Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 103066607
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: 103066607
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 238 characters in sequence are not A, C, G, or T
File 60 of 345
Found at i:16675203 original size:16 final size:16
Alignment explanation
Indices: 16675182--16675218 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
16675172 TTATATATAC
16675182 TATTATATTTTATTA-T
1 TATTATA-TTTATTATT
16675198 TATTATATTTATTATT
1 TATTATATTTATTATT
16675214 TATTA
1 TATTA
16675219 GCCTTAGCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TATTATATTTATTATT
Found at i:16675210 original size:25 final size:26
Alignment explanation
Indices: 16675150--16675212 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 26
16675140 CTTTTTCTCC
*
16675150 TTAT-TTTATTTTAATTTTAATATTA
1 TTATATTTATTATAATTTTAATATTA
* *
16675175 -TATATACTATTAT-ATTTTATTATTA
1 TTATAT-TTATTATAATTTTAATATTA
16675200 TTATATTTATTAT
1 TTATATTTATTAT
16675213 TTATTAGCCT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
24 3 0.10
25 18 0.58
26 10 0.32
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (26 bp):
TTATATTTATTATAATTTTAATATTA
Found at i:16676156 original size:2 final size:2
Alignment explanation
Indices: 16676149--16676181 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
16676139 TATTATTGTC
16676149 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16676182 AAAGAAACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16676200 original size:13 final size:13
Alignment explanation
Indices: 16676182--16676209 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
16676172 TATATATATA
16676182 AAAGAAACAAAAG
1 AAAGAAACAAAAG
16676195 AAAGAAACAAAAG
1 AAAGAAACAAAAG
16676208 AA
1 AA
16676210 TAAAAAGAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.79, C:0.07, G:0.14, T:0.00
Consensus pattern (13 bp):
AAAGAAACAAAAG
Found at i:16677012 original size:2 final size:2
Alignment explanation
Indices: 16676995--16677030 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
16676985 TAAATTGAAT
*
16676995 TA TA TA T- TA TA AA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16677031 GTGTGTGTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:16677035 original size:2 final size:2
Alignment explanation
Indices: 16677030--16677063 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
16677020 TATATATATA
16677030 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
16677064 AATGAGATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:16677237 original size:15 final size:15
Alignment explanation
Indices: 16677219--16677275 Score: 80
Period size: 15 Copynumber: 3.9 Consensus size: 15
16677209 TATCTGTTTT
16677219 ATTGAATTTATATTG
1 ATTGAATTTATATTG
* * *
16677234 ATTGAAATTATTTTA
1 ATTGAATTTATATTG
16677249 ATTGAATTTATATTG
1 ATTGAATTTATATTG
16677264 ATTGAA-TTATAT
1 ATTGAATTTATAT
16677276 AATATATATG
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
14 6 0.17
15 30 0.83
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.53
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:16677254 original size:30 final size:28
Alignment explanation
Indices: 16677215--16677273 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 28
16677205 TGAATATCTG
16677215 TTTTATTGAATTTATATTGATTGAAATTA
1 TTTTATTGAATTTATATTGATTG-AATTA
16677244 TTTTAATTGAATTTATATTGATTGAATTA
1 TTTT-ATTGAATTTATATTGATTGAATTA
16677273 T
1 T
16677274 ATAATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 10 0.34
30 19 0.66
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.56
Consensus pattern (28 bp):
TTTTATTGAATTTATATTGATTGAATTA
Found at i:16680834 original size:53 final size:53
Alignment explanation
Indices: 16680753--16680903 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
16680743 CTTACACGGT
* *
16680753 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
16680808 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
16680861 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
16680904 GCACACTTGT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:16688350 original size:53 final size:53
Alignment explanation
Indices: 16688269--16688419 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
16688259 CTTACACGGT
* *
16688269 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
16688324 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
16688377 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
16688420 GCACACTTGT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:16692781 original size:2 final size:2
Alignment explanation
Indices: 16692774--16692803 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
16692764 TTATTGTCAT
16692774 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
16692804 AGAAACAAAA
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):
TA
Found at i:16692821 original size:13 final size:13
Alignment explanation
Indices: 16692803--16692829 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
16692793 ATATATATAT
16692803 AAGAAACAAAAGA
1 AAGAAACAAAAGA
16692816 AAGAAACAAAAGA
1 AAGAAACAAAAGA
16692829 A
1 A
16692830 TAAAAAGAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.78, C:0.07, G:0.15, T:0.00
Consensus pattern (13 bp):
AAGAAACAAAAGA
Found at i:16693630 original size:2 final size:2
Alignment explanation
Indices: 16693614--16693658 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
16693604 TAAATTGAAT
16693614 TA TA TA T- TA TA -A 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
16693654 TA TA T
1 TA TA T
16693659 GTGTGTGTGT
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:16693663 original size:2 final size:2
Alignment explanation
Indices: 16693658--16693689 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
16693648 TATATATATA
16693658 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
16693690 AATGAGATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:16693863 original size:15 final size:15
Alignment explanation
Indices: 16693845--16693901 Score: 80
Period size: 15 Copynumber: 3.9 Consensus size: 15
16693835 TATCTGTTTT
16693845 ATTGAATTTATATTG
1 ATTGAATTTATATTG
* * *
16693860 ATTGAAATTATTTTA
1 ATTGAATTTATATTG
16693875 ATTGAATTTATATTG
1 ATTGAATTTATATTG
16693890 ATTGAA-TTATAT
1 ATTGAATTTATAT
16693902 AATATATATG
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
14 6 0.17
15 30 0.83
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.53
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:16693880 original size:30 final size:28
Alignment explanation
Indices: 16693841--16693899 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 28
16693831 TGAATATCTG
16693841 TTTTATTGAATTTATATTGATTGAAATTA
1 TTTTATTGAATTTATATTGATTG-AATTA
16693870 TTTTAATTGAATTTATATTGATTGAATTA
1 TTTT-ATTGAATTTATATTGATTGAATTA
16693899 T
1 T
16693900 ATAATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 10 0.34
30 19 0.66
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.56
Consensus pattern (28 bp):
TTTTATTGAATTTATATTGATTGAATTA
Found at i:16694330 original size:21 final size:23
Alignment explanation
Indices: 16694271--16694336 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
16694261 GCTTTACCGA
16694271 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACTTTATGTGTCGTATT
* **
16694294 TCAGGCACCTCGTGTGTCGT-TT
1 TCAGGCACTTTATGTGTCGTATT
16694316 T-AGGCACTTTATGTGTCGTAT
1 TCAGGCACTTTATGTGTCGTAT
16694337 ACTGATCAGG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
21 15 0.42
22 4 0.11
23 17 0.47
ACGTcount: A:0.15, C:0.20, G:0.24, T:0.41
Consensus pattern (23 bp):
TCAGGCACTTTATGTGTCGTATT
Found at i:16696215 original size:26 final size:26
Alignment explanation
Indices: 16696177--16696338 Score: 263
Period size: 26 Copynumber: 6.2 Consensus size: 26
16696167 TGATACAAAT
* *
16696177 TGATAATAGGTTAGGTAAATGTTTTA
1 TGATAATGGGTTAGGTAAATGTTTCA
*
16696203 TGATAATGTGTTAGGTAAAT-TTTCCA
1 TGATAATGGGTTAGGTAAATGTTT-CA
16696229 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
* *
16696255 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
16696281 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
16696307 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
16696333 TGATAA
1 TGATAA
16696339 GAATATCATG
Statistics
Matches: 126, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
25 3 0.02
26 120 0.95
27 3 0.02
ACGTcount: A:0.33, C:0.04, G:0.24, T:0.39
