAT
1499248 TAAGAAAATG
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
19 2 0.04
20 15 0.33
22 27 0.59
23 2 0.04
ACGTcount: A:0.35, C:0.29, G:0.17, T:0.19
Consensus pattern (22 bp):
ATCGCAACGCGATCTTCCAAGA
Found at i:1499256 original size:42 final size:42
Alignment explanation
Indices: 1499165--1499256 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
1499155 CAACGTTGAA
* *
1499165 AAGAAGATCGCAACACGATCTTCCAAGAATCGCAATGCGATT
1 AAGAAAATCGCAACACGATCTTCCAAGAATCGCAACGCGATT
* * *
1499207 CATAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATT
1 AAGAAAATCGCAACACGATCTTCCAAGAATCGCAACGCGATT
1499249 AAGAAAAT
1 AAGAAAAT
1499257 GAGTAAATTC
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.40, C:0.24, G:0.17, T:0.18
Consensus pattern (42 bp):
AAGAAAATCGCAACACGATCTTCCAAGAATCGCAACGCGATT
Found at i:1499363 original size:6 final size:6
Alignment explanation
Indices: 1499352--1499495 Score: 267
Period size: 6 Copynumber: 24.5 Consensus size: 6
1499342 GACACGTATT
1499352 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1499400 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1499448 ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG ACC-CG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1499493 ACC
1 ACC
1499496 CGAGACGAGA
Statistics
Matches: 138, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 15 0.11
6 123 0.89
ACGTcount: A:0.32, C:0.51, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1499897 original size:20 final size:20
Alignment explanation
Indices: 1499841--1500256 Score: 345
Period size: 20 Copynumber: 20.2 Consensus size: 20
1499831 GAATTTACTC
*
1499841 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
1499861 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
*
1499883 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
1499903 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
* *
1499925 ATTTACTGAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
*
1499945 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
1499965 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
**
1499987 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTAAATCGCGTTGCG
*
1500007 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
1500027 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTAAATCGCGTTGCG
*
1500047 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
1500067 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
*
1500089 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
*
1500109 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
1500129 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
* * *
1500151 ATTTTATGAATCGCATTGCG
1 ATTTTCTAAATCGCGTTGCG
**
1500171 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
* ** *
1500193 ATCTTCT-TTTCAACGTTGCG
1 ATTTTCTAAATC-GCGTTGCG
*
1500213 CTTTTCTAAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
* * *
1500233 GTTTT-GATATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
1500252 ATTTT
1 ATTTT
1500257 GTTGGTCATT
Statistics
Matches: 324, Mismatches: 55, Indels: 35
0.78 0.13 0.08
Matches are distributed among these distances:
19 22 0.07
20 180 0.56
21 37 0.11
22 85 0.26
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (20 bp):
ATTTTCTAAATCGCGTTGCG
Found at i:1499900 original size:42 final size:40
Alignment explanation
Indices: 1499841--1500256 Score: 420
Period size: 42 Copynumber: 10.1 Consensus size: 40
1499831 GAATTTACTC
1499841 ATTTTCTGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCG
*
1499883 ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCG
*
1499925 ATTTACTGAATCGCGTTGCGATTTTCTT--AATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGA--TTCTTGGAATCGCGTTGCG
*
1499965 ATTCTT-GGAAGATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1 ATT-TTCTG-A-ATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1500007 ATTTTCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
*
1500047 ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCG
*
1500089 ATTTTCTGAATCGCGTTGCGATT-TTCTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTT-GGAATCGCGTTGCG
* * *
1500129 ATTCTT-GGAAGATCGCGTTGCGATT-TTATGAATCGCATTGCG
1 ATT-TTCTG-A-ATCGCGTTGCGATTCTT-GGAATCGCGTTGCG
* **** *
1500171 ATTCTT-GGAAGATCGCGTTGCGA-TCTTCTTTTCAACGTTGCG
1 ATT-TTCTG-A-ATCGCGTTGCGATTCTTGGAATC-GCGTTGCG
* * *
1500213 CTTTTCTAAATCGCGTTGCGGTT-TT-GATATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTTGGA-ATCGCGTTGCG
1500252 ATTTT
1 ATTTT
1500257 GTTGGTCATT
Statistics
Matches: 328, Mismatches: 27, Indels: 41
0.83 0.07 0.10
Matches are distributed among these distances:
39 11 0.03
40 108 0.33
41 20 0.06
42 184 0.56
44 5 0.02
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (40 bp):
ATTTTCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
Found at i:1499949 original size:62 final size:60
Alignment explanation
Indices: 1499848--1500256 Score: 377
Period size: 62 Copynumber: 6.6 Consensus size: 60
1499838 CTCATTTTCT
*
1499848 GAATCGCGTTGCGATTCTT-GGAAGATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATT-TTCTG-A-ATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTG
*
1499910 GAAGATCGCGTTGCGATTTACTGAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTG
1 G-A-ATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTG
* *
1499972 GAAGATCGCGTTGCGATTCTT-GGAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTG
1 G-A-ATCGCGTTGCGATT-TTCTGAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTG
* *** *
1500034 GAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATT-TTCT
1 GAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATT-TTCTTA-ATCGCGTTGCGATTCTT-G
*** *
1500096 GAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATT-TTAT
1 GAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATT-TTCTTA-ATCGCGTTGCGATTCTT-G
* * * * * * *
1500158 GAATCGCATTGCGATTCTT-GGAAGATCGCGTTGCGATCTTCTT-TTCAACGTTGCGCTT-TTCT
1 GAATCGCGTTGCGATT-TTCTG-A-ATCGCGTTGCGATTTTCTTAATC-GCGTTGCGATTCTT-G
* *
1500220 AAATCGCGTTGCG-GTTT-TGATATCGCGTTGCGATTTT
1 GAATCGCGTTGCGATTTTCTGA-ATCGCGTTGCGATTTT
1500257 GTTGGTCATT
Statistics
Matches: 306, Mismatches: 29, Indels: 27
0.85 0.08 0.07
Matches are distributed among these distances:
59 18 0.06
60 32 0.10
61 9 0.03
62 210 0.69
63 9 0.03
64 28 0.09
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (60 bp):
GAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTG
Found at i:1500370 original size:27 final size:27
Alignment explanation
Indices: 1500340--1500397 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
1500330 GATTTTCTCT
1500340 ATTAAATATATAATGACATATTTAATA
1 ATTAAATATATAATGACATATTTAATA
1500367 ATTAAATATATAATGACATATTTAATA
1 ATTAAATATATAATGACATATTTAATA
1500394 ATTA
1 ATTA
1500398 TTGCTTATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.41
Consensus pattern (27 bp):
ATTAAATATATAATGACATATTTAATA
Found at i:1501647 original size:44 final size:45
Alignment explanation
Indices: 1501564--1501661 Score: 135
Period size: 44 Copynumber: 2.2 Consensus size: 45
1501554 GGATTATCTG
* *
1501564 CCGCCAGAACTTCCAACACCAGGAATCCCTCCGTCACCATCTGTA
1 CCGCCAGAACTTCCAACACCAGGAATCCCACCGCCACCATCTGTA
* * * *
1501609 CTGCCAGAACTTCCAA-GCCGGGAATCCCACTGCCACCATCTGTA
1 CCGCCAGAACTTCCAACACCAGGAATCCCACCGCCACCATCTGTA
1501653 CCGCCAGAA
1 CCGCCAGAA
1501662 ATTTTAACAC
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 31 0.67
45 15 0.33
ACGTcount: A:0.27, C:0.41, G:0.16, T:0.16
Consensus pattern (45 bp):
CCGCCAGAACTTCCAACACCAGGAATCCCACCGCCACCATCTGTA
Found at i:1507692 original size:2 final size:2
Alignment explanation
Indices: 1507687--1507713 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1507677 AAAAAAATGA
1507687 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1507714 AATAAATCCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1507901 original size:16 final size:16
Alignment explanation
Indices: 1507873--1507915 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
1507863 TTAAATTTCT
*
1507873 TTTAA-AATTTAAATA
1 TTTAAGAATTTAAAGA
*
1507888 TTTAAGATTTTAAAGA
1 TTTAAGAATTTAAAGA
1507904 TTTAAGAATTTA
1 TTTAAGAATTTA
1507916 GGGACAACAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 5 0.21
16 19 0.79
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (16 bp):
TTTAAGAATTTAAAGA
Found at i:1509008 original size:9 final size:9
Alignment explanation
Indices: 1508971--1509008 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
1508961 TGATTGGAAG
1508971 TTATTTTAT
1 TTATTTTAT
* *
1508980 TAATTTTAA
1 TTATTTTAT
1508989 TTATTTTAT
1 TTATTTTAT
1508998 TTATTTTAT
1 TTATTTTAT
1509007 TT
1 TT
1509009 TTCTCCAATC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (9 bp):
TTATTTTAT
Found at i:1509352 original size:23 final size:24
Alignment explanation
Indices: 1509323--1509382 Score: 79
Period size: 23 Copynumber: 2.6 Consensus size: 24
1509313 TTTCATATAT
1509323 TTTAAAATATAATTAATATAA-AA
1 TTTAAAATATAATTAATATAATAA
* * *
1509346 TTTAAAATAAAATTAATTTAATAT
1 TTTAAAATATAATTAATATAATAA
1509370 TTTAAAAT-TAATT
1 TTTAAAATATAATT
1509383 TCACCAAAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 23 0.72
24 9 0.28