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:16697755 original size:135 final size:135
Alignment explanation
Indices: 16697508--16697926 Score: 772
Period size: 135 Copynumber: 3.1 Consensus size: 135
16697498 GAGTAGTCTC
16697508 CCCAAATGGGCTTGCATATGTTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACT
1 CCCAAATGGGCTTGCATATGTTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACT
16697573 GTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGACTCTGCCCTAGTACCA
66 GTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGG-CTCTGCCCTAGTACCA
16697638 CTGTTA
130 CTGTTA
16697644 CCCAAATGGGCTTGCATATGTTATTGATGTTGCATGTATTTTGAAATGGGCCTAT-GGCCATACT
1 CCCAAATGGGCTTGCATATGTTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACT
16697708 GTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGCCC-AGTACCA
66 GTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAA-GGCTCTGCCCTAGTACCA
16697772 CTGTTA
130 CTGTTA
16697778 CCCAAATGGGCTTGCATATGTTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACT
1 CCCAAATGGGCTTGCATATGTTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACT
16697843 GTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAATGGCTCTGGCCCT-GTACC
66 GTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAA-GGCTCT-GCCCTAGTACC
16697907 ACTGTTA
129 ACTGTTA
*
16697914 CCTAAATGGGCTT
1 CCCAAATGGGCTT
16697927 AAGCCCAATA
Statistics
Matches: 277, Mismatches: 2, Indels: 8
0.97 0.01 0.03
Matches are distributed among these distances:
134 68 0.25
135 124 0.45
136 85 0.31
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (135 bp):
CCCAAATGGGCTTGCATATGTTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACT
GTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGCTCTGCCCTAGTACCAC
TGTTA
Found at i:16702081 original size:2 final size:2
Alignment explanation
Indices: 16702074--16702103 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
16702064 TTATTGTCAT
16702074 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
16702104 AGAAACAAAA
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):
TA
Found at i:16702121 original size:13 final size:13
Alignment explanation
Indices: 16702103--16702129 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
16702093 ATATATATAT
16702103 AAGAAACAAAAGA
1 AAGAAACAAAAGA
16702116 AAGAAACAAAAGA
1 AAGAAACAAAAGA
16702129 A
1 A
16702130 TAAAAAGAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.78, C:0.07, G:0.15, T:0.00
Consensus pattern (13 bp):
AAGAAACAAAAGA
Found at i:16702932 original size:2 final size:2
Alignment explanation
Indices: 16702915--16702959 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
16702905 TAAATTGAAT
*
16702915 TA TA TA T- TA TA AA 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
16702956 TA TA
1 TA TA
16702960 AGCGTGTGTG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:16702968 original size:2 final size:2
Alignment explanation
Indices: 16702963--16702989 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
16702953 ATATATAAGC
16702963 GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT G
16702990 AATGAGATAT
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:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:16703163 original size:15 final size:15
Alignment explanation
Indices: 16703145--16703201 Score: 80
Period size: 15 Copynumber: 3.9 Consensus size: 15
16703135 TATCTGTTTT
16703145 ATTGAATTTATATTG
1 ATTGAATTTATATTG
* * *
16703160 ATTGAAATTATTTTA
1 ATTGAATTTATATTG
16703175 ATTGAATTTATATTG
1 ATTGAATTTATATTG
16703190 ATTGAA-TTATAT
1 ATTGAATTTATAT
16703202 AATATATATG
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
14 6 0.17
15 30 0.83
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.53
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:16703180 original size:30 final size:28
Alignment explanation
Indices: 16703141--16703199 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 28
16703131 TGAATATCTG
16703141 TTTTATTGAATTTATATTGATTGAAATTA
1 TTTTATTGAATTTATATTGATTG-AATTA
16703170 TTTTAATTGAATTTATATTGATTGAATTA
1 TTTT-ATTGAATTTATATTGATTGAATTA
16703199 T
1 T
16703200 ATAATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 10 0.34
30 19 0.66
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.56
Consensus pattern (28 bp):
TTTTATTGAATTTATATTGATTGAATTA
Found at i:16703632 original size:21 final size:23
Alignment explanation
Indices: 16703573--16703638 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
16703563 GCTTTACCGA
16703573 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACTTTATGTGTCGTATT
* **
16703596 TCAGGCACCTCGTGTGTCGT-TT
1 TCAGGCACTTTATGTGTCGTATT
16703618 T-AGGCACTTTATGTGTCGTAT
1 TCAGGCACTTTATGTGTCGTAT
16703639 ACTGATCAGG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
21 15 0.42
22 4 0.11
23 17 0.47
ACGTcount: A:0.15, C:0.20, G:0.24, T:0.41
Consensus pattern (23 bp):
TCAGGCACTTTATGTGTCGTATT
Found at i:16704913 original size:18 final size:17
Alignment explanation
Indices: 16704885--16704926 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
16704875 TATACATGTA
16704885 TATATATATATACTTTT
1 TATATATATATACTTTT
**
16704902 TATATATGATATTTTTTT
1 TATATAT-ATATACTTTT
16704920 TATATAT
1 TATATAT
16704927 CATTATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (17 bp):
TATATATATATACTTTT
Found at i:16704923 original size:16 final size:15
Alignment explanation
Indices: 16704887--16704926 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
16704877 TACATGTATA
16704887 TATATATATACTTTT
1 TATATATATACTTTT
*
16704902 TATATATGATATTTTT
1 TATATAT-ATACTTTT
*
16704918 TTTATATAT
1 TATATATAT
16704927 CATTATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (15 bp):
TATATATATACTTTT
Found at i:16705158 original size:17 final size:18
Alignment explanation
Indices: 16705112--16705184 Score: 78
Period size: 17 Copynumber: 4.0 Consensus size: 18
16705102 TTTTTATTGC
*
16705112 TATTATTATTATTTTATT
1 TATTACTATTATTTTATT
*
16705130 TATTA-TAATATTTTATT
1 TATTACTATTATTTTATT
16705147 T-TTACTATTATTGTTATT
1 TATTACTATTATT-TTATT
*
16705165 ATCATTACTATTATATTATT
1 -T-ATTACTATTATTTTATT
16705185 AGCACATTAT
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
16 3 0.06
17 18 0.38
18 10 0.21
19 1 0.02
20 5 0.11
21 10 0.21
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.64
Consensus pattern (18 bp):
TATTACTATTATTTTATT
Found at i:16705203 original size:3 final size:3
Alignment explanation
Indices: 16705112--16705185 Score: 57
Period size: 3 Copynumber: 25.7 Consensus size: 3
16705102 TTTTTATTGC
* * *
16705112 TAT TAT TAT TAT T-T TATT TAT TA- TAA TAT T-T TAT TTT TAC TAT
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
16705155 TAT TGT TAT TAT CAT TAC TAT TA- TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
16705186 GCACATTATT
Statistics
Matches: 55, Mismatches: 11, Indels: 10
0.72 0.14 0.13
Matches are distributed among these distances:
2 8 0.15
3 44 0.80
4 3 0.05
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:16707046 original size:16 final size:16
Alignment explanation
Indices: 16707023--16707078 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 16
16707013 TTTATTAATG
16707023 ATTT-AAAAAAATAAA
1 ATTTAAAAAAAATAAA
*
16707038 ATTTAAAAAAAACTAAT
1 ATTTAAAAAAAA-TAAA
* *
16707055 ATTATAAAAATATTATAA
1 ATT-TAAAAAAAATA-AA
16707073 ATTTAA
1 ATTTAA
16707079 TATGTAACGA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
15 4 0.12
16 7 0.21
17 11 0.33
18 11 0.33
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (16 bp):
ATTTAAAAAAAATAAA
Found at i:16725955 original size:47 final size:47
Alignment explanation
Indices: 16725886--16725979 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
16725876 GAGAATATGA
16725886 CCCTCCAAATATATAGAAACACTTGCATGAATTAGAATTCTACTAAG
1 CCCTCCAAATATATAGAAACACTTGCATGAATTAGAATTCTACTAAG
16725933 CCCTCCAAATATATAGAAACACTTGCATGAATTAGAATTCTACTAAG
1 CCCTCCAAATATATAGAAACACTTGCATGAATTAGAATTCTACTAAG
16725980 AAATTGACGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.40, C:0.21, G:0.11, T:0.28
Consensus pattern (47 bp):
CCCTCCAAATATATAGAAACACTTGCATGAATTAGAATTCTACTAAG
Found at i:16729439 original size:3 final size:3
Alignment explanation
Indices: 16729433--16729458 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
16729423 AATAACAATA
16729433 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
16729459 AATAATAACC
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:16731371 original size:20 final size:22
Alignment explanation
Indices: 16731329--16731371 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
16731319 AATAAAAAAA
* *
16731329 ATATATTTTTAATTGATATTTT
1 ATATACTTTTAATTGATAATTT
16731351 ATATACTTTTAATT-A-AATTT
1 ATATACTTTTAATTGATAATTT
16731371 A
1 A
16731372 AAATTTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 5 0.26
21 1 0.05
22 13 0.68
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (22 bp):
ATATACTTTTAATTGATAATTT
Found at i:16731377 original size:7 final size:7
Alignment explanation
Indices: 16731365--16731389 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
16731355 ACTTTTAATT
16731365 AAATTTA
1 AAATTTA
16731372 AAATTTA
1 AAATTTA
16731379 AAATTTA
1 AAATTTA
16731386 AAAT
1 AAAT
16731390 AATTTTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
AAATTTA
Found at i:16733193 original size:14 final size:14
Alignment explanation
Indices: 16733174--16733215 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
16733164 TCTTGATACT
*
16733174 TTTTCAGTGGTTTA
1 TTTTCAGTGATTTA
16733188 TTTTCAGTGATTTA
1 TTTTCAGTGATTTA
16733202 -TTTCA-TGA-TTA
1 TTTTCAGTGATTTA
16733213 TTT
1 TTT
16733216 AGAAGGTAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
11 3 0.12
12 5 0.19
13 5 0.19
14 13 0.50
ACGTcount: A:0.19, C:0.07, G:0.14, T:0.60
Consensus pattern (14 bp):
TTTTCAGTGATTTA
Found at i:16740771 original size:3 final size:3
Alignment explanation
Indices: 16740765--16740801 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
16740755 TAATCAATTG
16740765 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
16740802 AAAGCTTTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:16756693 original size:13 final size:13
Alignment explanation
Indices: 16756660--16756696 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
16756650 CCCACCCTCC
*
16756660 CAAAAAAAAAAAA
1 CAAAAAAGAAAAA
16756673 CAAAAAAGAAAAA
1 CAAAAAAGAAAAA
*
16756686 GAAAAAAGAAA
1 CAAAAAAGAAA
16756697 CTCTAAAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.86, C:0.05, G:0.08, T:0.00
Consensus pattern (13 bp):
CAAAAAAGAAAAA
Found at i:16757567 original size:30 final size:30
Alignment explanation
Indices: 16757533--16757595 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
16757523 CCTTAAATGC
*
16757533 ATATCCTGAACCCCTCAAAGTAATTTAAAA
1 ATATCCTAAACCCCTCAAAGTAATTTAAAA
16757563 ATATCCTAAACCCCTCAAAGTAATTTAAAA
1 ATATCCTAAACCCCTCAAAGTAATTTAAAA
16757593 ATA
1 ATA
16757596 AGTAAAAATC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.46, C:0.22, G:0.05, T:0.27
Consensus pattern (30 bp):
ATATCCTAAACCCCTCAAAGTAATTTAAAA
Found at i:16763761 original size:42 final size:43
Alignment explanation
Indices: 16763674--16763774 Score: 134
Period size: 42 Copynumber: 2.4 Consensus size: 43
16763664 ATATTCCATA
*
16763674 ATAATATCATATAATATCCTATTAAGAATCAAATTGCTAAGAG
1 ATAATATCATATAATATCCTATTAAGAATCAAATTGCTAAAAG
* * *
16763717 ATAATATTATTTAATATCC-ATT-AGAAATCAAATTTCTAAAAG
1 ATAATATCATATAATATCCTATTAAG-AATCAAATTGCTAAAAG
*
16763759 ATAATATCACATAATA
1 ATAATATCATATAATA
16763775 ATATCCTAAC
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
41 2 0.04
42 31 0.62
43 17 0.34
ACGTcount: A:0.49, C:0.11, G:0.06, T:0.35
Consensus pattern (43 bp):
ATAATATCATATAATATCCTATTAAGAATCAAATTGCTAAAAG
Found at i:16765315 original size:40 final size:40
Alignment explanation
Indices: 16765169--16765304 Score: 191
Period size: 40 Copynumber: 3.4 Consensus size: 40
16765159 CGCTAGGACC
* *
16765169 AAAAACGCCACTATAGATTAAGCATTAGCGGCGCTTTTTG
1 AAAAACGCCGCTATAGATCAAGCATTAGCGGCGCTTTTTG
* * * *
16765209 AAAAATGCCGTTATAAATCAAGCATCAGCGGCGCTTTTTG
1 AAAAACGCCGCTATAGATCAAGCATTAGCGGCGCTTTTTG
* * *
16765249 AAAAACGCCGCTATAGATCGAGCATTAGCGGTGATTTTTG
1 AAAAACGCCGCTATAGATCAAGCATTAGCGGCGCTTTTTG
16765289 AAAAACGCCGCTATAG
1 AAAAACGCCGCTATAG
16765305 GTTGACCATT
Statistics
Matches: 83, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 83 1.00
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (40 bp):
AAAAACGCCGCTATAGATCAAGCATTAGCGGCGCTTTTTG
Found at i:16765333 original size:40 final size:40
Alignment explanation
Indices: 16765169--16765325 Score: 125
Period size: 40 Copynumber: 3.9 Consensus size: 40
16765159 CGCTAGGACC
* ** * * *
16765169 AAAAACGCCACTATAGATTAAGCATTAGCGGCGCTTTTTG
1 AAAAACGCCGCTATAGATCGACCATTAACAGCGCTTTTTG
* * * * * * * *
16765209 AAAAATGCCGTTATAAATCAAGCATCAGCGGCGCTTTTTG
1 AAAAACGCCGCTATAGATCGACCATTAACAGCGCTTTTTG
* * * * *
16765249 AAAAACGCCGCTATAGATCGAGCATTAGCGGTGATTTTTG
1 AAAAACGCCGCTATAGATCGACCATTAACAGCGCTTTTTG
* *
16765289 AAAAACGCCGCTATAGGTTGACCATTAACAGCGCTTT
1 AAAAACGCCGCTATAGATCGACCATTAACAGCGCTTT
16765326 CTAAAAAATG
Statistics
Matches: 97, Mismatches: 20, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 97 1.00
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (40 bp):
AAAAACGCCGCTATAGATCGACCATTAACAGCGCTTTTTG
Found at i:16765333 original size:80 final size:80
Alignment explanation
Indices: 16765169--16765333 Score: 177
Period size: 80 Copynumber: 2.1 Consensus size: 80
16765159 CGCTAGGACC
* * * * *
16765169 AAAAACGCCACTATAGATTAAGCATTAGCGGCGCTTTTTGAAAAATGCCGTTATAAATCAAGCAT
1 AAAAACGCCACTATAGATCAAGCATTAGCGGCGATTTTTGAAAAACGCCGCTATAAATCAACCAT
* * * *
16765234 CAGCGGCGCTTTTTG
66 CAACAGCGCTTTCTA
* * * ** **
16765249 AAAAACGCCGCTATAGATCGAGCATTAGCGGTGATTTTTGAAAAACGCCGCTATAGGTTGACCAT
1 AAAAACGCCACTATAGATCAAGCATTAGCGGCGATTTTTGAAAAACGCCGCTATAAATCAACCAT
*
16765314 TAACAGCGCTTTCTA
66 CAACAGCGCTTTCTA
16765329 AAAAA
1 AAAAA
16765334 TGCAACGAAA
Statistics
Matches: 68, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
80 68 1.00
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (80 bp):
AAAAACGCCACTATAGATCAAGCATTAGCGGCGATTTTTGAAAAACGCCGCTATAAATCAACCAT
CAACAGCGCTTTCTA
Found at i:16766748 original size:39 final size:39
Alignment explanation
Indices: 16766700--16766800 Score: 139
Period size: 39 Copynumber: 2.6 Consensus size: 39
16766690 GCTCTGATGA
* **
16766700 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTTT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAACACTTGCAT
* *
16766739 GTTTCAGTTAGCCTTTGGGCTTCCGTTTAACACTTGCAT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAACACTTGCAT
* *
16766778 GCTTCAGCTAGACTTCGGGCTTC
1 GCTTCAGTTAGCCTTCGGGCTTC
16766801 AGATCACGAT
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 53 1.00
ACGTcount: A:0.13, C:0.26, G:0.23, T:0.39
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCGGGCTTCCGTTTAACACTTGCAT
Found at i:16768721 original size:8 final size:7
Alignment explanation
Indices: 16768675--16768721 Score: 60
Period size: 7 Copynumber: 6.4 Consensus size: 7
16768665 TATGCCTTAT
16768675 GGTTTAG
1 GGTTTAG
16768682 GGTTTAG
1 GGTTTAG
16768689 GGTTTAG
1 GGTTTAG
16768696 GGTTT-G
1 GGTTTAG
16768702 GAGTTTAGG
1 G-GTTTA-G
16768711 GGTTTAAG
1 GGTTT-AG
16768719 GGT
1 GGT
16768722 GAATATGGTG
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
6 2 0.06
7 23 0.64
8 8 0.22
9 3 0.08
ACGTcount: A:0.15, C:0.00, G:0.45, T:0.40
Consensus pattern (7 bp):
GGTTTAG
Found at i:16769275 original size:28 final size:29
Alignment explanation
Indices: 16769244--16769373 Score: 85
Period size: 28 Copynumber: 4.6 Consensus size: 29
16769234 TGTTTATTAT
*
16769244 TTTAGGGTTTAGAGTTTATAATTTAAGA-
1 TTTAAGGTTTAGAGTTTATAATTTAAGAG
* **
16769272 TTTAAGGTTTA-ATGTCTATGGTTTAAGAG
1 TTTAAGGTTTAGA-GTTTATAATTTAAGAG
**
16769301 TTTAAGGTTTATG-G--TATAATGTTTATTA-
1 TTTAAGGTTTA-GAGTTTATAA--TTTAAGAG
* * *
16769329 TTTTAGGTTTAGAGTTTTTAATTT-AGGG
1 TTTAAGGTTTAGAGTTTATAATTTAAGAG
*
16769357 TTTATGGTTTAGAGTTT
1 TTTAAGGTTTAGAGTTT
16769374 GTGGTTTTCT
Statistics
Matches: 77, Mismatches: 15, Indels: 20
0.69 0.13 0.18
Matches are distributed among these distances:
27 5 0.06
28 51 0.66
29 17 0.22
30 4 0.05
ACGTcount: A:0.26, C:0.01, G:0.22, T:0.51
Consensus pattern (29 bp):
TTTAAGGTTTAGAGTTTATAATTTAAGAG
Found at i:16769305 original size:8 final size:7
Alignment explanation
Indices: 16769265--16769325 Score: 50
Period size: 7 Copynumber: 8.6 Consensus size: 7
16769255 GAGTTTATAA
*
16769265 TTTAAGA
1 TTTAAGG
16769272 TTTAAGG
1 TTTAAGG
*
16769279 TTTAATG
1 TTTAAGG
* *
16769286 TCTATGG
1 TTTAAGG
16769293 TTTAAGAG
1 TTTAAG-G
16769301 TTTAAGG
1 TTTAAGG
*
16769308 TTTATGG
1 TTTAAGG
* *
16769315 TATAATG
1 TTTAAGG
16769322 TTTA
1 TTTA
16769326 TTATTTTAGG
Statistics
Matches: 41, Mismatches: 12, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