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTAAAATATAATTAATATAATAA
Found at i:1517181 original size:2 final size:2
Alignment explanation
Indices: 1517174--1517203 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1517164 TTGAATTTCG
1517174 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
1517204 GTGGTATTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1518398 original size:14 final size:15
Alignment explanation
Indices: 1518379--1518408 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1518369 TTTTTTTGTG
1518379 TTTTTT-AAAAAATT
1 TTTTTTGAAAAAATT
1518393 TTTTTTGAAAAAATT
1 TTTTTTGAAAAAATT
1518408 T
1 T
1518409 ATATAATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (15 bp):
TTTTTTGAAAAAATT
Found at i:1518450 original size:38 final size:36
Alignment explanation
Indices: 1518402--1518663 Score: 332
Period size: 36 Copynumber: 7.1 Consensus size: 36
1518392 TTTTTTTGAA
* * *
1518402 AAAATTTATATAATATATAATTTTTTTATATCATTTTG
1 AAAACTTATATAATATAT-A-TTTTTTAAAACATTTTG
* * *
1518440 AAAA-TATATATAATATATAGTTTTTAAATCATATTG
1 AAAACT-TATATAATATATATTTTTTAAAACATTTTG
*
1518476 AAAACTTGTATATAATATATAGTTTTTAAAACATTTTG
1 AAAAC-T-TATATAATATATATTTTTTAAAACATTTTG
1518514 AAAACTTATATAATATA-ATTTTTTTAAAACATTTTG
1 AAAACTTATATAATATATA-TTTTTTAAAACATTTTG
*
1518550 AAAA-TATATATAATATATAGTTTTTTAAAATATTTTG
1 AAAACT-TATATAATATATA-TTTTTTAAAACATTTTG
*
1518587 AAAACTTATATAATATATAGTTTTTAAAACATTTTG
1 AAAACTTATATAATATATATTTTTTAAAACATTTTG
*
1518623 AAAACTTATATAATACATAGTTTTTTAAAACATTTTG
1 AAAACTTATATAATATATA-TTTTTTAAAACATTTTG
1518660 AAAA
1 AAAA
1518664 TATATAGGTT
Statistics
Matches: 203, Mismatches: 13, Indels: 17
0.87 0.06 0.07
Matches are distributed among these distances:
35 2 0.01
36 93 0.46
37 57 0.28
38 51 0.25
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (36 bp):
AAAACTTATATAATATATATTTTTTAAAACATTTTG
Found at i:1518591 original size:73 final size:73
Alignment explanation
Indices: 1518402--1518663 Score: 361
Period size: 73 Copynumber: 3.6 Consensus size: 73
1518392 TTTTTTTGAA
* * * *
1518402 AAAATTTATATAATATATAATTTTTTTATATCATTTTGAAAA-TATATATAATATATAGTTTTTA
1 AAAACTTATATAATATAT-AGTTTTTTAAAACATTTTGAAAACT-TATATAATATATAGTTTTTA
* *
1518466 AATCATATTG
64 AAACATTTTG
*
1518476 AAAACTTGTATATAATATATAG-TTTTTAAAACATTTTGAAAACTTATATAATATA-ATTTTTTT
1 AAAAC-T-TATATAATATATAGTTTTTTAAAACATTTTGAAAACTTATATAATATATA-GTTTTT
1518539 AAAACATTTTG
63 AAAACATTTTG
*
1518550 AAAA-TATATATAATATATAGTTTTTTAAAATATTTTGAAAACTTATATAATATATAGTTTTTAA
1 AAAACT-TATATAATATATAGTTTTTTAAAACATTTTGAAAACTTATATAATATATAGTTTTTAA
1518614 AACATTTTG
65 AACATTTTG
*
1518623 AAAACTTATATAATACATAGTTTTTTAAAACATTTTGAAAA
1 AAAACTTATATAATATATAGTTTTTTAAAACATTTTGAAAA
1518664 TATATAGGTT
Statistics
Matches: 169, Mismatches: 12, Indels: 15
0.86 0.06 0.08
Matches are distributed among these distances:
72 15 0.09
73 86 0.51
74 53 0.31
75 3 0.02
76 12 0.07
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (73 bp):
AAAACTTATATAATATATAGTTTTTTAAAACATTTTGAAAACTTATATAATATATAGTTTTTAAA
ACATTTTG
Found at i:1518691 original size:27 final size:26
Alignment explanation
Indices: 1518618--1518694 Score: 66
Period size: 28 Copynumber: 2.8 Consensus size: 26
1518608 TTTTAAAACA
* *
1518618 TTTTGAAAAC-TTATATAATACATAGT
1 TTTTGAAAACTTTTTA-AATACATAGG
* * *
1518644 TTTTTAAAACATTTTGAAAATATATAGG
1 TTTTGAAAAC-TTTT-TAAATACATAGG
1518672 TTTTGAAAACGTTTTTAAATACA
1 TTTTGAAAAC-TTTTTAAATACA
1518695 CATAATAAAA
Statistics
Matches: 39, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
26 9 0.23
27 6 0.15
28 23 0.59
29 1 0.03
ACGTcount: A:0.42, C:0.06, G:0.09, T:0.43
Consensus pattern (26 bp):
TTTTGAAAACTTTTTAAATACATAGG
Found at i:1521410 original size:24 final size:22
Alignment explanation
Indices: 1521383--1521444 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 22
1521373 GTTTTAGTGG
1521383 TTTTTATTTTATTTATTTTTAAT
1 TTTTTATTTTATTTATTTTT-AT
1521406 TTTTTACTTCTTA-TTATTTTTAT
1 TTTTTA-TT-TTATTTATTTTTAT
*
1521429 TTTATTACTTTATTTA
1 TTT-TTATTTTATTTA
1521445 ACATTTTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 3 0.09
23 15 0.44
24 13 0.38
25 3 0.09
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (22 bp):
TTTTTATTTTATTTATTTTTAT
Found at i:1521491 original size:24 final size:23
Alignment explanation
Indices: 1521452--1521506 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
1521442 TTAACATTTT
*
1521452 TTTATTTTTTCCTTTTTATTTAA
1 TTTATTTTTTCCTTTTCATTTAA
* * *
1521475 TTTATTTTTATCTTTTTCCTTTGA
1 TTTATTTTT-TCCTTTTCATTTAA
1521499 TTTATTTT
1 TTTATTTT
1521507 ATTATTATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
23 9 0.33
24 18 0.67
ACGTcount: A:0.15, C:0.09, G:0.02, T:0.75
Consensus pattern (23 bp):
TTTATTTTTTCCTTTTCATTTAA
Found at i:1521501 original size:29 final size:27
Alignment explanation
Indices: 1521385--1521515 Score: 101
Period size: 29 Copynumber: 4.8 Consensus size: 27
1521375 TTTAGTGGTT
* *
1521385 TTTATTTTATTTATTTTTAATTTTTTAC
1 TTTATTTAATTTATTTTT-ATTTTTTCC
* *
1521413 -TT-CTT-A-TTATTTTTATTTTATTAC
1 TTTATTTAATTTATTTTTATTTT-TTCC
*
1521437 TTTATTTAACATT-TTTTTATTTTTTCC
1 TTTATTTAA-TTTATTTTTATTTTTTCC
1521464 TTTTTATTTAATTTATTTTTATCTTTTTCC
1 --TTTATTTAATTTATTTTTAT-TTTTTCC
* *
1521494 TTTGATTTATTTTATTATTATT
1 TTT-ATTTAATTTATTTTTATT
1521516 ATTATTATTA
Statistics
Matches: 86, Mismatches: 6, Indels: 22
0.75 0.05 0.19
Matches are distributed among these distances:
23 5 0.06
24 12 0.14
25 3 0.03
26 4 0.05
27 6 0.07
28 16 0.19
29 33 0.38
30 7 0.08
ACGTcount: A:0.20, C:0.07, G:0.01, T:0.73
Consensus pattern (27 bp):
TTTATTTAATTTATTTTTATTTTTTCC
Found at i:1521534 original size:81 final size:79
Alignment explanation
Indices: 1521383--1521535 Score: 177
Period size: 81 Copynumber: 1.9 Consensus size: 79
1521373 GTTTTAGTGG
* *
1521383 TTTTTATTTTATTTATTTTTAATTTTTTACTTCTTATTATTTTTATTTTATTACTTTATTTAACA
1 TTTTTATTTAATTTATTTTTAATTTTTTACTTCTGATTATTTTTATTTTATTACTTTATTT-A-A
1521448 TTTTTTTATTTTTTCC
64 TTTTTTTATTTTTTCC
* *
1521464 TTTTTATTTAATTTATTTTT-ATCTTTTTCCTT-TGATTTATTTTATTATTATTATTATTATTAT
1 TTTTTATTTAATTTATTTTTAAT-TTTTTACTTCTGA-TTA-TTT-TTATT-TTATTACT-TTAT
1521527 TT-ATTTTTT
60 TTAATTTTTT
1521536 CTCTTTGATT
Statistics
Matches: 62, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
80 4 0.06
81 30 0.48
82 10 0.16
83 5 0.08
84 7 0.11
85 6 0.10
ACGTcount: A:0.20, C:0.06, G:0.01, T:0.73
Consensus pattern (79 bp):
TTTTTATTTAATTTATTTTTAATTTTTTACTTCTGATTATTTTTATTTTATTACTTTATTTAATT
TTTTTATTTTTTCC
Found at i:1521577 original size:17 final size:17
Alignment explanation
Indices: 1521555--1521608 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
1521545 TATTTTAATC
1521555 ATTTATTTTTTCCTTTG
1 ATTTATTTTTTCCTTTG
1521572 ATTTATTTTCTT-CTTT-
1 ATTTATTTT-TTCCTTTG
*
1521588 -TCT-TTTTTTCCTTTG
1 ATTTATTTTTTCCTTTG
1521603 ATTTAT
1 ATTTAT
1521609 ATAATATCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
13 2 0.07
14 8 0.27
15 2 0.07
16 2 0.07
17 14 0.47
18 2 0.07
ACGTcount: A:0.11, C:0.13, G:0.04, T:0.72
Consensus pattern (17 bp):
ATTTATTTTTTCCTTTG
Found at i:1521595 original size:31 final size:30
Alignment explanation
Indices: 1521525--1521608 Score: 107
Period size: 30 Copynumber: 2.8 Consensus size: 30
1521515 TATTATTATT
1521525 ATTTATTTTTTCTCTTTGA-TTATTTTAATC
1 ATTTATTTTTTC-CTTTGATTTATTTTAATC
**
1521555 ATTTATTTTTTCCTTTGATTTATTTTCTTC
1 ATTTATTTTTTCCTTTGATTTATTTTAATC
* *
1521585 TTTTCTTTTTTTCCTTTGATTTAT
1 ATTT-ATTTTTTCCTTTGATTTAT
1521609 ATAATATCTA
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
29 6 0.12
30 24 0.50
31 18 0.38
ACGTcount: A:0.14, C:0.12, G:0.04, T:0.70
Consensus pattern (30 bp):
ATTTATTTTTTCCTTTGATTTATTTTAATC
Found at i:1522327 original size:2 final size:2
Alignment explanation
Indices: 1522320--1522345 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1522310 ATGCTTTTCG
1522320 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
1522346 TATCATTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1524976 original size:193 final size:189
Alignment explanation
Indices: 1524650--1525032 Score: 689
Period size: 193 Copynumber: 2.0 Consensus size: 189
1524640 TTTTTAATAA
1524650 GTTATTAAGTTAGCATGGTGGTTGGTGTTTAGTTTTAATCTTAAAGGTTTATGATATGATCTCAT
1 GTTATTAAGTTAGCATGGTGGTTGGTGTTTAGTTTTAATCTTAAAGGTTTATGATATGATCTCAT
1524715 TGAAATCATTTTTTCTATCACAAACACGTCGTTTTGAGCATCAAAACGGTCGTGCCAAAACGATG
66 TGAAATCATTTTTTCTATCACAAACACGTCGTTTTGAGCATCAAAACGGTCGTGCCAAAACGATG
1524780 TCGTTTTGATGAGGGAGTCACATCATCGCCATCACGGAATGGAGA-TCATGTCATCGTT
131 TCGTTTTGATGAGGGAGTCACATCATCGCCATCACGGAATGGAGAGTCATGTCATCGTT
1524838 GTTATTAAGTTAGCATGGTGGTTGGATGTTTAGTTTTAATTCTTAAAGGTTTATGAT-TGAATCT
1 GTTATTAAGTTAGCATGGTGGTTGG-TGTTTAGTTTTAA-TCTTAAAGGTTTATGATATG-ATCT
1524902 CATTGAAATCATTTTTTCTATCAACAAAACGACGTCGTTTTGAGCATCAAAACGGTCGTGCCAAA
63 CATTGAAATCATTTTTTCTATC-AC-AAAC-ACGTCGTTTTGAGCATCAAAACGGTCGTGCCAAA
1524967 ACGATGTCGTTTTGATGAGGGAGTCACATCATCGCCATCACGGAATGGAGATGTCATGTCATCGT
125 ACGATGTCGTTTTGATGAGGGAGTCACATCATCGCCATCACGGAATGGAGA-GTCATGTCATCGT
1525032 T
189 T
1525033 CCGTTAATGG
Statistics
Matches: 187, Mismatches: 0, Indels: 9
0.95 0.00 0.05
Matches are distributed among these distances:
188 25 0.13
189 15 0.08
190 43 0.23
191 2 0.01
192 4 0.02
193 85 0.45
195 13 0.07
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (189 bp):
GTTATTAAGTTAGCATGGTGGTTGGTGTTTAGTTTTAATCTTAAAGGTTTATGATATGATCTCAT
TGAAATCATTTTTTCTATCACAAACACGTCGTTTTGAGCATCAAAACGGTCGTGCCAAAACGATG
TCGTTTTGATGAGGGAGTCACATCATCGCCATCACGGAATGGAGAGTCATGTCATCGTT
Found at i:1525928 original size:20 final size:21
Alignment explanation
Indices: 1525903--1525954 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1525893 TTTTCCCAAT
*
1525903 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1525923 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1525944 TCGCAATGCGA
1 TCGCAATGCGA
1525955 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1525968 original size:20 final size:20
Alignment explanation
Indices: 1525943--1526056 Score: 113
Period size: 20 Copynumber: 5.7 Consensus size: 20
1525933 AATTGGGAAA
*
1525943 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1525963 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTGACT
* * *
1525983 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
1526004 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1526024 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
1526044 TTCGCAACGCGAT
1 ATCGCAACGCGAT
1526057 TTACATAGCG
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
19 2 0.02
20 64 0.79
21 13 0.16
22 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1525987 original size:61 final size:61
Alignment explanation
Indices: 1525940--1526056 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
1525930 GCGAATTGGG
* * * * *
1525940 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
1526001 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGAT
1526057 TTACATAGCG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:1526632 original size:19 final size:19
Alignment explanation
Indices: 1526608--1526644 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1526598 ACGAGAGAAT
*
1526608 CGCAACGCGAAATAAAAAA
1 CGCAACGCGAAACAAAAAA
1526627 CGCAACGCGAAACAAAAA
1 CGCAACGCGAAACAAAAA
1526645 TCACATTGCG
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:0.57, C:0.24, G:0.16, T:0.03
Consensus pattern (19 bp):
CGCAACGCGAAACAAAAAA
Found at i:1526670 original size:19 final size:19
Alignment explanation
Indices: 1526650--1526776 Score: 120
Period size: 19 Copynumber: 6.8 Consensus size: 19
1526640 AAAAATCACA
*
1526650 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCG
**
1526669 TTATGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
1526688 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
* *
1526707 TTGCGA--TTC---TCTCA
1 TTGCGATTTTCATTTCGCG
**
1526721 TTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTT-CGCG
* *
1526741 TTGCGATTCTCATTATCTCG
1 TTGCGATTTTCATT-TCGCG
1526761 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1526777 AACCAAAAGA
Statistics
Matches: 87, Mismatches: 14, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
14 9 0.10
16 2 0.02
17 3 0.03
19 42 0.48
20 30 0.34
21 1 0.01
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:1526734 original size:33 final size:34
Alignment explanation
Indices: 1526688--1526751 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
1526678 TCATTTCGCG
**
1526688 TTGCGATTTTCATTT-CGCGTTGCGATTCTCTCA
1 TTGCGATAGTCATTTCCGCGTTGCGATTCTCTCA
1526721 TTGCGATAGTCATTTCCGCGTTGCGATTCTC
1 TTGCGATAGTCATTTCCGCGTTGCGATTCTC
1526752 ATTATCTCGT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
33 13 0.46
34 15 0.54
ACGTcount: A:0.12, C:0.25, G:0.20, T:0.42
Consensus pattern (34 bp):
TTGCGATAGTCATTTCCGCGTTGCGATTCTCTCA
Found at i:1526753 original size:20 final size:19
Alignment explanation
Indices: 1526730--1526776 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
1526720 ATTGCGATAG
*
1526730 TCATTTCCGCGTTGCGATTC
1 TCATTT-CGCGTTGCGATTT
*
1526750 TCATTATCTCGTTGCGATTT
1 TCATT-TCGCGTTGCGATTT
1526770 TCATTTC
1 TCATTTC
1526777 AACCAAAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.88
21 1 0.04
ACGTcount: A:0.13, C:0.26, G:0.15, T:0.47
Consensus pattern (19 bp):
TCATTTCGCGTTGCGATTT
Found at i:1528851 original size:21 final size:21
Alignment explanation
Indices: 1528827--1528893 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1528817 TCATTCCTCG
1528827 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
1528848 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
1528869 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
1528890 AGAG
1 AGAG
1528894 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:1528851 original size:42 final size:42
Alignment explanation
Indices: 1528775--1528893 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
1528765 GACTCGCCTG
* * * * * * *
1528775 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
1528817 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
1528859 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
1528894 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:1530455 original size:19 final size:19
Alignment explanation
Indices: 1530393--1530446 Score: 90
Period size: 20 Copynumber: 2.8 Consensus size: 19
1530383 AAAAAGTACT
*
1530393 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
1530412 ATCGCAACGCGAAAATGAAA
1 ATCGCAACGCG-AAATGAAA
1530432 ATCGCAACGCGAAAT
1 ATCGCAACGCGAAAT
1530447 TAAATTCGCG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
19 14 0.42
20 19 0.58
ACGTcount: A:0.46, C:0.20, G:0.20, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:1530473 original size:19 final size:19
Alignment explanation
Indices: 1530451--1530620 Score: 100
Period size: 19 Copynumber: 9.7 Consensus size: 19
1530441 CGAAATTAAA
1530451 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* **
1530470 TTCGCATTGCGA--TTCCC
1 TTCGCGTTGCGATTTTCAT
*
1530487 TT---GTTGCAATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
1530503 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
* *
1530517 TTAGCGTTGCAATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1530536 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
1530551 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
1530569 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
1530588 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
1530607 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
1530621 AGACATTAAG
Statistics
Matches: 110, Mismatches: 25, Indels: 31
0.66 0.15 0.19
Matches are distributed among these distances:
14 24 0.22
16 8 0.07
17 8 0.07
19 60 0.55
20 10 0.09
ACGTcount: A:0.16, C:0.22, G:0.19, T:0.43
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:1530499 original size:33 final size:32
Alignment explanation
Indices: 1530456--1530582 Score: 157
Period size: 33 Copynumber: 3.9 Consensus size: 32
1530446 TTAAATTCGC
*
1530456 GTTGCGATTTTCATTTCGCATTGCGATTCCCTT
1 GTTGCAATTTTCATTTCGCATTGCGATTCCC-T
**
1530489 GTTGCAATTTTCATTTCGCATTGCGAAATTAGC-
1 GTTGCAATTTTCATTTCGCATTGCG--ATTCCCT
*
1530522 GTTGCAATTTTCATTTCGCATTGCGATTCTCT
1 GTTGCAATTTTCATTTCGCATTGCGATTCCCT
* *
1530554 CGTTGCGATTTTCATTTCGCGTTGCGATT
1 -GTTGCAATTTTCATTTCGCATTGCGATT
1530583 TTCATTTCGC
Statistics
Matches: 83, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
31 4 0.05
33 75 0.90
35 4 0.05
ACGTcount: A:0.16, C:0.21, G:0.19, T:0.44
Consensus pattern (32 bp):
GTTGCAATTTTCATTTCGCATTGCGATTCCCT
Found at i:1530544 original size:66 final size:66
Alignment explanation
Indices: 1530448--1530580 Score: 212
Period size: 66 Copynumber: 2.0 Consensus size: 66
1530438 ACGCGAAATT
* * *
1530448 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTTGTTGCAATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCAATTTTCATTTCGCATTGCGATTCCCTCGTTGCAATTTTCATTTCGCATTGC
1530513 G
66 G
* * *
1530514 AAATTAGCGTTGCAATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCGTTGC
1 AAATTAGCGTTGCAATTTTCATTTCGCATTGCGATTCCCTCGTTGCAATTTTCATTTCGCATTGC
1530579 G
66 G
1530580 A
1 A
1530581 TTTTCATTTC
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.17, C:0.22, G:0.19, T:0.42
Consensus pattern (66 bp):
AAATTAGCGTTGCAATTTTCATTTCGCATTGCGATTCCCTCGTTGCAATTTTCATTTCGCATTGC
G
Found at i:1532782 original size:23 final size:23
Alignment explanation
Indices: 1532751--1532795 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1532741 ATCATCAAAA
* *
1532751 TCCGTGTATTGACCAATATCAAG
1 TCCGGGTATTGACCAAGATCAAG
1532774 TCCGGGTATTGACCAAGATCAA
1 TCCGGGTATTGACCAAGATCAA
1532796 ATTTCGAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (23 bp):
TCCGGGTATTGACCAAGATCAAG
Found at i:1533872 original size:20 final size:20
Alignment explanation
Indices: 1533844--1533904 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
1533834 GACATTCATT
1533844 TGACTATCGCAACGCGAAAA
1 TGACTATCGCAACGCGAAAA
*
1533864 TGGCTATCGCAACGCGAAAA
1 TGACTATCGCAACGCGAAAA
*
1533884 TGACTATCGCAACGAGAAAA
1 TGACTATCGCAACGCGAAAA
1533904 T
1 T
1533905 CGCAATGCGA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.39, C:0.23, G:0.21, T:0.16
Consensus pattern (20 bp):
TGACTATCGCAACGCGAAAA
Found at i:1533947 original size:14 final size:14
Alignment explanation
Indices: 1533928--1533981 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
1533918 GAAAACCGCA