7 34 0.83
8 7 0.17
ACGTcount: A:0.30, C:0.02, G:0.21, T:0.48
Consensus pattern (7 bp):
TTTAAGG
Found at i:16769345 original size:21 final size:22
Alignment explanation
Indices: 16769321--16769360 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
16769311 ATGGTATAAT
16769321 GTTTATTATTTTA-GGTTTAGA
1 GTTTATTATTTTAGGGTTTAGA
*
16769342 GTTT-TTAATTTAGGGTTTA
1 GTTTATTATTTTAGGGTTTA
16769361 TGGTTTAGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.23, C:0.00, G:0.20, T:0.57
Consensus pattern (22 bp):
GTTTATTATTTTAGGGTTTAGA
Found at i:16769378 original size:14 final size:14
Alignment explanation
Indices: 16769244--16769380 Score: 59
Period size: 14 Copynumber: 9.7 Consensus size: 14
16769234 TGTTTATTAT
*
16769244 TTTAGGGTTTAGAG
1 TTTATGGTTTAGAG
**
16769258 TTTATAATTTA-AG
1 TTTATGGTTTAGAG
*
16769271 ATTTAAGGTTTA-ATG
1 -TTTATGGTTTAGA-G
*
16769286 TCTATGGTTTAAGAG
1 TTTATGGTTT-AGAG
*
16769301 TTTAAGGTTTATG-G
1 TTTATGGTTTA-GAG
* * *
16769315 TATAAT-GTTTATTAT
1 T-TTATGGTTTA-GAG
16769330 TTTA-GGTTTAGAG
1 TTTATGGTTTAGAG
* ** *
16769343 TTTTTAATTTAGGG
1 TTTATGGTTTAGAG
16769357 TTTATGGTTTAGAG
1 TTTATGGTTTAGAG
*
16769371 TTTGTGGTTT
1 TTTATGGTTT
16769381 TCTGTTTTAT
Statistics
Matches: 88, Mismatches: 26, Indels: 18
0.67 0.20 0.14
Matches are distributed among these distances:
13 6 0.07
14 66 0.75
15 15 0.17
16 1 0.01
ACGTcount: A:0.25, C:0.01, G:0.23, T:0.51
Consensus pattern (14 bp):
TTTATGGTTTAGAG
Found at i:16769560 original size:7 final size:7
Alignment explanation
Indices: 16769548--16769606 Score: 66
Period size: 7 Copynumber: 8.6 Consensus size: 7
16769538 AATATATATA
16769548 TTTAGGG
1 TTTAGGG
16769555 TTTAGGG
1 TTTAGGG
*
16769562 TGTA-GG
1 TTTAGGG
*
16769568 TTTATGG
1 TTTAGGG
*
16769575 TTTGGGG
1 TTTAGGG
**
16769582 TTTAAAG
1 TTTAGGG
16769589 TTTAGGG
1 TTTAGGG
16769596 TTTAGGG
1 TTTAGGG
16769603 TTTA
1 TTTA
16769607 TTGTTAGAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
6 5 0.12
7 37 0.88
ACGTcount: A:0.17, C:0.00, G:0.37, T:0.46
Consensus pattern (7 bp):
TTTAGGG
Found at i:16769597 original size:21 final size:21
Alignment explanation
Indices: 16769548--16769606 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
16769538 AATATATATA
* *
16769548 TTTAGGGTTTAGGGTGT-AGG
1 TTTAGGGTTTAGGGTTTAAAG
* *
16769568 TTTATGGTTTGGGGTTTAAAG
1 TTTAGGGTTTAGGGTTTAAAG
16769589 TTTAGGGTTTAGGGTTTA
1 TTTAGGGTTTAGGGTTTA
16769607 TTGTTAGAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 14 0.44
21 18 0.56
ACGTcount: A:0.17, C:0.00, G:0.37, T:0.46
Consensus pattern (21 bp):
TTTAGGGTTTAGGGTTTAAAG
Found at i:16769803 original size:17 final size:18
Alignment explanation
Indices: 16769781--16769814 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16769771 TATTTATTTT
16769781 AATATA-TTAAAATTATC
1 AATATAGTTAAAATTATC
*
16769798 AATATAGTTTAAATTAT
1 AATATAGTTAAAATTAT
16769815 TTAAGAGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (18 bp):
AATATAGTTAAAATTATC
Found at i:16771669 original size:22 final size:22
Alignment explanation
Indices: 16771620--16771672 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
16771610 GTACTATTGC
*
16771620 AATGCCTTGGTCAGGTACTGTG
1 AATGCTTTGGTCAGGTACTGTG
16771642 AATGCTTTGGTCAGGTACTGTG
1 AATGCTTTGGTCAGGTACTGTG
16771664 AATGCTTTG
1 AATGCTTTG
16771673 CATCTGGCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.19, C:0.15, G:0.30, T:0.36
Consensus pattern (22 bp):
AATGCTTTGGTCAGGTACTGTG
Found at i:16774133 original size:43 final size:43
Alignment explanation
Indices: 16774086--16774242 Score: 183
Period size: 43 Copynumber: 3.7 Consensus size: 43
16774076 GAAAGCGCCA
* *
16774086 CTAAAGGCCATGTTCTTTAGTGGCGTTTGTGGGAGAAA-TACTG
1 CTAAAGGTCATGTTCTTTAGTGGCGTTTGTGGGA-AAAGTACCG
*
16774129 CTAAAGGTCATGTTCTTTAGTGGCGTTTGTGGGAAAAGTGCCG
1 CTAAAGGTCATGTTCTTTAGTGGCGTTTGTGGGAAAAGTACCG
* * * ** *
16774172 CTAAAGGTTATGCTCTTTAGCGGCGTTTGTGGCTAAAG-AGCCA
1 CTAAAGGTCATGTTCTTTAGTGGCGTTTGTGGGAAAAGTA-CCG
* *
16774215 CTAAAGGTCATGCTCTTTAGCGGCGTTT
1 CTAAAGGTCATGTTCTTTAGTGGCGTTT
16774243 TTTGCGGCAC
Statistics
Matches: 101, Mismatches: 11, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
42 3 0.03
43 98 0.97
ACGTcount: A:0.22, C:0.17, G:0.29, T:0.32
Consensus pattern (43 bp):
CTAAAGGTCATGTTCTTTAGTGGCGTTTGTGGGAAAAGTACCG
Found at i:16782288 original size:6 final size:6
Alignment explanation
Indices: 16782277--16782343 Score: 74
Period size: 6 Copynumber: 12.2 Consensus size: 6
16782267 TAGGAAGATA
* *
16782277 TTATTT TTATTT TTATTT TTATTT TTGTTT TTA--A TTATTT TTA-TT
1 TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT
16782322 TTA-TT TTA-TT TTA-TT TTATTT T
1 TTATTT TTATTT TTATTT TTATTT T
16782344 ATTATTAAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
4 3 0.06
5 20 0.37
6 31 0.57
ACGTcount: A:0.18, C:0.00, G:0.01, T:0.81
Consensus pattern (6 bp):
TTATTT
Found at i:16782295 original size:5 final size:5
Alignment explanation
Indices: 16782281--16782346 Score: 66
Period size: 5 Copynumber: 13.4 Consensus size: 5
16782271 AAGATATTAT
* * *
16782281 TTTTA TTTTTA TTTTTA TTTT- TGTT- TTTAA TTAT- TTTTA TTTTA TTTTA
1 TTTTA -TTTTA -TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
16782330 TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TT
16782347 ATTAAATTAG
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
4 8 0.15
5 33 0.63
6 11 0.21
ACGTcount: A:0.18, C:0.00, G:0.02, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:16782970 original size:15 final size:15
Alignment explanation
Indices: 16782952--16782983 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
16782942 ATTTCAACTA
*
16782952 TTATTATATTTTTAT
1 TTATTATATTTATAT
16782967 TTATTATATTTATAT
1 TTATTATATTTATAT
16782982 TT
1 TT
16782984 GTATTTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTATTATATTTATAT
Found at i:16783066 original size:21 final size:22
Alignment explanation
Indices: 16783013--16783085 Score: 60
Period size: 21 Copynumber: 3.2 Consensus size: 22
16783003 ATTTTCTTTA
* *
16783013 TTATTTTTCTTATATATGTTTTT
1 TTATTTTTATTACATAT-TTTTT
16783036 TTACTCTTTTTATTA-ATATTTTTT
1 TTA---TTTTTATTACATATTTTTT
* *
16783060 TTATTTTTTTTACAT-TTTTTG
1 TTATTTTTATTACATATTTTTT
16783081 TTATT
1 TTATT
16783086 ATCTATTTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
21 18 0.42
22 2 0.05
23 3 0.07
24 8 0.19
25 4 0.09
26 8 0.19
ACGTcount: A:0.18, C:0.05, G:0.03, T:0.74
Consensus pattern (22 bp):
TTATTTTTATTACATATTTTTT
Found at i:16783068 original size:23 final size:24
Alignment explanation
Indices: 16783002--16783069 Score: 75
Period size: 26 Copynumber: 2.8 Consensus size: 24
16782992 ATACTAATAT
* *
16783002 TATTTTCTTTATTATTTTTCTTATA
1 TATTTTTTTTATT-TTTTTATTATA
*
16783027 TATGTTTTTTTACTCTTTTTATTA-A
1 TAT-TTTTTTTA-TTTTTTTATTATA
16783052 TATTTTTTTTATTTTTTT
1 TATTTTTTTTATTTTTTT
16783070 TACATTTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
23 6 0.16
24 8 0.22
25 7 0.19
26 15 0.41
27 1 0.03
ACGTcount: A:0.18, C:0.06, G:0.01, T:0.75
Consensus pattern (24 bp):
TATTTTTTTTATTTTTTTATTATA
Found at i:16783095 original size:33 final size:33
Alignment explanation
Indices: 16783031--16783095 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
16783021 CTTATATATG
* *
16783031 TTTTTTTACTCTTTTTATTAATATTTTTTTTAT
1 TTTTTTTACTCTTTTTATTAATATCTATTTTAT
* *
16783064 TTTTTTTACAT-TTTTTGTTATTATCTATTTTA
1 TTTTTTTAC-TCTTTTTATTAATATCTATTTTA
16783096 AGTTTTTATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 26 0.96
34 1 0.04
ACGTcount: A:0.18, C:0.06, G:0.02, T:0.74
Consensus pattern (33 bp):
TTTTTTTACTCTTTTTATTAATATCTATTTTAT
Found at i:16783149 original size:25 final size:27
Alignment explanation
Indices: 16783121--16783187 Score: 66
Period size: 25 Copynumber: 2.6 Consensus size: 27
16783111 TTCATTTCAA
*
16783121 ATTTTTATACATTATTTACTTT-AA-T
1 ATTTTTATACATTATGTACTTTAAACT
* * *
16783146 ATTTTCATATATTATGTATTTTAAACT
1 ATTTTTATACATTATGTACTTTAAACT
* *
16783173 TTTTTTACACATTAT
1 ATTTTTATACATTAT
16783188 ATATTTTGAA
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
25 18 0.56
26 2 0.06
27 12 0.38
ACGTcount: A:0.31, C:0.09, G:0.01, T:0.58
Consensus pattern (27 bp):
ATTTTTATACATTATGTACTTTAAACT
Found at i:16791894 original size:26 final size:27
Alignment explanation
Indices: 16791865--16791916 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
16791855 GTACAAATGG
*
16791865 TAATGA-AGAAATA-GTTTAGGTACCAC