1533928 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
1533942 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
1533959 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
1533975 TTGCGAT
1 TTGCGAT
1533982 AGCCATTTCG
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
16 3 0.09
17 3 0.09
19 11 0.31
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:1533947 original size:33 final size:33
Alignment explanation
Indices: 1533910--1533980 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 33
1533900 AAAATCGCAA
1533910 TGCGAAATGAAAACCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAACCGCATTGCGATTTTCTCGT
** ** ***
1533943 TGCGATTTTCATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAACCGCATTGCGATTTTCTCGT
1533976 TGCGA
1 TGCGA
1533981 TAGCCATTTC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (33 bp):
TGCGAAATGAAAACCGCATTGCGATTTTCTCGT
Found at i:1533981 original size:33 final size:33
Alignment explanation
Indices: 1533924--1534000 Score: 118
Period size: 33 Copynumber: 2.3 Consensus size: 33
1533914 AAATGAAAAC
***
1533924 CGCATTGCGATTTTCTCGTTGCGATTTTCATTT
1 CGCATTGCGATTTTCTCGTTGCGATAGCCATTT
1533957 CGCATTGCGATTTTCTCGTTGCGATAGCCATTT
1 CGCATTGCGATTTTCTCGTTGCGATAGCCATTT
*
1533990 CGCGTTGCGAT
1 CGCATTGCGAT
1534001 AGTCTGTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.13, C:0.23, G:0.22, T:0.42
Consensus pattern (33 bp):
CGCATTGCGATTTTCTCGTTGCGATAGCCATTT
Found at i:1534106 original size:14 final size:14
Alignment explanation
Indices: 1534087--1534123 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1534077 CATCAATTAA
1534087 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
1534101 ACAAATCATCTTTT
1 ACAAATCAACATTT
1534115 ACAAATCAA
1 ACAAATCAA
1534124 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:1535873 original size:20 final size:19
Alignment explanation
Indices: 1535850--1535916 Score: 71
Period size: 19 Copynumber: 3.5 Consensus size: 19
1535840 GAAACTTAAA
1535850 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCG-AAATGACT
* *
1535870 ATCGCAACGCGGAATGGCT
1 ATCGCAACGCGAAATGACT
* * **
1535889 ATCACAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
1535908 ATCGCAACG
1 ATCGCAACG
1535917 ACAAAATCGC
Statistics
Matches: 37, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
19 26 0.70
20 11 0.30
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:1535924 original size:14 final size:14
Alignment explanation
Indices: 1535905--1535960 Score: 78
Period size: 14 Copynumber: 3.9 Consensus size: 14
1535895 ATGCGAAATG
1535905 AAAATCGCAACGAC
1 AAAATCGCAACGAC
1535919 AAAATCGCAACG-C
1 AAAATCGCAACGAC
1535932 GAAATGATCGCAACGAC
1 -AAA--ATCGCAACGAC
1535949 AAAATCGCAACG
1 AAAATCGCAACG
1535961 CGAAACACAA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
13 1 0.03
14 24 0.63
16 12 0.32
17 1 0.03
ACGTcount: A:0.46, C:0.27, G:0.18, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1535944 original size:30 final size:30
Alignment explanation
Indices: 1535908--1535965 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
1535898 CGAAATGAAA
1535908 ATCGCAACGACAAAATCGCAACGCGAAATG
1 ATCGCAACGACAAAATCGCAACGCGAAATG
1535938 ATCGCAACGACAAAATCGCAACGCGAAA
1 ATCGCAACGACAAAATCGCAACGCGAAA
1535966 CACAAATCGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.45, C:0.28, G:0.19, T:0.09
Consensus pattern (30 bp):
ATCGCAACGACAAAATCGCAACGCGAAATG
Found at i:1535994 original size:19 final size:19
Alignment explanation
Indices: 1535972--1536053 Score: 104
Period size: 19 Copynumber: 4.6 Consensus size: 19
1535962 GAAACACAAA
1535972 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
1535991 TCGCGTTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
1536007 TCG--TTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
1536023 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1536042 TCGCATTGCGAT
1 TCGCATTGCGAT
1536054 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
14 9 0.16
16 8 0.15
18 9 0.16
19 29 0.53
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1536060 original size:19 final size:19
Alignment explanation
Indices: 1536018--1536081 Score: 83
Period size: 19 Copynumber: 3.3 Consensus size: 19
1536008 CGTTGCGATT
**
1536018 TCATTTCGCATTGCGATTT
1 TCATTTCGCATTGCGATAG
1536037 TCATTTCGCATTGCGATAG
1 TCATTTCGCATTGCGATAG
* *
1536056 CCATTTCCGCGTTGCGATAG
1 TCATTT-CGCATTGCGATAG
1536076 TCATTT
1 TCATTT
1536082 TCGTGTTGCG
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
19 22 0.56
20 17 0.44
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.41
Consensus pattern (19 bp):
TCATTTCGCATTGCGATAG
Found at i:1536072 original size:20 final size:19
Alignment explanation
Indices: 1536019--1536092 Score: 67
Period size: 20 Copynumber: 3.8 Consensus size: 19
1536009 GTTGCGATTT
* ***
1536019 CATTTCGCATTGCGATTTT
1 CATTTCGCGTTGCGATAGC
*
1536038 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
1536057 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
1536077 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
1536093 AAGTAAACTA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
19 21 0.45
20 23 0.49
21 3 0.06
ACGTcount: A:0.16, C:0.23, G:0.22, T:0.39
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:1536594 original size:18 final size:18
Alignment explanation
Indices: 1536568--1536612 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1536558 GTCGATCAGA
*
1536568 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
1536586 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
1536604 TGATGGCTC
1 TGATGGCTC
1536613 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:1537679 original size:106 final size:101
Alignment explanation
Indices: 1537483--1537690 Score: 371
Period size: 106 Copynumber: 2.0 Consensus size: 101
1537473 CGGTGGGAAA
1537483 ATCAAACATATCTCTCATCACGACGTTGTATAGTATCTGGTAGATCCCTAGTGGTTTGAAGAAAT
1 ATCAAACATATCTCTCATCACGACGTTGTATAGTATCTGGTAGATCCCTAGTGGTTTGAAGAAAT
1537548 AGGTGTGTCAACATCGCATCTCCACCGGGATGTTGT
66 AGGTGTGTCAACATCGCATCTCCACCGGGATGTTGT
1537584 ATCAAACCATATCTCTTCATCACGACGTTGTATAGTATCTGGTAGATCCCTAGTCATGGTTTGAA
1 ATCAAA-CATATCTC-TCATCACGACGTTGTATAGTATCTGGTAGATCCCTAG---TGGTTTGAA
1537649 GAAATAGGTGTGTCAACATCGCATCTCCACCGGGATGTTGT
61 GAAATAGGTGTGTCAACATCGCATCTCCACCGGGATGTTGT
1537690 A
1 A
1537691 CTTTCAGCCA
Statistics
Matches: 102, Mismatches: 0, Indels: 5
0.95 0.00 0.05
Matches are distributed among these distances:
101 6 0.06
102 8 0.08
103 37 0.36
106 51 0.50
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (101 bp):
ATCAAACATATCTCTCATCACGACGTTGTATAGTATCTGGTAGATCCCTAGTGGTTTGAAGAAAT
AGGTGTGTCAACATCGCATCTCCACCGGGATGTTGT
Found at i:1538343 original size:22 final size:22
Alignment explanation
Indices: 1538315--1538358 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1538305 GATGGAGATA
*
1538315 GACGGATTTCGCCGGATATGGG
1 GACGGATTTCGCCGGAGATGGG
*
1538337 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
1538359 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.18, C:0.16, G:0.43, T:0.23
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:1538592 original size:20 final size:20
Alignment explanation
Indices: 1538541--1538634 Score: 82
Period size: 20 Copynumber: 4.7 Consensus size: 20
1538531 GATTATGTAT
*
1538541 TATCGCGTTGCAAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1538561 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* ** *
1538581 TATCTCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
* *
1538602 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1538622 TATCGCATTGCGA
1 TATCGCGTTGCGA
1538635 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
19 3 0.05
20 43 0.72
21 12 0.20
22 2 0.03
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.32
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:1538635 original size:20 final size:20
Alignment explanation
Indices: 1538521--1538635 Score: 81
Period size: 20 Copynumber: 5.7 Consensus size: 20
1538511 CACTTTGAAA
*
1538521 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * * *
1538542 ATCGCGTTGCAAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
1538562 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
1538582 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
1538603 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
1538623 ATCGCATTGCGAT
1 ATCGCATTGCGAT
1538636 TTTCCCAATT
Statistics
Matches: 75, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
19 5 0.07
20 46 0.61
21 22 0.29
22 2 0.03
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.34
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:1538653 original size:21 final size:21
Alignment explanation
Indices: 1538624--1538737 Score: 142
Period size: 21 Copynumber: 5.5 Consensus size: 21
1538614 ATAGTCAGTA
1538624 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
1538645 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
1538665 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
*
1538686 TCACATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* **
1538707 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
1538727 TCGCATTGCGA
1 TCGCATTGCGA
1538738 ATTGGGAAAA
Statistics