1 TAATGACAGAAA-AGGTTTAGATACCAC
16791891 TAATGACAGAAAAGGTTTAGATACCA
1 TAATGACAGAAAAGGTTTAGATACCA
16791917 ATTTGAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.25
Consensus pattern (27 bp):
TAATGACAGAAAAGGTTTAGATACCAC
Found at i:16792663 original size:16 final size:17
Alignment explanation
Indices: 16792624--16792663 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
16792614 GTTTTTAAAG
16792624 TTTT-TATATTATGTTA
1 TTTTATATATTATGTTA
16792640 TTTGTATATATTATG-TA
1 TTT-TATATATTATGTTA
16792657 TTTTATA
1 TTTTATA
16792664 ACACATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 7 0.32
17 6 0.27
18 9 0.41
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (17 bp):
TTTTATATATTATGTTA
Found at i:16793792 original size:2 final size:2
Alignment explanation
Indices: 16793785--16793811 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
16793775 TTTAACTGTA
16793785 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
16793812 AAGTTAAGGT
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:16795218 original size:14 final size:15
Alignment explanation
Indices: 16795199--16795258 Score: 52
Period size: 16 Copynumber: 3.9 Consensus size: 15
16795189 ATCTAAAAAA
16795199 AAAATTAAATATA-T
1 AAAATTAAATATATT
16795213 AAAATTTATAATA-ATT
1 AAAA-TTA-AATATATT
*
16795229 AAAATAAAATATAATT
1 AAAATTAAATAT-ATT
*
16795245 ATAATTATAATATA
1 AAAATTA-AATATA
16795259 CATAATTGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 8 0.22
15 6 0.16
16 18 0.49
17 5 0.14
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAAATTAAATATATT
Found at i:16795343 original size:39 final size:38
Alignment explanation
Indices: 16795300--16795410 Score: 125
Period size: 39 Copynumber: 2.8 Consensus size: 38
16795290 CATTTTTTAA
16795300 AAATTGTAAAAATTATAAATAAATTTAAAAAGGTATTAG
1 AAATTGTAAAAATTATAAATAAATTTAAAAAGG-ATTAG
* * *
16795339 AAATTGTAAACTATTGTAAA-AAATTATAAAAATGATTAG
1 AAATTGTAAA-AATTATAAATAAATT-TAAAAAGGATTAG
*
16795378 AAATCGTAAAATATTATAAATAATTATTTAAAA
1 AAATTGTAAAA-ATTATAAATAA--ATTTAAAA
16795411 TTTTAAAAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
39 36 0.60
40 16 0.27
41 5 0.08
42 3 0.05
ACGTcount: A:0.56, C:0.02, G:0.08, T:0.34
Consensus pattern (38 bp):
AAATTGTAAAAATTATAAATAAATTTAAAAAGGATTAG
Found at i:16795800 original size:19 final size:19
Alignment explanation
Indices: 16795778--16795817 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
16795768 AATAATTTAT
*
16795778 TTTGAAATAGTAAAAAATA
1 TTTGAAATAATAAAAAATA
*
16795797 TTTGAAATAATTAAAAATA
1 TTTGAAATAATAAAAAATA
16795816 TT
1 TT
16795818 ATTGATTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (19 bp):
TTTGAAATAATAAAAAATA
Found at i:16796044 original size:18 final size:17
Alignment explanation
Indices: 16796021--16796106 Score: 59
Period size: 18 Copynumber: 4.7 Consensus size: 17
16796011 CTAATGTGTT
16796021 TTTTTTTAATTTTAGTAA
1 TTTTTTTAATTTTA-TAA
*
16796039 TTTTTTTATATTTTTATAT
1 TTTTTTTA-A-TTTTATAA
*
16796058 TATTTTTTAATTTTTTAA
1 T-TTTTTTAATTTTATAA
16796076 TGTTATATTT--TTTTATAA
1 T-TT-T-TTTAATTTTATAA
*
16796094 TTTATTGTAATTT
1 TTT-TTTTAATTT
16796107 CTTTTCATTT
Statistics
Matches: 55, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
16 2 0.04
17 4 0.07
18 28 0.51
19 6 0.11
20 15 0.27
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (17 bp):
TTTTTTTAATTTTATAA
Found at i:16796044 original size:19 final size:17
Alignment explanation
Indices: 16796020--16796071 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 17
16796010 TCTAATGTGT
16796020 TTTTTTTTAATTTTAGTAA
1 TTTTTTTTAATTTTA-T-A
*
16796039 TTTTTTTATATTTTTATA
1 TTTTTTT-TAATTTTATA
16796057 TTATTTTTTAATTTT
1 TT-TTTTTTAATTTT
16796072 TTAATGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
18 9 0.31
19 13 0.45
20 7 0.24
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (17 bp):
TTTTTTTTAATTTTATA
Found at i:16796062 original size:21 final size:21
Alignment explanation
Indices: 16796038--16796088 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
16796028 AATTTTAGTA
16796038 ATTTTTTTATATTTTT-ATATT
1 ATTTTTTTAT-TTTTTAATATT
* *
16796059 ATTTTTTAATTTTTTAATGTT
1 ATTTTTTTATTTTTTAATATT
16796080 ATATTTTTT
1 AT-TTTTTT
16796089 TATAATTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 5 0.20
21 15 0.60
22 5 0.20
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.75
Consensus pattern (21 bp):
ATTTTTTTATTTTTTAATATT
Found at i:16796071 original size:26 final size:26
Alignment explanation
Indices: 16796042--16796096 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
16796032 TTAGTAATTT
* * * *
16796042 TTTTATATTTTTATATTATTTTTTAA
1 TTTTATAATGTTATATTTTTTTATAA
*
16796068 TTTTTTAATGTTATATTTTTTTATAA
1 TTTTATAATGTTATATTTTTTTATAA
16796094 TTT
1 TTT
16796097 ATTGTAATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (26 bp):
TTTTATAATGTTATATTTTTTTATAA
Found at i:16796072 original size:19 final size:19
Alignment explanation
Indices: 16796021--16796072 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
16796011 CTAATGTGTT
16796021 TTTTTTTAA-TTTTAGTAA
1 TTTTTTTAATTTTTAGTAA
*
16796039 TTTTTTTATATTTTTA-TAT
1 TTTTTTTA-ATTTTTAGTAA
16796058 TATTTTTTAATTTTT
1 T-TTTTTTAATTTTT
16796073 TAATGTTATA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 8 0.27
19 10 0.33
20 12 0.40
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (19 bp):
TTTTTTTAATTTTTAGTAA
Found at i:16797097 original size:27 final size:26
Alignment explanation
Indices: 16797058--16797111 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 26
16797048 TCGAGTGATT
16797058 AAATAAAAATAAAATAAAATATTCAAAA
1 AAATAAAAATAAAATAAAAT-TT-AAAA
*
16797086 AAAT-AAAATAAATTAAAATTTAAAA
1 AAATAAAAATAAAATAAAATTTAAAA
16797111 A
1 A
16797112 TAATGATTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 5 0.20
26 2 0.08
27 14 0.56
28 4 0.16
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (26 bp):
AAATAAAAATAAAATAAAATTTAAAA
Found at i:16797291 original size:6 final size:6
Alignment explanation
Indices: 16797280--16797321 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
16797270 GCCAGCTTAG
16797280 CATATA CATATA CATATA CATATA CATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA
16797322 TTCTTTTTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (6 bp):
CATATA
Found at i:16801072 original size:22 final size:24
Alignment explanation
Indices: 16801047--16801092 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 24
16801037 AGTCCGGCCC
*
16801047 ATATTATTTT-TTTTAA-ATATTT
1 ATATTATTTTAATTTAATATATTT
16801069 ATATTATTTTAATTTAATATATTT
1 ATATTATTTTAATTTAATATATTT
16801093 TTTATATAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 10 0.48
23 5 0.24
24 6 0.29
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (24 bp):
ATATTATTTTAATTTAATATATTT
Found at i:16803089 original size:19 final size:19
Alignment explanation
Indices: 16803039--16803090 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
16803029 TGTTTAATAT
*
16803039 AATAATATAATAATTATTTA
1 AATAATATAA-AAATATTTA
*
16803059 AAAAAT-TAAAAATATTTA
1 AATAATATAAAAATATTTA
*
16803077 GATAATATAAAAAT
1 AATAATATAAAAAT
16803091 GACATTGATA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 12 0.44
19 10 0.37
20 5 0.19
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (19 bp):
AATAATATAAAAATATTTA
Found at i:16811823 original size:24 final size:24
Alignment explanation
Indices: 16811796--16811843 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
16811786 ATCTCAAAAA
16811796 GAGGTATCTTACAAATTCAACACT
1 GAGGTATCTTACAAATTCAACACT
16811820 GAGGTATCTTACAAATTCAACACT
1 GAGGTATCTTACAAATTCAACACT
16811844 CGGTTTGTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (24 bp):
GAGGTATCTTACAAATTCAACACT
Found at i:16813283 original size:2 final size:2
Alignment explanation
Indices: 16813278--16813308 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
16813268 GTGACTACCC
16813278 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16813309 CATGTACGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16813588 original size:2 final size:2
Alignment explanation
Indices: 16813581--16813617 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
16813571 ATTTCTCATA
16813581 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16813618 CACGATATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:16814363 original size:2 final size:2
Alignment explanation
Indices: 16814356--16814387 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