Matches: 79, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
20 33 0.42
21 46 0.58
ACGTcount: A:0.19, C:0.25, G:0.16, T:0.39
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:1538654 original size:41 final size:41
Alignment explanation
Indices: 1538563--1538697 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
1538553 AAAGTCAGAA
* * * * ** *
1538563 TCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTT-GTATT
1 TCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1538603 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
* * *
1538645 TCGCGTTGCGAT--TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATAGTCA-GTA-TCGCATTGCGATTTTCCCAAT
*
1538686 TCACATTGCGAT
1 TCGCATTGCGAT
1538698 TTTCCCAATT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
39 2 0.03
40 2 0.03
41 73 0.92
42 2 0.03
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.38
Consensus pattern (41 bp):
TCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
Found at i:1538698 original size:41 final size:42
Alignment explanation
Indices: 1538624--1538720 Score: 142
Period size: 41 Copynumber: 2.3 Consensus size: 42
1538614 ATAGTCAGTA
* * **
1538624 TCGCATTGCGATTTTCCCAATTCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCACATTGCGATTTTACCAAT
*
1538665 TCGCATTGCGATTTTCCCAATTCACATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAATTCACATTGCGATTTTACCAAT
1538707 TCGCATTGCGATTT
1 TCGCATTGCGATTT
1538721 ACTTATTCGC
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 30 0.60
42 20 0.40
ACGTcount: A:0.19, C:0.26, G:0.15, T:0.40
Consensus pattern (42 bp):
TCGCATTGCGATTTTCCCAATTCACATTGCGATTTTACCAAT
Found at i:1539129 original size:2 final size:2
Alignment explanation
Indices: 1539122--1539151 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1539112 TCAAATTCGA
1539122 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
1539152 TAGGGCAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1545227 original size:9 final size:9
Alignment explanation
Indices: 1545213--1545242 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
1545203 TATTGATTGG
1545213 TTTTTTATT
1 TTTTTTATT
1545222 TTTTTTA-T
1 TTTTTTATT
1545230 TTTTTTATT
1 TTTTTTATT
1545239 TTTT
1 TTTT
1545243 ACTAACGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (9 bp):
TTTTTTATT
Found at i:1545261 original size:9 final size:8
Alignment explanation
Indices: 1545213--1545242 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
1545203 TATTGATTGG
1545213 TTTTTTATT
1 TTTTTTA-T
1545222 TTTTTTAT
1 TTTTTTAT
1545230 TTTTTTAT
1 TTTTTTAT
1545238 TTTTT
1 TTTTT
1545243 ACTAACGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 14 0.67
9 7 0.33
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTTAT
Found at i:1545306 original size:23 final size:27
Alignment explanation
Indices: 1545266--1545313 Score: 68
Period size: 24 Copynumber: 1.9 Consensus size: 27
1545256 TTGTTTTATC
1545266 TTTTTATTATATTAATAT-TTTTTTCT
1 TTTTTATTATATTAATATATTTTTTCT
1545292 TTTTTA-TATA-T-ATATATTTTTT
1 TTTTTATTATATTAATATATTTTTT
1545314 AATCTAACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 7 0.33
25 4 0.19
26 6 0.29
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (27 bp):
TTTTTATTATATTAATATATTTTTTCT
Found at i:1549834 original size:105 final size:105
Alignment explanation
Indices: 1548902--1550065 Score: 1692
Period size: 105 Copynumber: 11.4 Consensus size: 105
1548892 AGCTACACCT
* **
1548902 CAACAACTTCCCAATTTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCTTGACAAC
1 CAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAAC
*
1548967 GCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
66 GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
*
1549007 CAAACAACTTCTCAA-TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAA
1 C-AACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAA
1549071 CGCAAGTTC-ACTTCACGACGAAGGGACCGCTGGTTGTCAA
65 CGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
* * * * * *
1549111 TAAACAATTTTCCAATTT-AGAGTCAATTTCAACTTCACAGCGAAGGATAGTGGACTCCAGACAA
1 -CAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAA
1549175 CGCAAGTTCAACTTCACGACGAAGGGACCG-TGGTTGTCAA
65 CGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
*
1549215 AAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCA-ACAAC
1 CAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAAC
1549279 GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT---
66 GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
*
1549316 C-ACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAA-
1 CAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAAC
1549379 -C--GTTCAACTTC-CGACGAAGGGACCGCT-G-TGT---
66 GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
1549410 CAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAAC
1 CAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAAC
*
1549475 GCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAA
66 GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
* **
1549515 CAA-AA-TT-TC-A-TTCAGAATCAATTTCAACTTCAC-ACGAAGGATATTGGACTCCAGACAAC
1 CAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAAC
* *
1549574 GCATGTTCAACTTCACGATGAAGGGACCGC---TTGTCAA
66 GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
*
1549611 -AA-AA-TT--CAAATTCAGAG-CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAAC
1 CAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAAC
1549670 GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
66 GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
* * *
1549710 CAAACAACTTTCCAA-TTCAGAGCCAATTTCAACTTCAGAGCGAAGGATATTGGACTCCAGACAA
1 C-AACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAA
1549774 CGCAAGTTCAACTTCAC-ACGAAGGGACCGCTGGTTGTCAA
65 CGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
**
1549814 CAACAACTTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCTTGACAA
1 CAACAAC-TTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAA
*
1549879 CGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
65 CGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
*
1549920 CAAACAACTTCTCAATTTCAGAGCC-ATTTCAACTTCACAACGAAGGATA-TGGACTCCAGAC-A
1 C-AACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAA
1549982 CGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
65 CGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
* * * *
1550023 TAAACAATTTTCCAA-TTCTAGAGTCAA-TTCAACTTCAC-ACGAA
1 -CAACAACTTCCCAATTTC-AGAGCCAATTTCAACTTCACAACGAA
1550066 TGGGTCACCA
Statistics
Matches: 975, Mismatches: 46, Indels: 79
0.89 0.04 0.07
Matches are distributed among these distances:
94 5 0.01
95 84 0.09
96 83 0.09
97 11 0.01
99 72 0.07
100 93 0.10
101 7 0.01
102 14 0.01
103 126 0.13
104 198 0.20
105 224 0.23
106 52 0.05
107 6 0.01
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (105 bp):
CAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAAC
GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
Found at i:1554431 original size:195 final size:198
Alignment explanation
Indices: 1554096--1554488 Score: 756
Period size: 195 Copynumber: 2.0 Consensus size: 198
1554086 AAGGTGCCCT
1554096 CCCCTTTAAGCTCTTCAATTTTTTTTTACGTGTACGATAGGTAATATTATAATATTTGAGTGATT
1 CCCCTTTAAGCTCTTCAATTTTTTTTTACGTGTACGATAGGTAATATTATAATATTTGAGTGATT
1554161 TTTTTCGTAAAAACGCCCTCTCCTAAATATATATTTTCTTCCATTTTGCCCATGCTATGAGAGAT
66 TTTTTCGTAAAAACGCCCTCTCCTAAATATATATTTTCTTCCATTTTGCCCATGCTATGAGAGAT
1554226 TCGCCCTTTGATTTTTTTGCTACATCGAATTAAGCTTTCAATCGGGTAAGGTCTTTTTCTTTTTA
131 TCGCCCTTTGATTTTTTTGCTACATCGAATTAAGCTTTCAATCGGGTAAGGTCTTTTTCTTTTTA
1554291 ATC
196 ATC
1554294 CCCCTTTAAGCTCTTCAA-TTTTTTTTACGTGTACGATAGGT-A-ATTATAATATTTGAGTGATT
1 CCCCTTTAAGCTCTTCAATTTTTTTTTACGTGTACGATAGGTAATATTATAATATTTGAGTGATT
*
1554356 TTTTTCGTAAAAACGCCCTCTCCTAAATATATATTTTCTTCCATTTTGCCCATGCTCTGAGAGAT
66 TTTTTCGTAAAAACGCCCTCTCCTAAATATATATTTTCTTCCATTTTGCCCATGCTATGAGAGAT
1554421 TCGCCCTTTGATTTTTTTGCTACATCGAATTAAGCTTTCAATCGGGTAAGGTCTTTTTCTTTTTA
131 TCGCCCTTTGATTTTTTTGCTACATCGAATTAAGCTTTCAATCGGGTAAGGTCTTTTTCTTTTTA
1554486 ATC
196 ATC
1554489 ATCGAAATCG
Statistics
Matches: 194, Mismatches: 1, Indels: 3
0.98 0.01 0.02
Matches are distributed among these distances:
195 152 0.78
196 1 0.01
197 23 0.12
198 18 0.09
ACGTcount: A:0.23, C:0.19, G:0.13, T:0.44
Consensus pattern (198 bp):
CCCCTTTAAGCTCTTCAATTTTTTTTTACGTGTACGATAGGTAATATTATAATATTTGAGTGATT
TTTTTCGTAAAAACGCCCTCTCCTAAATATATATTTTCTTCCATTTTGCCCATGCTATGAGAGAT
TCGCCCTTTGATTTTTTTGCTACATCGAATTAAGCTTTCAATCGGGTAAGGTCTTTTTCTTTTTA
ATC
Found at i:1556833 original size:12 final size:12
Alignment explanation
Indices: 1556818--1556849 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
1556808 GATAAAATGC
1556818 AATACATATATA
1 AATACATATATA
*
1556830 AATAAATATATA
1 AATACATATATA
1556842 AATACATA
1 AATACATA
1556850 GTTGAACAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.31
Consensus pattern (12 bp):
AATACATATATA
Found at i:1560395 original size:40 final size:41
Alignment explanation
Indices: 1560330--1560406 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 41
1560320 GAACAATGAA
1560330 AAAAATACAGATCCAGTAAAACCTACTCAAAG-AAAAGTAC
1 AAAAATACAGATCCAGTAAAACCTACTCAAAGCAAAAGTAC
* * * *
1560370 AAAAATATAGATCCCGTAGATCCTACTCAAAGCAAAA
1 AAAAATACAGATCCAGTAAAACCTACTCAAAGCAAAA
1560407 ATGATTTTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
40 28 0.88
41 4 0.12
ACGTcount: A:0.52, C:0.21, G:0.10, T:0.17
Consensus pattern (41 bp):
AAAAATACAGATCCAGTAAAACCTACTCAAAGCAAAAGTAC
Found at i:1562220 original size:23 final size:23
Alignment explanation
Indices: 1562191--1562247 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
1562181 CTAGTTAGAC
1562191 CCGGGTCGGGTCTTAGTTGGGC-
1 CCGGGTCGGGTCTTAGTTGGGCG
1562213 CCTGGGTCGGGTCTTAGTTGGGCG
1 CC-GGGTCGGGTCTTAGTTGGGCG
1562237 CCGGGTCGGGT
1 CCGGGTCGGGT
1562248 TCCAGGTCTA
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
22 2 0.06
23 29 0.88
24 2 0.06
ACGTcount: A:0.04, C:0.23, G:0.47, T:0.26
Consensus pattern (23 bp):
CCGGGTCGGGTCTTAGTTGGGCG
Found at i:1562631 original size:14 final size:14
Alignment explanation
Indices: 1562612--1562640 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1562602 GTCTCCATTG
1562612 ATATCAATTCAAGA
1 ATATCAATTCAAGA
1562626 ATATCAATTCAAGA
1 ATATCAATTCAAGA
1562640 A
1 A
1562641 AAAGGTAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.14, G:0.07, T:0.28
Consensus pattern (14 bp):
ATATCAATTCAAGA
Found at i:1564146 original size:42 final size:42
Alignment explanation
Indices: 1564095--1564444 Score: 293
Period size: 42 Copynumber: 8.2 Consensus size: 42
1564085 TCAATTATAA
* * *
1564095 AATTATAAAGGTAAAAAGTGAAATTAAAAAAGTGGGGACCTC
1 AATTATAAAGGTAAAAAGTGAGATTAAAAAATTAGGGACCTC
* *
1564137 AATTTTAAAGGTAAAAAGTGAGATTAAAAAAATTAGGGACCTA
1 AATTATAAAGGTAAAAAGTGAGATT-AAAAAATTAGGGACCTC
1564180 AATTATATAA-GTAAAAA-TGAGATTGAAAAAATTAGGG-CCAT-
1 AATTATA-AAGGTAAAAAGTGAGATT-AAAAAATTAGGGACC-TC
** * *
1564221 AATTATAAAAATAAAAAAGTGAGATTAAAAAATTAGAGTCCTC
1 AATTATAAAGGT-AAAAAGTGAGATTAAAAAATTAGGGACCTC
* * * *
1564264 ATTTATAAAGATAGAAAGTAAGATTAAAAAAGTTA-GGACCTC
1 AATTATAAAGGTAAAAAGTGAGATTAAAAAA-TTAGGGACCTC
* * ** * *
1564306 AATTATAAAAGTACAAAGT-AGGATTAAAAAACTTAAAGTCATC
1 AATTATAAAGGTAAAAAGTGA-GATTAAAAAA-TTAGGGACCTC
* * *
1564349 AATTATAAATGTAAAAAAGTGAGATTTAAAGAATTAAGGACCTC
1 AATTATAAAGGT-AAAAAGTGAGA-TTAAAAAATTAGGGACCTC
* ** *
1564393 AATTATAAAGATAAAAA-ACATGATTACAAAAATTAAGGG-CTTC
1 AATTATAAAGGTAAAAAGTGA-GATTA-AAAAATT-AGGGACCTC
1564436 AATTATAAA
1 AATTATAAA
1564445 AAAAAAATTA
Statistics
Matches: 255, Mismatches: 36, Indels: 33
0.79 0.11 0.10
Matches are distributed among these distances:
40 2 0.01
41 11 0.04
42 114 0.45
43 89 0.35
44 31 0.12
45 8 0.03
ACGTcount: A:0.52, C:0.07, G:0.15, T:0.26
Consensus pattern (42 bp):
AATTATAAAGGTAAAAAGTGAGATTAAAAAATTAGGGACCTC
Found at i:1564194 original size:85 final size:84
Alignment explanation
Indices: 1564094--1564409 Score: 270
Period size: 85 Copynumber: 3.7 Consensus size: 84
1564084 CTCAATTATA
* * *
1564094 AAATTATAAAGGTAAAAAGTGAAATTAAAAAAGTGGGGACCTCAATTTTAAAGGTAAAAAGTGAG
1 AAATTATAAA-GTAAAAAGTGAAATTAAAAAAGTAGGGACCTCAATTATAAAAGTAAAAAGTGAG
*
1564159 ATTAAAAAAATTAGGGACCT
65 ATTAAAAAAATTAGAGACCT
* * *
1564179 AAATTATATAAGTAAAAA-TGAGATTGAAAAAATTAGGG-CCAT-AATTATAAAAATAAAAAAGT
1 AAATTATA-AAGTAAAAAGTGAAATT-AAAAAAGTAGGGACC-TCAATTATAAAAGT-AAAAAGT
*
1564241 GAGATT-AAAAAATTAGAGTCCT
62 GAGATTAAAAAAATTAGAGACCT
* * * *
1564263 CATTTATAAAGATAGAAAGT-AAGATTAAAAAAGTTA-GGACCTCAATTATAAAAGTACAAAGT-
1 AAATTATAAAG-TAAAAAGTGAA-ATTAAAAAAG-TAGGGACCTCAATTATAAAAGTAAAAAGTG
* * * *
1564325 AGGATTAAAAAACTTAAAGTCAT
63 A-GATTAAAAAAATTAGAGACCT
* * * * *
1564348 CAATTATAAATGTAAAAAAGTGAGATTTAAAGAATTAAGGACCTCAATTAT-AAAGATAAAAA
1 AAATTATAAA-GT-AAAAAGTGA-AATTAAAAAAGTAGGGACCTCAATTATAAAAG-TAAAAA
1564410 ACATGATTAC
Statistics
Matches: 189, Mismatches: 24, Indels: 34
0.77 0.10 0.14
Matches are distributed among these distances:
83 4 0.02
84 62 0.33
85 81 0.43
86 15 0.08
87 26 0.14
88 1 0.01
ACGTcount: A:0.53, C:0.06, G:0.16, T:0.25
Consensus pattern (84 bp):
AAATTATAAAGTAAAAAGTGAAATTAAAAAAGTAGGGACCTCAATTATAAAAGTAAAAAGTGAGA
TTAAAAAAATTAGAGACCT
Found at i:1564418 original size:87 final size:82
Alignment explanation
Indices: 1564180--1564444 Score: 225
Period size: 87 Copynumber: 3.1 Consensus size: 82
1564170 TAGGGACCTA
* * *
1564180 AATTATATAAGT-AAAAA-TGAGATTGAAAAAATTAGGGCCAT-AATTATAAAAATAAAAAAGTG
1 AATTATA-AAGTAAAAAAGTGAGATTTAAAAAATTAGGACC-TCAATTAT-AAAATAAAAAAAT-
* *
1564242 AGATTAAAAAATTAGAGTCCTC
62 -GATTAAAAAATTAAAGTCATC
* * * ** *
1564264 ATTTATAAAG-ATAGAAAGTAAGA-TTAAAAAAGTTAGGACCTCAATTATAAAAGTACAAAGTAG
1 AATTATAAAGTA-AAAAAGTGAGATTTAAAAAA-TTAGGACCTCAATTATAAAA-TA-AAAAAAT
1564327 GATTAAAAAACTTAAAGTCATC
62 GATTAAAAAA-TTAAAGTCATC
*
1564349 AATTATAAATGTAAAAAAGTGAGATTTAAAGAATTAAGGACCTCAATTATAAAGATAAAAAACAT
1 AATTATAAA-GTAAAAAAGTGAGATTTAAAAAATT-AGGACCTCAATTATAAA-ATAAAAAA-AT
* * *
1564414 GATTACAAAAATTAAGGGCTTC
62 GATTA-AAAAATTAAAGTCATC
1564436 AATTATAAA
1 AATTATAAA
1564445 AAAAAAATTA
Statistics
Matches: 145, Mismatches: 21, Indels: 27
0.75 0.11 0.14
Matches are distributed among these distances:
83 3 0.02
84 32 0.22
85 36 0.25
86 18 0.12
87 50 0.34
88 6 0.04
ACGTcount: A:0.53, C:0.07, G:0.14, T:0.26
Consensus pattern (82 bp):
AATTATAAAGTAAAAAAGTGAGATTTAAAAAATTAGGACCTCAATTATAAAATAAAAAAATGATT
AAAAAATTAAAGTCATC
Found at i:1564451 original size:27 final size:28
Alignment explanation
Indices: 1564420--1564479 Score: 88
Period size: 27 Copynumber: 2.2 Consensus size: 28
1564410 ACATGATTAC
*
1564420 AAAAATT-AAGGGCTTCAATTATAAAAA-
1 AAAAATTAAAGGAC-TCAATTATAAAAAT
1564447 AAAAATTAAAGGACTCAATTATAAAAAT
1 AAAAATTAAAGGACTCAATTATAAAAAT
1564475 AAAAA
1 AAAAA
1564480 AATATACTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 20 0.67
28 10 0.33
ACGTcount: A:0.62, C:0.07, G:0.08, T:0.23
Consensus pattern (28 bp):
AAAAATTAAAGGACTCAATTATAAAAAT
Found at i:1564676 original size:19 final size:19
Alignment explanation
Indices: 1564636--1564678 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1564626 TGTTTCTATC
*
1564636 AAAAAATGATATTTTGGTT
1 AAAAAATGATATTTTGGAT
*
1564655 AAAAAATGGTTATTTT-GAT
1 AAAAAAT-GATATTTTGGAT
1564674 AAAAA
1 AAAAA
1564679 TAAACATTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.37
Consensus pattern (19 bp):
AAAAAATGATATTTTGGAT
Found at i:1564678 original size:20 final size:19
Alignment explanation
Indices: 1564636--1564678 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
1564626 TGTTTCTATC
* *
1564636 AAAAAATGATATTTTGGTT
1 AAAAAATGATATTTTGATA
*
1564655 AAAAAATGGTTATTTTGATA
1 AAAAAAT-GATATTTTGATA
1564675 AAAA
1 AAAA
1564679 TAAACATTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.37
Consensus pattern (19 bp):
AAAAAATGATATTTTGATA
Found at i:1572317 original size:15 final size:16
Alignment explanation
Indices: 1572295--1572340 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
1572285 ATTTAGTTCT
1572295 ATTTTTATTTCATTTC
1 ATTTTTATTTCATTTC
* *
1572311 A-TTTTATTTCGTTTT
1 ATTTTTATTTCATTTC
*
1572326 ATTTTTATTTTATTT
1 ATTTTTATTTCATTT
1572341 TTAGCAAACT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
15 13 0.52
16 12 0.48
ACGTcount: A:0.17, C:0.07, G:0.02, T:0.74
Consensus pattern (16 bp):
ATTTTTATTTCATTTC
Found at i:1572383 original size:14 final size:14
Alignment explanation
Indices: 1572366--1572392 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1572356 TTTATTATAT
1572366 TTATTATATTTTAA
1 TTATTATATTTTAA
1572380 TTATTATATTTTA
1 TTATTATATTTTA
1572393 TTTCTCTCTC
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTATTATATTTTAA
Found at i:1573626 original size:34 final size:36
Alignment explanation
Indices: 1573578--1573678 Score: 125
Period size: 35 Copynumber: 2.9 Consensus size: 36
1573568 AAAATAGTCC
* *
1573578 TCAATTTCATTCTAAACCCTAATTTCC-AAAGTAAT
1 TCAATTTCATTCTAAACCCTAAATTCCAAAAATAAT
1573613 TCAATTT-ATTCTAAACCCTAAATTCCAAAAATAAT
1 TCAATTTCATTCTAAACCCTAAATTCCAAAAATAAT
** * * *
1573648 TCAATTAAATTTTAAACCCCAAATTCTAAAA
1 TCAATTTCATTCTAAACCCTAAATTCCAAAA
1573679 TTCTTTAATT
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
34 18 0.31
35 20 0.34
36 20 0.34
ACGTcount: A:0.44, C:0.21, G:0.01, T:0.35
Consensus pattern (36 bp):
TCAATTTCATTCTAAACCCTAAATTCCAAAAATAAT
Found at i:1573672 original size:36 final size:35
Alignment explanation
Indices: 1573586--1573678 Score: 116
Period size: 36 Copynumber: 2.7 Consensus size: 35
1573576 CCTCAATTTC
* * *
1573586 ATTCTAAACCCTAATTTCC-AAAGTAATTCAATTT
1 ATTCTAAACCCTAAATTCCAAAAATAATTCAATTA
1573620 ATTCTAAACCCTAAATTCCAAAAATAATTCAATTAA
1 ATTCTAAACCCTAAATTCCAAAAATAATTCAATT-A
* * *
1573656 ATTTTAAACCCCAAATTCTAAAA
1 ATTCTAAACCCTAAATTCCAAAA
1573679 TTCTTTAATT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
34 18 0.35
35 13 0.25
36 20 0.39
ACGTcount: A:0.45, C:0.20, G:0.01, T:0.33
Consensus pattern (35 bp):
ATTCTAAACCCTAAATTCCAAAAATAATTCAATTA
Found at i:1573753 original size:35 final size:35
Alignment explanation
Indices: 1573685--1573759 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 35
1573675 AAAATTCTTT
* * *
1573685 AATTTAAGGTTTAGAATGTAATTGAATTATTTTGG
1 AATTTAAGGTTTAGAATGAAATTGAAGTATTTTGA
* *
1573720 AATTTAGGGTTTAGAATGAAATT-AAGGTGTTTTGA
1 AATTTAAGGTTTAGAATGAAATTGAA-GTATTTTGA
1573755 AATTT
1 AATTT
1573760 TGAACATGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