16814346 ATTGAATTGC
16814356 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16814388 CTTTTGAGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16821736 original size:9 final size:9
Alignment explanation
Indices: 16821722--16821750 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
16821712 GATGTAAAAA
16821722 TAGTTATGC
1 TAGTTATGC
16821731 TAGTTATGC
1 TAGTTATGC
16821740 TAGTTATGC
1 TAGTTATGC
16821749 TA
1 TA
16821751 ATTTTAAGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.24, C:0.10, G:0.21, T:0.45
Consensus pattern (9 bp):
TAGTTATGC
Found at i:16827906 original size:5 final size:5
Alignment explanation
Indices: 16827860--16827904 Score: 72
Period size: 5 Copynumber: 9.0 Consensus size: 5
16827850 AAGATGGCGC
* *
16827860 TGAGT TGAGT TGAGT TGAGT TGAGT TGAGT TGAGT AGAGT AGAGT
1 TGAGT TGAGT TGAGT TGAGT TGAGT TGAGT TGAGT TGAGT TGAGT
16827905 AGTGTACAGT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.24, C:0.00, G:0.40, T:0.36
Consensus pattern (5 bp):
TGAGT
Found at i:16828208 original size:21 final size:20
Alignment explanation
Indices: 16828165--16828207 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
16828155 CAGAAAATAA
*
16828165 TTTCTGAAAAATAATTTATT
1 TTTCTGAAAAATAATATATT
16828185 TTTCTGGAAAAATAA-ATATT
1 TTTCT-GAAAAATAATATATT
16828205 TTT
1 TTT
16828208 TGGTGTTTGA
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:0.40, C:0.05, G:0.07, T:0.49
Consensus pattern (20 bp):
TTTCTGAAAAATAATATATT
Found at i:16828607 original size:15 final size:15
Alignment explanation
Indices: 16828587--16828652 Score: 55
Period size: 15 Copynumber: 4.3 Consensus size: 15
16828577 ATTACAAAAC
16828587 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
16828602 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
16828621 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
*
16828636 ATTGA-TATTAA-AT
1 ATTTATTATTAATAT
16828649 ATTT
1 ATTT
16828653 TCAATAATAT
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
13 5 0.12
14 6 0.14
15 13 0.31
16 1 0.02
17 7 0.17
18 1 0.02
19 9 0.21
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:16828702 original size:16 final size:16
Alignment explanation
Indices: 16828671--16828707 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
16828661 ATGTTAATAA
16828671 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
16828687 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
16828703 TATTA
1 TATTA
16828708 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:16828759 original size:22 final size:22
Alignment explanation
Indices: 16828719--16828774 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
16828709 AATAAAATTG
*
16828719 AAATATTAAA-TA-ATTTATTA
1 AAATAATAAATTATATTTATTA
16828739 AAATAATAAATTATATTTATTA
1 AAATAATAAATTATATTTATTA
* * *
16828761 TATTAATAATTTAT
1 AAATAATAAATTAT
16828775 TATATGACTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 9 0.30
21 2 0.07
22 19 0.63
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AAATAATAAATTATATTTATTA
Found at i:16836371 original size:30 final size:28
Alignment explanation
Indices: 16836299--16836381 Score: 78
Period size: 30 Copynumber: 2.8 Consensus size: 28
16836289 TAATTTTAAA
*
16836299 AAATAATTGAGAAAATAAAATAAAATTTT
1 AAATAATT-AGAAAATAAAATAAAATATT
* *
16836328 AAA-AGTGATGAAAATTAAAATTAAAATATT
1 AAATAATTA-GAAAA-TAAAA-TAAAATATT
*
16836358 AAATAATTAGAAAAAATAAATAAA
1 AAATAATTAGAAAATA-AAATAAA
16836382 TAAATTATAA
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
27 1 0.02
28 7 0.16
29 13 0.30
30 19 0.44
31 3 0.07
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (28 bp):
AAATAATTAGAAAATAAAATAAAATATT
Found at i:16838204 original size:17 final size:17
Alignment explanation
Indices: 16838182--16838216 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
16838172 TTACGATTTA
16838182 TCTCTCAATACTTTTCG
1 TCTCTCAATACTTTTCG
16838199 TCTCTCAATACTTTTCG
1 TCTCTCAATACTTTTCG
16838216 T
1 T
16838217 TTGATGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.29, G:0.06, T:0.49
Consensus pattern (17 bp):
TCTCTCAATACTTTTCG
Found at i:16842281 original size:311 final size:310
Alignment explanation
Indices: 16841708--16842294 Score: 704
Period size: 311 Copynumber: 1.9 Consensus size: 310
16841698 AGACAAGAAA
16841708 AAAAAGCAACTACAATATTGAGGAAGAAAAGGGTTGCAAATTGGATTCAAAAGCTCTTAATGCAA
1 AAAAAGCAACTACAATATTGAGGAAGAAAAGGGTTGCAAATTGGATTCAAAAGCTCTTAATGCAA
* *
16841773 TATGCAATGATGTTGACATTGAACAATTCGAAATCATTTCCATATGTGAATCCATCAAAGATATT
66 TATGCAATGATGTTGACATTGAACAATTCAAAATCATTTCCATATGTGAATCCATCAAAGATAGT
* * * * * * *
16841838 TGGACAAATCTCTAAAATCAACATGAAGGGAATGCAATCAATCTATATGTCTAAACTCTAGATTC
131 CGGACAAATCTCTAAAATCAACATGAAAGGAATACAATCAATCTACATGTCCAAACTCTACATCC
** * * *
16841903 TTACTTTGAAATTTGAAAATTTAAGAATGAGTTAAGAAGAAACTATTTTTGGTTTTAAAGTTCAT
196 TTACTTCCAAATTTGAAAATTTAAGAATGAATGAAGAAGAAACTATTTTTAGTTTTAAAG-TCAT
16841968 TTATGTGAAATTTCTATTGAAGTAGCTACAACATTGTGAGTTCTAAGACAG
260 TTATGTGAAATTTCTATTGAAGTAGCTACAACATTGTGAGTTCTAAGACAG
* * * * *
16842019 AAAAA-CAACTACGATATTGTGGAAG-AAAGGGTTGCCAATTTGGAATTGAAAAGCTCTTAATGT
1 AAAAAGCAACTACAATATTGAGGAAGAAAAGGGTTG-CAAATTGG-ATTCAAAAGCTCTTAATGC
* * * * * * * *
16842082 AATATGCAGTTATGTTGTCATTGAATAATTCAAAATCTTTTCTATGTGTGAATTCA-CTAAAGAT
64 AATATGCAATGATGTTGACATTGAACAATTCAAAATCATTTCCATATGTGAATCCATC-AAAGAT
* * *
16842146 -GTCGGACAATTCTTTAAAATCAACACT-AAAGGAATAC-ATCAGTCTACATGTCCAAACT-TCA
128 AGTCGGACAAATCTCTAAAATCAACA-TGAAAGGAATACAATCAATCTACATGTCCAAACTCT-A
* ** * * *
16842207 CATCCTTACTTCCAAGTTTGAATTTTTAAGAATGAATGAAGAATAAACTTTTTTTTTTATTTTTA
191 CATCCTTACTTCCAAATTTGAAAATTTAAGAATGAATGAAGAAGAAAC---TATTTTTAGTTTTA
16842272 CAA-TCATTTATGTGAAATTTCTA
253 -AAGTCATTTATGTGAAATTTCTA
16842295 ACGAAGCCCT
Statistics
Matches: 231, Mismatches: 36, Indels: 18
0.81 0.13 0.06
Matches are distributed among these distances:
308 1 0.00
309 66 0.29
310 55 0.24
311 96 0.42
312 11 0.05
313 2 0.01
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (310 bp):
AAAAAGCAACTACAATATTGAGGAAGAAAAGGGTTGCAAATTGGATTCAAAAGCTCTTAATGCAA
TATGCAATGATGTTGACATTGAACAATTCAAAATCATTTCCATATGTGAATCCATCAAAGATAGT
CGGACAAATCTCTAAAATCAACATGAAAGGAATACAATCAATCTACATGTCCAAACTCTACATCC
TTACTTCCAAATTTGAAAATTTAAGAATGAATGAAGAAGAAACTATTTTTAGTTTTAAAGTCATT
TATGTGAAATTTCTATTGAAGTAGCTACAACATTGTGAGTTCTAAGACAG
Found at i:16844612 original size:42 final size:43
Alignment explanation
Indices: 16844520--16844623 Score: 131
Period size: 43 Copynumber: 2.4 Consensus size: 43
16844510 AATGCCAACG
* *
16844520 TCCCAGACATGGTCTTACATGTAATCAAATATCGATGCCACTA
1 TCCCAGACATGGTCTTACACGAAATCAAATATCGATGCCACTA
* *
16844563 TCCCAGACAGGGTCTTACACGAAATCAAATA-CGATGCCGA-TG
1 TCCCAGACATGGTCTTACACGAAATCAAATATCGATGCC-ACTA
* *
16844605 TCTCAGACATGATCTTACA
1 TCCCAGACATGGTCTTACA
16844624 TATAAATCAT
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
42 24 0.45
43 29 0.55
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (43 bp):
TCCCAGACATGGTCTTACACGAAATCAAATATCGATGCCACTA
Found at i:16846207 original size:89 final size:90
Alignment explanation
Indices: 16846054--16846232 Score: 238
Period size: 89 Copynumber: 2.0 Consensus size: 90
16846044 TATAGGCAAT
* * * *
16846054 TGGGTGCGCAATAATTGAAAAAAAAAAGAGGTAACTGACGAATCTGAAATTATCTTGGGATTCTC
1 TGGGTGCGCAAGAATT-AAAAAAAAAAGAGGTAACAGACGAATCTAAAATTATCTCGGGATTCTC
16846119 -GAGATGTCT-AAAAACTTATCCTGGGA
65 AG-GATGTCTGAAAAA-TTATCCTGGGA
* * *
16846145 TGGGTGGGCAAGAATT-AAAAAAAAAGATGTAACAGATGAATCTAAAATTATCTCGGGATTCTCA
1 TGGGTGCGCAAGAATTAAAAAAAAAAGAGGTAACAGACGAATCTAAAATTATCTCGGGATTCTCA
*
16846209 GGATGTTTGAAAAATTATCCTGGG
66 GGATGTCTGAAAAATTATCCTGGG
16846233 GTTTTAGAAA
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
89 58 0.74
90 6 0.08
91 14 0.18
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.27
Consensus pattern (90 bp):
TGGGTGCGCAAGAATTAAAAAAAAAAGAGGTAACAGACGAATCTAAAATTATCTCGGGATTCTCA
GGATGTCTGAAAAATTATCCTGGGA
Found at i:16847819 original size:6 final size:6
Alignment explanation
Indices: 16847787--16847830 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
16847777 ACAGTACCTA
* * *
16847787 AACAGT AATCAGT AACGGT AGCAGT AACAGT AATAGT AACAGT A
1 AACAGT AA-CAGT AACAGT AACAGT AACAGT AACAGT AACAGT A
16847831 TTCAACACAC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
6 25 0.81
7 6 0.19
ACGTcount: A:0.45, C:0.14, G:0.20, T:0.20
Consensus pattern (6 bp):
AACAGT
Found at i:16847858 original size:45 final size:45