34 2 0.06
35 32 0.94
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (35 bp):
AATTTAAGGTTTAGAATGAAATTGAAGTATTTTGA
Found at i:1573778 original size:48 final size:48
Alignment explanation
Indices: 1573719--1573821 Score: 206
Period size: 48 Copynumber: 2.1 Consensus size: 48
1573709 AATTATTTTG
1573719 GAATTTAGGGTTTAGAATGAAATTAAGGTGTTTTGAAATTTTGAACAT
1 GAATTTAGGGTTTAGAATGAAATTAAGGTGTTTTGAAATTTTGAACAT
1573767 GAATTTAGGGTTTAGAATGAAATTAAGGTGTTTTGAAATTTTGAACAT
1 GAATTTAGGGTTTAGAATGAAATTAAGGTGTTTTGAAATTTTGAACAT
1573815 GAATTTA
1 GAATTTA
1573822 CTATTTGACA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 55 1.00
ACGTcount: A:0.36, C:0.02, G:0.22, T:0.40
Consensus pattern (48 bp):
GAATTTAGGGTTTAGAATGAAATTAAGGTGTTTTGAAATTTTGAACAT
Found at i:1576245 original size:18 final size:18
Alignment explanation
Indices: 1576222--1576264 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
1576212 TCTTAGATTA
*
1576222 TTTATTTAATTATTTTCT
1 TTTATTTAATTATTATCT
*
1576240 TTTATTTAATTCTTATCT
1 TTTATTTAATTATTATCT
1576258 TTTATTT
1 TTTATTT
1576265 TAAAAACAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:1576384 original size:31 final size:30
Alignment explanation
Indices: 1576312--1576384 Score: 76
Period size: 31 Copynumber: 2.3 Consensus size: 30
1576302 ACTATTACTT
1576312 ATTATTTTATTATTTTCCCTTTTTATTAATA
1 ATTA-TTTATTATTTTCCCTTTTTATTAATA
* **
1576343 TTTATCTTATTATTTTTTCTTTTTAAATT-ATA
1 ATTAT-TTATTATTTTCCCTTTTT--ATTAATA
1576375 ATTATTTATT
1 ATTATTTATT
1576385 TTATTTTATT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
30 1 0.03
31 24 0.69
32 7 0.20
33 3 0.09
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (30 bp):
ATTATTTATTATTTTCCCTTTTTATTAATA
Found at i:1576645 original size:35 final size:35
Alignment explanation
Indices: 1576559--1576723 Score: 149
Period size: 35 Copynumber: 4.7 Consensus size: 35
1576549 ACAGTTATCA
* * * **
1576559 GAAGCATCACACTTTAGATTCAAGTAGAATGGAAG
1 GAAGCATCGCACTTTCGATTCAAGTAAAAACGAAG
* * *
1576594 GAAGTATCGCAGTTTCGATTCAAGTAAAAACGAAT
1 GAAGCATCGCACTTTCGATTCAAGTAAAAACGAAG
* * *
1576629 GAAGCATTGCACTTTCGATTCAAGT-AGAACAAACG
1 GAAGCATCGCACTTTCGATTCAAGTAAAAACGAA-G
*
1576664 GAAGCATCACACTTTCGATTCAA--AAAGAACGAAAG
1 GAAGCATCGCACTTTCGATTCAAGTAAA-AACG-AAG
*
1576699 GAAGCATTAG-ACTTTCGATTCAAGT
1 GAAGCA-TCGCACTTTCGATTCAAGT
1576724 GTTTGTCTTT
Statistics
Matches: 103, Mismatches: 20, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
34 7 0.07
35 93 0.90
36 3 0.03
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (35 bp):
GAAGCATCGCACTTTCGATTCAAGTAAAAACGAAG
Found at i:1576680 original size:70 final size:70
Alignment explanation
Indices: 1576559--1576723 Score: 185
Period size: 70 Copynumber: 2.4 Consensus size: 70
1576549 ACAGTTATCA
** * ** * * *
1576559 GAAGCATCACACTTTAGATTCAAGTAGAATGGAAGGAAGTATCGCAGTTTCGATTCAAGTAAA-A
1 GAAGCATTGCACTTTCGATTCAAGTAGAATCAAAGGAAGCATCACACTTTCGATTCAA--AAAGA
*
1576623 ACG-AAT
64 ACGAAAG
1576629 GAAGCATTGCACTTTCGATTCAAGTAGAA-CAAACGGAAGCATCACACTTTCGATTCAAAAAGAA
1 GAAGCATTGCACTTTCGATTCAAGTAGAATCAAA-GGAAGCATCACACTTTCGATTCAAAAAGAA
1576693 CGAAAG
65 CGAAAG
1576699 GAAGCATTAG-ACTTTCGATTCAAGT
1 GAAGCATT-GCACTTTCGATTCAAGT
1576724 GTTTGTCTTT
Statistics
Matches: 82, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
68 3 0.04
69 6 0.07
70 72 0.88
71 1 0.01
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (70 bp):
GAAGCATTGCACTTTCGATTCAAGTAGAATCAAAGGAAGCATCACACTTTCGATTCAAAAAGAAC
GAAAG
Found at i:1576787 original size:54 final size:54
Alignment explanation
Indices: 1576723--1576830 Score: 198
Period size: 54 Copynumber: 2.0 Consensus size: 54
1576713 TCGATTCAAG
* *
1576723 TGTTTGTCTTTATATCAAGAAGGTTGAAGAAGTCGAGTGAATGTTAGATGAAAC
1 TGTTTGTCTTTACATCAAGAAGGTCGAAGAAGTCGAGTGAATGTTAGATGAAAC
1576777 TGTTTGTCTTTACATCAAGAAGGTCGAAGAAGTCGAGTGAATGTTAGATGAAAC
1 TGTTTGTCTTTACATCAAGAAGGTCGAAGAAGTCGAGTGAATGTTAGATGAAAC
1576831 AAATAGTTGT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.33, C:0.09, G:0.26, T:0.31
Consensus pattern (54 bp):
TGTTTGTCTTTACATCAAGAAGGTCGAAGAAGTCGAGTGAATGTTAGATGAAAC
Found at i:1578318 original size:20 final size:20
Alignment explanation
Indices: 1578295--1578337 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
1578285 AAAATAATTT
1578295 AAAT-TTTAAAAAAATGTAAA
1 AAATGTTTAAAAAAA-GTAAA
*
1578315 AAATGTTTAAAAATAGTAAA
1 AAATGTTTAAAAAAAGTAAA
1578335 AAA
1 AAA
1578338 AAGAACATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (20 bp):
AAATGTTTAAAAAAAGTAAA
Found at i:1579000 original size:351 final size:351
Alignment explanation
Indices: 1578357--1579058 Score: 1404
Period size: 351 Copynumber: 2.0 Consensus size: 351
1578347 TTAAGAAAAG
1578357 AAGAAGAGGAAAATGATAATAAAAAAGCACAAAATTTTAAAGGATTAAATTAAAACAAGTTGAAA
1 AAGAAGAGGAAAATGATAATAAAAAAGCACAAAATTTTAAAGGATTAAATTAAAACAAGTTGAAA
1578422 TTGAGGGACCAAATTAATGCTAAAGATGTGTTGCAAGGAAAAATAAAGAGTTATAGGGGTTAAAT
66 TTGAGGGACCAAATTAATGCTAAAGATGTGTTGCAAGGAAAAATAAAGAGTTATAGGGGTTAAAT
1578487 TGCAAAAATATAAATTATAAATAGGGATTAAATCGAATTAATCGAAAATTCAGAGGCAAAATTGC
131 TGCAAAAATATAAATTATAAATAGGGATTAAATCGAATTAATCGAAAATTCAGAGGCAAAATTGC
1578552 AATAGGTGACCAAAATGAATTACGCTTAAAAAATGCACAAATTGCGAAAATGATTTAACTATTTG
196 AATAGGTGACCAAAATGAATTACGCTTAAAAAATGCACAAATTGCGAAAATGATTTAACTATTTG
1578617 CAAATTACAAGGCGGTCCCTCCCCTATAAATAGCCCAAAACTTAGAAAAAATCATTTTTACCCTC
261 CAAATTACAAGGCGGTCCCTCCCCTATAAATAGCCCAAAACTTAGAAAAAATCATTTTTACCCTC
1578682 TTTCCAAAAACTCTCAACAACTCTCT
326 TTTCCAAAAACTCTCAACAACTCTCT
1578708 AAGAAGAGGAAAATGATAATAAAAAAGCACAAAATTTTAAAGGATTAAATTAAAACAAGTTGAAA
1 AAGAAGAGGAAAATGATAATAAAAAAGCACAAAATTTTAAAGGATTAAATTAAAACAAGTTGAAA
1578773 TTGAGGGACCAAATTAATGCTAAAGATGTGTTGCAAGGAAAAATAAAGAGTTATAGGGGTTAAAT
66 TTGAGGGACCAAATTAATGCTAAAGATGTGTTGCAAGGAAAAATAAAGAGTTATAGGGGTTAAAT
1578838 TGCAAAAATATAAATTATAAATAGGGATTAAATCGAATTAATCGAAAATTCAGAGGCAAAATTGC
131 TGCAAAAATATAAATTATAAATAGGGATTAAATCGAATTAATCGAAAATTCAGAGGCAAAATTGC
1578903 AATAGGTGACCAAAATGAATTACGCTTAAAAAATGCACAAATTGCGAAAATGATTTAACTATTTG
196 AATAGGTGACCAAAATGAATTACGCTTAAAAAATGCACAAATTGCGAAAATGATTTAACTATTTG
1578968 CAAATTACAAGGCGGTCCCTCCCCTATAAATAGCCCAAAACTTAGAAAAAATCATTTTTACCCTC
261 CAAATTACAAGGCGGTCCCTCCCCTATAAATAGCCCAAAACTTAGAAAAAATCATTTTTACCCTC
1579033 TTTCCAAAAACTCTCAACAACTCTCT
326 TTTCCAAAAACTCTCAACAACTCTCT
1579059 TAACCCTTCC
Statistics
Matches: 351, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
351 351 1.00
ACGTcount: A:0.46, C:0.14, G:0.15, T:0.25
Consensus pattern (351 bp):
AAGAAGAGGAAAATGATAATAAAAAAGCACAAAATTTTAAAGGATTAAATTAAAACAAGTTGAAA
TTGAGGGACCAAATTAATGCTAAAGATGTGTTGCAAGGAAAAATAAAGAGTTATAGGGGTTAAAT
TGCAAAAATATAAATTATAAATAGGGATTAAATCGAATTAATCGAAAATTCAGAGGCAAAATTGC
AATAGGTGACCAAAATGAATTACGCTTAAAAAATGCACAAATTGCGAAAATGATTTAACTATTTG
CAAATTACAAGGCGGTCCCTCCCCTATAAATAGCCCAAAACTTAGAAAAAATCATTTTTACCCTC
TTTCCAAAAACTCTCAACAACTCTCT
Found at i:1579293 original size:16 final size:17
Alignment explanation
Indices: 1579255--1579300 Score: 67
Period size: 18 Copynumber: 2.7 Consensus size: 17
1579245 TGTTTATGAG
*
1579255 GGAATTGGAATTTGTGAA
1 GGAATTGGAATCTGT-AA
1579273 GGAATTGGAATCTGT-A
1 GGAATTGGAATCTGTAA
1579289 GGAATTGGAATC
1 GGAATTGGAATC
1579301 CAATTCCATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 13 0.48
18 14 0.52
ACGTcount: A:0.33, C:0.04, G:0.33, T:0.30
Consensus pattern (17 bp):
GGAATTGGAATCTGTAA
Found at i:1579959 original size:37 final size:39
Alignment explanation
Indices: 1579872--1579966 Score: 131
Period size: 39 Copynumber: 2.5 Consensus size: 39
1579862 TTTTCACCCT
* *
1579872 AAACCCGAACCTGACCTGACCCGAATATCACACTTAAAAA
1 AAACCCG-ACCCGACCCGACCCGAATATCACACTTAAAAA
*
1579912 AAACCCGACCCGACCCGACCCGAATATCACA-TT-TAAA
1 AAACCCGACCCGACCCGACCCGAATATCACACTTAAAAA
*
1579949 AAACCCGACCCTACCCGA
1 AAACCCGACCCGACCCGA
1579967 ATATATGAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
37 20 0.39
38 2 0.04
39 22 0.43
40 7 0.14
ACGTcount: A:0.39, C:0.38, G:0.11, T:0.13
Consensus pattern (39 bp):
AAACCCGACCCGACCCGACCCGAATATCACACTTAAAAA
Found at i:1580491 original size:19 final size:20
Alignment explanation
Indices: 1580463--1580501 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
1580453 AAGGTTCGGG
*
1580463 TTTTACCTTTTCTGATGACT
1 TTTTACCTTTCCTGATGACT
*
1580483 TTTTA-CTTTCCTGGTGACT
1 TTTTACCTTTCCTGATGACT
1580502 CTTCCTTGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.13, C:0.21, G:0.13, T:0.54
Consensus pattern (20 bp):
TTTTACCTTTCCTGATGACT
Found at i:1581207 original size:11 final size:10
Alignment explanation
Indices: 1581187--1581234 Score: 59
Period size: 8 Copynumber: 5.1 Consensus size: 10
1581177 AATAAATTAG
1581187 ATAAATAAAT
1 ATAAATAAAT
1581197 ATAATATAAAT
1 ATAA-ATAAAT
1581208 ATAAA-AAA-
1 ATAAATAAAT
1581216 ATAAA-AAA-
1 ATAAATAAAT
1581224 ATAAATAAAT
1 ATAAATAAAT
1581234 A
1 A
1581235 AGAAAAAACA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
8 13 0.37
9 6 0.17
10 6 0.17
11 10 0.29
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (10 bp):
ATAAATAAAT
Found at i:1581221 original size:8 final size:8
Alignment explanation
Indices: 1581189--1581241 Score: 52
Period size: 8 Copynumber: 6.4 Consensus size: 8
1581179 TAAATTAGAT
1581189 AAATAAATA