Alignment explanation
Indices: 16847808--16847920 Score: 145
Period size: 45 Copynumber: 2.5 Consensus size: 45
16847798 GTAACGGTAG
* **
16847808 CAGTAACAGTAATAGTAACAGTATTCAACACACAAAGTGTTTAAT
1 CAGTAACAGTAACAGTAACAGTATTCAACACACAAAGTGTCAAAT
* * **
16847853 CAGTAACGGTAACAGTAATAGTATTTGACACACAAAGTGTCAAAT
1 CAGTAACAGTAACAGTAACAGTATTCAACACACAAAGTGTCAAAT
* *
16847898 CGGTAACAGTAACGGTAACAGTA
1 CAGTAACAGTAACAGTAACAGTA
16847921 ATAGTAGCCG
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 57 1.00
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.24
Consensus pattern (45 bp):
CAGTAACAGTAACAGTAACAGTATTCAACACACAAAGTGTCAAAT
Found at i:16849490 original size:20 final size:19
Alignment explanation
Indices: 16849463--16849504 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
16849453 ATATAAAACC
16849463 ATAACAATTA-ATAATTATA
1 ATAACAATTATATAA-TATA
16849482 ATAATCAATTATATAATATA
1 ATAA-CAATTATATAATATA
16849502 ATA
1 ATA
16849505 TATATAATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.19
20 13 0.62
21 4 0.19
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
ATAACAATTATATAATATA
Found at i:16851093 original size:12 final size:12
Alignment explanation
Indices: 16851076--16851159 Score: 54
Period size: 12 Copynumber: 7.1 Consensus size: 12
16851066 ATTATTTTAA
16851076 TAAATTTAATAT
1 TAAATTTAATAT
16851088 TAAATTTAAT-T
1 TAAATTTAATAT
* *
16851099 TAATACTT-ATCT
1 TAA-ATTTAATAT
16851111 TGATAGCA-TTA-TAT
1 T-A-A--ATTTAATAT
16851125 T-AATTTAATAT
1 TAAATTTAATAT
*
16851136 TAATTTTAATAT
1 TAAATTTAATAT
16851148 TAAA-TTAATAT
1 TAAATTTAATAT
16851159 T
1 T
16851160 TATCTTATAG
Statistics
Matches: 58, Mismatches: 5, Indels: 19
0.71 0.06 0.23
Matches are distributed among these distances:
9 1 0.02
10 3 0.05
11 19 0.33
12 27 0.47
13 1 0.02
14 6 0.10
15 1 0.02
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (12 bp):
TAAATTTAATAT
Found at i:16851137 original size:11 final size:11
Alignment explanation
Indices: 16851121--16851159 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
16851111 TGATAGCATT
16851121 ATATTAATTTA
1 ATATTAATTTA
16851132 ATATTAATTTTA
1 ATATTAA-TTTA
*
16851144 ATATTAAATTA
1 ATATTAATTTA
16851155 ATATT
1 ATATT
16851160 TATCTTATAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 15 0.58
12 11 0.42
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
ATATTAATTTA
Found at i:16851144 original size:6 final size:6
Alignment explanation
Indices: 16851121--16851159 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
16851111 TGATAGCATT
*
16851121 ATATTA AT-TTA ATATTA ATTTTA ATATTA A-ATTA ATATT
1 ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA ATATT
16851160 TATCTTATAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 10 0.34
6 19 0.66
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
ATATTA
Found at i:16855149 original size:12 final size:12
Alignment explanation
Indices: 16855134--16855159 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
16855124 TGGTCTGAAT
16855134 ATAAAAAAATAA
1 ATAAAAAAATAA
16855146 ATAAAAAAATAA
1 ATAAAAAAATAA
16855158 AT
1 AT
16855160 TTAATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (12 bp):
ATAAAAAAATAA
Found at i:16855854 original size:14 final size:14
Alignment explanation
Indices: 16855835--16855868 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
16855825 GTACTAGTTG
16855835 TTGCTTTATTGAAT
1 TTGCTTTATTGAAT
16855849 TTGCTTTATTGAAT
1 TTGCTTTATTGAAT
16855863 TTGCTT
1 TTGCTT
16855869 CATTAATAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.18, C:0.09, G:0.15, T:0.59
Consensus pattern (14 bp):
TTGCTTTATTGAAT
Found at i:16856984 original size:6 final size:6
Alignment explanation
Indices: 16856973--16857003 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
16856963 CCCTATCTAG
16856973 ACGATC ACGATC ACGATC ACGATC ACGATC A
1 ACGATC ACGATC ACGATC ACGATC ACGATC A
16857004 TCATCATCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.35, C:0.32, G:0.16, T:0.16
Consensus pattern (6 bp):
ACGATC
Found at i:16865603 original size:28 final size:28
Alignment explanation
Indices: 16865549--16865605 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
16865539 AAAAGAAAAG
*
16865549 TAGTGTTATGAATATGCAAACAGAATCA
1 TAGTGTTATGAATACGCAAACAGAATCA
16865577 TAGTGTTATGAATACGCAAACAGAATCA
1 TAGTGTTATGAATACGCAAACAGAATCA
16865605 T
1 T
16865606 GTCACAGGGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.42, C:0.12, G:0.18, T:0.28
Consensus pattern (28 bp):
TAGTGTTATGAATACGCAAACAGAATCA
Found at i:16885476 original size:3 final size:3
Alignment explanation
Indices: 16885470--16885524 Score: 101
Period size: 3 Copynumber: 18.3 Consensus size: 3
16885460 TACCATCATC
16885470 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
16885518 AGT AAT A
1 AAT AAT A
16885525 CTATTCTCAC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:16888428 original size:24 final size:24
Alignment explanation
Indices: 16888400--16888449 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
16888390 TGCTGGGCTT
*
16888400 CTCTTTGGATCTTGTCTATTAATG
1 CTCTTTGGATCTTGTATATTAATG
16888424 CTCTTTGGATCTTGTATATTAATG
1 CTCTTTGGATCTTGTATATTAATG
16888448 CT
1 CT
16888450 ATGTAGTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.18, C:0.16, G:0.16, T:0.50
Consensus pattern (24 bp):
CTCTTTGGATCTTGTATATTAATG
Found at i:16890151 original size:12 final size:12
Alignment explanation
Indices: 16890114--16890168 Score: 58
Period size: 12 Copynumber: 4.7 Consensus size: 12
16890104 TGTACTTTTA
16890114 TATT-TTAGTAT
1 TATTATTAGTAT
* * *
16890125 CATTGTTATTAT
1 TATTATTAGTAT
16890137 TATTATTAGTAT
1 TATTATTAGTAT
*
16890149 TATTATTATTAT
1 TATTATTAGTAT
*
16890161 CATTATTA
1 TATTATTA
16890169 TTTATTTTTC
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
11 3 0.08
12 33 0.92
ACGTcount: A:0.31, C:0.04, G:0.05, T:0.60
Consensus pattern (12 bp):
TATTATTAGTAT
Found at i:16890188 original size:3 final size:3
Alignment explanation
Indices: 16890130--16890170 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
16890120 AGTATCATTG
* *
16890130 TTA TTA TTA TTA TTA GTA TTA TTA TTA TTA TCA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
16890171 TATTTTTCCT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:16895182 original size:19 final size:19
Alignment explanation
Indices: 16895158--16895198 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
16895148 AGAGAAGGAG
16895158 ACAACAATGCTTTTCATAA
1 ACAACAATGCTTTTCATAA
16895177 ACAACAATGCTTTTCATAA
1 ACAACAATGCTTTTCATAA
16895196 ACA
1 ACA
16895199 CTCTAAAAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.44, C:0.22, G:0.05, T:0.29
Consensus pattern (19 bp):
ACAACAATGCTTTTCATAA
Found at i:16902323 original size:44 final size:46
Alignment explanation
Indices: 16902254--16902352 Score: 134
Period size: 44 Copynumber: 2.2 Consensus size: 46
16902244 CACTGTGGTG
*
16902254 AATCTTATC-TCCTTGAAGTCACAGTGGAGTAGATTGAAG-TCA-CA
1 AATCTTATCTTCCTTGAAGTCACAGTGGAGCAGATTGAAGAT-ATCA
**
16902298 AATCTTATCTTCC-TGAAGTTGCAGTGGAGCAGATTGAAGATATCA
1 AATCTTATCTTCCTTGAAGTCACAGTGGAGCAGATTGAAGATATCA
16902343 AATCTTATCT
1 AATCTTATCT
16902353 CTCTAAAGTT
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
44 33 0.67
45 16 0.33
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32
Consensus pattern (46 bp):
AATCTTATCTTCCTTGAAGTCACAGTGGAGCAGATTGAAGATATCA
Found at i:16902362 original size:45 final size:44
Alignment explanation
Indices: 16902254--16902367 Score: 126
Period size: 44 Copynumber: 2.6 Consensus size: 44
16902244 CACTGTGGTG
* * *
16902254 AATCTTATC-TCCTTGAAGTCACAGTGGAGTAGATTGAAGTCACA
1 AATCTTATCTTCC-TAAAGTTACAGTGGAGCAGATTGAAGTCACA
* *
16902298 AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGAT-ATCA
1 AATCTTATCTTCCTAAAGTTACAGTGGAGCAGATTGAAG-TCA-CA
16902343 AATCTTATC-TCTCTAAAGTTACAGT
1 AATCTTATCTTC-CTAAAGTTACAGT
16902368 AGAATAGATT
Statistics
Matches: 61, Mismatches: 5, Indels: 7
0.84 0.07 0.10
Matches are distributed among these distances:
44 35 0.57
45 26 0.43
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (44 bp):
AATCTTATCTTCCTAAAGTTACAGTGGAGCAGATTGAAGTCACA
Found at i:16902377 original size:45 final size:44
Alignment explanation
Indices: 16902254--16902434 Score: 145
Period size: 45 Copynumber: 4.1 Consensus size: 44
16902244 CACTGTGGTG
* * * *
16902254 AATCTTATCTC-CTTGAAGTCACAGTGGAGTAGATTGAAG-TCACA
1 AATCTTATCTCTC-TAAAGTTACAGTAGAATAGATTGAAGAT-ACA