1 AAATAAA-A
* *
1581198 TAATATAA
1 AAATAAAA
*
1581206 ATATAAAA
1 AAATAAAA
1581214 AAATAAAA
1 AAATAAAA
*
1581222 AAATAAAT
1 AAATAAAA
1581230 AAATAAGAA
1 AAATAA-AA
1581239 AAA
1 AAA
1581242 ACATATAATA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
8 26 0.74
9 9 0.26
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (8 bp):
AAATAAAA
Found at i:1581457 original size:12 final size:12
Alignment explanation
Indices: 1581440--1581501 Score: 52
Period size: 12 Copynumber: 4.8 Consensus size: 12
1581430 ATTATATTCG
1581440 TTTTCAAAAATA
1 TTTTCAAAAATA
1581452 TTTTCAAAATCATTTA
1 TTTTCAAAA--A--TA
*
1581468 TTTTCCAAAAATG
1 TTTT-CAAAAATA
* *
1581481 TTTTCAAACATG
1 TTTTCAAAAATA
1581493 TTTTCAAAA
1 TTTTCAAAA
1581502 CCATATAATA
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
12 24 0.57
13 5 0.12
14 1 0.02
15 1 0.02
16 6 0.14
17 5 0.12
ACGTcount: A:0.40, C:0.13, G:0.03, T:0.44
Consensus pattern (12 bp):
TTTTCAAAAATA
Found at i:1581533 original size:12 final size:12
Alignment explanation
Indices: 1581516--1581575 Score: 66
Period size: 12 Copynumber: 4.7 Consensus size: 12
1581506 ATAATATACG
1581516 TTTCAAAAATGT
1 TTTCAAAAATGT
1581528 TTTCAAAACCATATGT
1 TTTC-AAA--A-ATGT
1581544 TTTCAAAAATGT
1 TTTCAAAAATGT
* *
1581556 TTTCAAACACGT
1 TTTCAAAAATGT
1581568 TTTCAAAA
1 TTTCAAAA
1581576 CCTATAGCCA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
12 25 0.61
13 4 0.10
15 4 0.10
16 8 0.20
ACGTcount: A:0.40, C:0.15, G:0.07, T:0.38
Consensus pattern (12 bp):
TTTCAAAAATGT
Found at i:1581571 original size:74 final size:77
Alignment explanation
Indices: 1581414--1581581 Score: 236
Period size: 74 Copynumber: 2.2 Consensus size: 77
1581404 TTTCCAAAAG
* * * *
1581414 GTTTTCAAAACTATATATTATATTCGTTTTCAAAAATATTTTCAAAATCATTTATTTTCCAAAAA
1 GTTTTCAAAACCATATA-TATATACGTTTTCAAAAATATTTTCAAAACCATATATTTTCCAAAAA
*
1581479 TGTTTTCAAACAT
65 TGTTTTCAAACAC
* *
1581492 GTTTTCAAAACCATATA-ATATACG-TTTCAAAAATGTTTTCAAAACCATATGTTTT-CAAAAAT
1 GTTTTCAAAACCATATATATATACGTTTTCAAAAATATTTTCAAAACCATATATTTTCCAAAAAT
1581554 GTTTTCAAACAC
66 GTTTTCAAACAC
1581566 GTTTTCAAAACC-TATA
1 GTTTTCAAAACCATATA
1581582 GCCAAAAATT
Statistics
Matches: 83, Mismatches: 7, Indels: 5
0.87 0.07 0.05
Matches are distributed among these distances:
73 4 0.05
74 30 0.36
75 27 0.33
76 6 0.07
78 16 0.19
ACGTcount: A:0.39, C:0.15, G:0.05, T:0.40
Consensus pattern (77 bp):
GTTTTCAAAACCATATATATATACGTTTTCAAAAATATTTTCAAAACCATATATTTTCCAAAAAT
GTTTTCAAACAC
Found at i:1583592 original size:12 final size:12
Alignment explanation
Indices: 1583575--1583607 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
1583565 TTGCCCCAGT
1583575 CGAAGTTTGTAC
1 CGAAGTTTGTAC
1583587 CGAAGTTTGTAC
1 CGAAGTTTGTAC
1583599 CGAAGTTTG
1 CGAAGTTTG
1583608 GTAAGAAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.33
Consensus pattern (12 bp):
CGAAGTTTGTAC
Found at i:1592287 original size:16 final size:17
Alignment explanation
Indices: 1592268--1592301 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1592258 TGAAAATGAT
1592268 AAAATAAAAGA-AAACA
1 AAAATAAAAGAGAAACA
*
1592284 AAAATGAAAGAGAAACA
1 AAAATAAAAGAGAAACA
1592301 A
1 A
1592302 GTCAGTAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.76, C:0.06, G:0.12, T:0.06
Consensus pattern (17 bp):
AAAATAAAAGAGAAACA
Found at i:1594762 original size:4 final size:4
Alignment explanation
Indices: 1594715--1594782 Score: 63
Period size: 4 Copynumber: 17.2 Consensus size: 4
1594705 ACCTGGACTG
* *
1594715 AATA AATTA GATA AAT- AA-A AATA ATATC AATA TAAT- AA-A AATA AATA
1 AATA AA-TA AATA AATA AATA AATA A-ATA AATA -AATA AATA AATA AATA
1594762 AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA A
1594783 GAAAAAACAT
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
3 8 0.15
4 36 0.68
5 9 0.17
ACGTcount: A:0.71, C:0.01, G:0.01, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:1594776 original size:20 final size:18
Alignment explanation
Indices: 1594715--1594782 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 18
1594705 ACCTGGACTG
*
1594715 AATAAATTAGATAAATAAA
1 AATAAA-TAAATAAATAAA
*
1594734 AATAATATCAATATAATAAA
1 AATAA-ATAAATA-AATAAA
1594754 AATAAATAAATAAAT--A
1 AATAAATAAATAAATAAA
1594770 AATAAATAAATAA
1 AATAAATAAATAA
1594783 GAAAAAACAT
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
16 14 0.32
18 3 0.07
19 15 0.34
20 12 0.27
ACGTcount: A:0.71, C:0.01, G:0.01, T:0.26
Consensus pattern (18 bp):
AATAAATAAATAAATAAA
Found at i:1594955 original size:34 final size:37
Alignment explanation
Indices: 1594892--1595121 Score: 173
Period size: 36 Copynumber: 6.1 Consensus size: 37
1594882 AAAAAACATA
*
1594892 TATACATGTTTTCAAAATATGTTTTCAAAA-T-TATAT
1 TATATATGTTTTCAAAA-ATGTTTTCAAAACTATATAT
*
1594928 TATATATGTTTTC-AAAACGTTTTCAAAACTATATAT
1 TATATATGTTTTCAAAAATGTTTTCAAAACTATATAT
** * *
1594964 TATATACATTTTCAAAAATGTTTTCAAAACCATATGTTT
1 TATATATGTTTTCAAAAATGTTTTCAAAA-C-TATATAT
* * *
1595003 TCCAAAAATGTTTTCAAACATGTTTTCAAAAC-A-ATAT
1 T--ATATATGTTTTCAAAAATGTTTTCAAAACTATATAT
* * * * *
1595040 AATATACGCTTTCAAAAATGTTTTCAAAACCATATGTTT
1 TATATATGTTTTCAAAAATGTTTTCAAAA-C-TATATAT
* * * * *
1595079 TCAAAAATGTTTTCAAACACGTTTTCAAAACCTATATAA
1 T-ATATATGTTTTCAAAAATGTTTTCAAAA-CTATATAT
1595118 TATA
1 TATA
1595122 AATTTCCAAA
Statistics
Matches: 149, Mismatches: 33, Indels: 22
0.73 0.16 0.11
Matches are distributed among these distances:
34 11 0.07
35 27 0.18
36 29 0.19
37 16 0.11
38 5 0.03
39 13 0.09
40 25 0.17
41 23 0.15
ACGTcount: A:0.40, C:0.13, G:0.06, T:0.40
Consensus pattern (37 bp):
TATATATGTTTTCAAAAATGTTTTCAAAACTATATAT
Found at i:1594989 original size:12 final size:12
Alignment explanation
Indices: 1594972--1595108 Score: 82
Period size: 12 Copynumber: 10.8 Consensus size: 12
1594962 ATTATATACA
1594972 TTTTCAAAAATG
1 TTTTCAAAAATG
1594984 TTTTCAAAACCATATG
1 TTTTC-AAA--A-ATG
1595000 TTTTCCAAAAATG
1 TTTT-CAAAAATG
*
1595013 TTTTCAAACATG
1 TTTTCAAAAATG
1595025 TTTTCAAAACA--
1 TTTTCAAAA-ATG
* * * *
1595036 ATAT-AATATACG
1 TTTTCAA-AAATG
*
1595048 CTTTCAAAAATG
1 TTTTCAAAAATG
1595060 TTTTCAAAACCATATG
1 TTTTC-AAA--A-ATG
1595076 TTTTCAAAAATG
1 TTTTCAAAAATG
* *
1595088 TTTTCAAACACG
1 TTTTCAAAAATG
1595100 TTTTCAAAA
1 TTTTCAAAA
1595109 CCTATATAAT
Statistics
Matches: 98, Mismatches: 13, Indels: 28
0.71 0.09 0.20
Matches are distributed among these distances:
10 3 0.03
11 3 0.03
12 50 0.51
13 17 0.17
14 1 0.01
15 5 0.05
16 18 0.18
17 1 0.01
ACGTcount: A:0.40, C:0.15, G:0.07, T:0.38
Consensus pattern (12 bp):
TTTTCAAAAATG
Found at i:1595021 original size:28 final size:27
Alignment explanation
Indices: 1594972--1595096 Score: 113
Period size: 28 Copynumber: 4.8 Consensus size: 27
1594962 ATTATATACA
1594972 TTTTCAAAAATGTTTTCAAAACCATATG
1 TTTTCAAAAATGTTTTC-AAACCATATG
1595000 TTTTCCAAAAATGTTTTCAAA-C--ATG
1 TTTT-CAAAAATGTTTTCAAACCATATG
* * * *
1595025 TTTTCAAAACA--ATAT--AA-TATACG
1 TTTTCAAAA-ATGTTTTCAAACCATATG
*
1595048 CTTTCAAAAATGTTTTCAAAACCATATG
1 TTTTCAAAAATGTTTTC-AAACCATATG
1595076 TTTTCAAAAATGTTTTCAAAC
1 TTTTCAAAAATGTTTTCAAAC
1595097 ACGTTTTCAA
Statistics
Matches: 77, Mismatches: 10, Indels: 21
0.71 0.09 0.19
Matches are distributed among these distances:
21 2 0.03
22 1 0.01
23 12 0.16
24 7 0.09
25 8 0.10
27 7 0.09
28 27 0.35
29 13 0.17
ACGTcount: A:0.40, C:0.15, G:0.06, T:0.38
Consensus pattern (27 bp):
TTTTCAAAAATGTTTTCAAACCATATG
Found at i:1595059 original size:76 final size:75
Alignment explanation
Indices: 1594933--1595121 Score: 290
Period size: 76 Copynumber: 2.5 Consensus size: 75
1594923 TATATTATAT
* *
1594933 ATGTTTTCAAA-ACGTTTTCAAAACTATATATTATATACATTTTCAAAAATGTTTTCAAAACCAT
1 ATGTTTTCAAACACGTTTTCAAAAC-A-ATATAATATACACTTTCAAAAATGTTTTCAAAACCAT
1594997 ATGTTTTCCAAAA
64 ATGTTTT-CAAAA
* *
1595010 ATGTTTTCAAACATGTTTTCAAAACAATATAATATACGCTTTCAAAAATGTTTTCAAAACCATAT
1 ATGTTTTCAAACACGTTTTCAAAACAATATAATATACACTTTCAAAAATGTTTTCAAAACCATAT
1595075 GTTTTCAAAA
66 GTTTTCAAAA
*
1595085 ATGTTTTCAAACACGTTTTCAAAACCTATATAATATA
1 ATGTTTTCAAACACGTTTTCAAAA-CAATATAATATA
1595122 AATTTCCAAA
Statistics
Matches: 104, Mismatches: 6, Indels: 5
0.90 0.05 0.04
Matches are distributed among these distances:
75 28 0.27
76 52 0.50
77 12 0.12
78 12 0.12
ACGTcount: A:0.41, C:0.15, G:0.06, T:0.39
Consensus pattern (75 bp):
ATGTTTTCAAACACGTTTTCAAAACAATATAATATACACTTTCAAAAATGTTTTCAAAACCATAT
GTTTTCAAAA
Found at i:1595163 original size:24 final size:24
Alignment explanation
Indices: 1595100--1595163 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 24
1595090 TTCAAACACG
1595100 TTTTCAAAACCTATATAATATAAA
1 TTTTCAAAACCTATATAATATAAA
* * **
1595124 TTTCCAAAAACTATAT-ATCATGTA
1 TTTTCAAAACCTATATAAT-ATAAA
*
1595148 TTTTCAAAACCCATAT
1 TTTTCAAAACCTATAT
1595164 TTAAGGCCTC
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
23 2 0.06
24 30 0.94
ACGTcount: A:0.44, C:0.17, G:0.02, T:0.38
Consensus pattern (24 bp):
TTTTCAAAACCTATATAATATAAA
Found at i:1595577 original size:2 final size:2
Alignment explanation
Indices: 1595570--1595595 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1595560 TTAACGTCTG
1595570 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
1595596 TATTTTTAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.