* * * **
16902298 AATCTTATCT-TCCTGAAGTTGCAGTGGAGCAGATTGAAGATATCA
1 AATCTTATCTCT-CTAAAGTTACAGTAGAATAGATTGAAGATA-CA
* *
16902343 AATCTTATCTCTCTAAAGTTACAGTAGAATAGATT-AAAACTAGA
1 AATCTTATCTCTCTAAAGTTACAGTAGAATAGATTGAAGA-TACA
* * * *
16902387 AATCTTATTTCCCTAAAAGTTACAGTAGAATAGATTAAAGCTACA
1 AATCTTATCTCTCT-AAAGTTACAGTAGAATAGATTGAAGATACA
16902432 AAT
1 AAT
16902435 TACAAATCTT
Statistics
Matches: 114, Mismatches: 15, Indels: 15
0.79 0.10 0.10
Matches are distributed among these distances:
44 50 0.44
45 61 0.54
46 3 0.03
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (44 bp):
AATCTTATCTCTCTAAAGTTACAGTAGAATAGATTGAAGATACA
Found at i:16903293 original size:2 final size:2
Alignment explanation
Indices: 16903286--16903325 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
16903276 AATTTGTTAT
16903286 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
16903326 AAAGAAAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:16904080 original size:12 final size:12
Alignment explanation
Indices: 16904063--16904101 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
16904053 AAACAAACTG
16904063 TTTTATTTATTA
1 TTTTATTTATTA
16904075 TTTTATTTATT-
1 TTTTATTTATTA
*
16904086 TATCTATTTATTA
1 T-TTTATTTATTA
16904099 TTT
1 TTT
16904102 CTTCAACCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 1 0.04
12 21 0.91
13 1 0.04
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTATTTATTA
Found at i:16904183 original size:3 final size:3
Alignment explanation
Indices: 16904161--16904211 Score: 59
Period size: 3 Copynumber: 17.3 Consensus size: 3
16904151 TGTACTTTTA
* * * *
16904161 TAT T-T TAT TAT CAT TGT TAT TAT TAT TAG TAT TAT TAT TAT CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
16904208 TAT T
1 TAT T
16904212 TATTTTTCCT
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:16904193 original size:12 final size:11
Alignment explanation
Indices: 16904178--16904215 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
16904168 TTATCATTGT
16904178 TATTATTATTA
1 TATTATTATTA
16904189 GTATTATTATTA
1 -TATTATTATTA
16904201 TCATTATTATT-
1 T-ATTATTATTA
16904212 TATT
1 TATT
16904216 TTTCCTTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 3 0.12
11 2 0.08
12 20 0.80
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (11 bp):
TATTATTATTA
Found at i:16908211 original size:79 final size:81
Alignment explanation
Indices: 16908102--16908284 Score: 241
Period size: 79 Copynumber: 2.3 Consensus size: 81
16908092 TACTCGTTCA
* *
16908102 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
16908165 ATTTAGTAAC-TCGCACC
65 ATATAGTAACTTAGCA-C
**
16908182 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
*
16908245 TATAGTCACTTAGCAC
66 TATAGTAACTTAGCAC
*
16908261 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
16908285 CGCCATTCGA
Statistics
Matches: 91, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
78 3 0.03
79 60 0.66
80 28 0.31
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:16908284 original size:40 final size:40
Alignment explanation
Indices: 16908081--16908284 Score: 247
Period size: 40 Copynumber: 5.1 Consensus size: 40
16908071 CGAAATTTAA
** *
16908081 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
16908121 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
16908161 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
16908200 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* *
16908240 CCGGATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
16908280 CCGGA
1 CCGGA
16908285 CGCCATTCGA
Statistics
Matches: 142, Mismatches: 15, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.23
40 95 0.67
41 12 0.08
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:16924332 original size:40 final size:40
Alignment explanation
Indices: 16924295--16924519 Score: 262
Period size: 40 Copynumber: 5.7 Consensus size: 40
16924285 GCTACTCGTT
*
16924295 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
* * *
16924335 CAAATGCTTTCGAGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
16924375 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
16924414 CAAATGCTTTC-GGATCTTAGTCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCGCA
* * * * *
16924454 CAAATGCCTTC-GGATCTTAGTCCGAATATAGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
16924495 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
16924520 CACCATTCGA
Statistics
Matches: 160, Mismatches: 20, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
38 2 0.01
39 32 0.20
40 113 0.71
41 13 0.08
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:16924410 original size:79 final size:79
Alignment explanation
Indices: 16924295--16924519 Score: 278
Period size: 79 Copynumber: 2.8 Consensus size: 79
16924285 GCTACTCGTT
* * *
16924295 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCTTTCGAGACTTAACCCG
1 CAAATGCCTTCGGG-CTTAGCCCGGAATATAGTAACTCGCACAAATGCTTTCG-GACTTAGCCCG
16924359 GATTTAGTAACTCGCA
64 GATTTAGTAACTCGCA
* *
16924375 CCAATGCCTTCGGGCTTAGCCCGGAAT-TAGTAACTCGCACAAATGCTTTCGGATCTTAGTCCGG
1 CAAATGCCTTCGGGCTTAGCCCGGAATATAGTAACTCGCACAAATGCTTTCGGA-CTTAGCCCGG
16924439 ATTTAGTAACTCGCA
65 ATTTAGTAACTCGCA
* * * * *
16924454 CAAATGCCTTCGGATCTTAGTCC-GAATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGG-GCTTAGCCCGGAATATAGTAAC-TCGCACAAATGCTTTC-GGACTTAGCCC
16924517 GGA
63 GGA
16924520 CACCATTCGA
Statistics
Matches: 127, Mismatches: 12, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
78 2 0.02
79 72 0.57
80 42 0.33
81 11 0.09
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.26
Consensus pattern (79 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATATAGTAACTCGCACAAATGCTTTCGGACTTAGCCCGGA
TTTAGTAACTCGCA
Found at i:16932184 original size:79 final size:77
Alignment explanation
Indices: 16932077--16932308 Score: 261
Period size: 79 Copynumber: 2.9 Consensus size: 77
16932067 AGATATAGCT
* *
16932077 ACTCGTTCAAATGCCTTCGGGACATAGCCTGGTTATAGTAACTCACACAAATGCCTTCGGGACTT
1 ACTCGTACAAATGCCTTCGGG-CTTAGCC-GG-TATAGTAACTCACACAAATGCCTTCGGGACTT
*
16932142 AACCCGGATTTAGTA
63 AGCCCGGATTTAGTA
* *
16932157 ACTCGTACCAATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCACACAAATGCCTTC-GGATCTT
1 ACTCGTACAAATGCCTTCGGGCTTAG-CCGGTA-TAGTAACTCACACAAATGCCTTCGGGA-CTT
*
16932221 AGTCCGGATTTAGTA
63 AGCCCGGATTTAGTA
** * * *
16932236 ACTCACACAAATGCCTTCGGATCTTAGTCCGGATATAGTCACTTAGCACAAA-GCCTTCGGGACT
1 ACTCGTACAAATGCCTTCGG-GCTTAG-CCGG-TATAGTAACTCA-CACAAATGCCTTCGGGACT
16932300 TAGCCCGGA
62 TAGCCCGGA
16932309 CACCATTCGA
Statistics
Matches: 130, Mismatches: 15, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
78 4 0.03
79 62 0.48
80 54 0.42
81 10 0.08
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (77 bp):
ACTCGTACAAATGCCTTCGGGCTTAGCCGGTATAGTAACTCACACAAATGCCTTCGGGACTTAGC
CCGGATTTAGTA
Found at i:16932308 original size:40 final size:40
Alignment explanation
Indices: 16932084--16932308 Score: 262
Period size: 40 Copynumber: 5.7 Consensus size: 40
16932074 GCTACTCGTT
* * *
16932084 CAAATGCCTTCGGGACATAGCCTGGTTATAGTAACTCACA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCACA
* * **
16932124 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGTA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCACA
*
16932164 CCAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCACA
* *
16932203 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCACA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAACTCACA
* * *
16932243 CAAATGCCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAACTCA-CA
16932284 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
16932309 CACCATTCGA
Statistics
Matches: 160, Mismatches: 19, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
38 2 0.01
39 30 0.19
40 119 0.74
41 9 0.06
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCACA
Found at i:16941190 original size:12 final size:11
Alignment explanation
Indices: 16941155--16941214 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 11
16941145 TTAAGTATGT
*
16941155 ATAAAAAATAA
1 ATAAATAATAA
* *
16941166 AGAAGTAATAA
1 ATAAATAATAA
16941177 ATAAATAGATAA
1 ATAAATA-ATAA
*
16941189 ATAGATAATAA
1 ATAAATAATAA
16941200 A-ATAATAAT-A
1 ATA-AATAATAA
16941210 ATAAA
1 ATAAA
16941215 GGCGCAAAAG
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
10 5 0.13
11 24 0.62
12 10 0.26
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (11 bp):
ATAAATAATAA
Done.