Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A07
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: 92880876
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2857347 characters in sequence are not A, C, G, or T
File 51 of 290
Found at i:16252768 original size:20 final size:19
Alignment explanation
Indices: 16252743--16252791 Score: 73
Period size: 20 Copynumber: 2.6 Consensus size: 19
16252733 AAAATTTTAT
16252743 TTTATATATTTTAAAATTA
1 TTTATATATTTTAAAATTA
16252762 TTATATATATTTTAAAA-TA
1 TT-TATATATTTTAAAATTA
*
16252781 TTTATGTATTT
1 TTTATATATTT
16252792 ATGTATCTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 8 0.29
19 6 0.21
20 14 0.50
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (19 bp):
TTTATATATTTTAAAATTA
Found at i:16253180 original size:34 final size:34
Alignment explanation
Indices: 16253132--16253196 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 34
16253122 CATGTCTGTG
16253132 TTTCAAGTTATTACCCAATAAAAAGCTCCTAGTA
1 TTTCAAGTTATTACCCAATAAAAAGCTCCTAGTA
*
16253166 TTTCAAGTTGTTACCCAATAAAAAGCTCCTA
1 TTTCAAGTTATTACCCAATAAAAAGCTCCTA
16253197 CTTGAACTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.37, C:0.22, G:0.09, T:0.32
Consensus pattern (34 bp):
TTTCAAGTTATTACCCAATAAAAAGCTCCTAGTA
Found at i:16257012 original size:55 final size:55
Alignment explanation
Indices: 16256928--16257046 Score: 220
Period size: 55 Copynumber: 2.2 Consensus size: 55
16256918 AAGGGTCTTT
16256928 CCTTAAATTCATTGTTGGAAAGAATGGAACACCTCTCCAATATTTACCACAGTGC
1 CCTTAAATTCATTGTTGGAAAGAATGGAACACCTCTCCAATATTTACCACAGTGC
*
16256983 CCTTAAATTCATTGTTGGAAGGAATGGAACACCTCTCCAATATTTACCACAGTGC
1 CCTTAAATTCATTGTTGGAAAGAATGGAACACCTCTCCAATATTTACCACAGTGC
*
16257038 CCTTCAATT
1 CCTTAAATT
16257047 TCCTCTCAGA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
55 62 1.00
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.30
Consensus pattern (55 bp):
CCTTAAATTCATTGTTGGAAAGAATGGAACACCTCTCCAATATTTACCACAGTGC
Found at i:16260756 original size:3 final size:3
Alignment explanation
Indices: 16260748--16260913 Score: 56
Period size: 3 Copynumber: 54.3 Consensus size: 3
16260738 ATTAGTTAAT
* * *
16260748 TTA TTA TTA TTC TTA TTAA TGTA -TA TTA TTA TTC TTA TTAA TGTA TTC
1 TTA TTA TTA TTA TTA TT-A T-TA TTA TTA TTA TTA TTA TT-A T-TA TTA
* * * * * * * *
16260796 TTA TTA TT- GTA CTA TTG CTA TTA TTT TTA TTA TTA TCA CTA TTA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
** **
16260843 TTA -TA TT- TCC TT- TCTA TGC TTA TGTA TTTA TTTA TTA TTA TTA -TA
1 TTA TTA TTA TTA TTA T-TA TTA TTA T-TA -TTA -TTA TTA TTA TTA TTA
* *
16260888 TTT TGTA TTA TTA TTA CTA TTA TTA T
1 TTA T-TA TTA TTA TTA TTA TTA TTA T
16260914 ATCTCTATTT
Statistics
Matches: 118, Mismatches: 31, Indels: 28
0.67 0.18 0.16
Matches are distributed among these distances:
2 9 0.08
3 88 0.75
4 18 0.15
5 3 0.03
ACGTcount: A:0.28, C:0.07, G:0.04, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:16260777 original size:22 final size:23
Alignment explanation
Indices: 16260748--16260803 Score: 96
Period size: 22 Copynumber: 2.5 Consensus size: 23
16260738 ATTAGTTAAT
16260748 TTATTATTATTCTTATTAATGTA
1 TTATTATTATTCTTATTAATGTA
16260771 -TATTATTATTCTTATTAATGTA
1 TTATTATTATTCTTATTAATGTA
*
16260793 TTCTTATTATT
1 TTATTATTATT
16260804 GTACTATTGC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 22 0.71
23 9 0.29
ACGTcount: A:0.29, C:0.05, G:0.04, T:0.62
Consensus pattern (23 bp):
TTATTATTATTCTTATTAATGTA
Found at i:16260796 original size:14 final size:14
Alignment explanation
Indices: 16260755--16260806 Score: 53
Period size: 14 Copynumber: 4.1 Consensus size: 14
16260745 AATTTATTAT
16260755 TATTCTTATTAATG
1 TATTCTTATTAATG
16260769 TA----TATT-AT-
1 TATTCTTATTAATG
16260777 TATTCTTATTAATG
1 TATTCTTATTAATG
*
16260791 TATTCTTATTATTG
1 TATTCTTATTAATG
16260805 TA
1 TA
16260807 CTATTGCTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 12
0.70 0.02 0.27
Matches are distributed among these distances:
8 2 0.06
9 2 0.06
10 4 0.13
12 4 0.13
13 2 0.06
14 17 0.55
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.60
Consensus pattern (14 bp):
TATTCTTATTAATG
Found at i:16261991 original size:26 final size:26
Alignment explanation
Indices: 16261911--16261994 Score: 132
Period size: 26 Copynumber: 3.2 Consensus size: 26
16261901 TGATACAAAT
* *
16261911 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
16261937 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
* *
16261963 TGATAATGGGTTAGGTAAATATTTGA
1 TGATAATGGGTTAGGTAAATGTTTCA
16261989 TGATAA
1 TGATAA
16261995 GAATTTCATG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 54 1.00
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:16268965 original size:26 final size:26
Alignment explanation
Indices: 16268929--16269010 Score: 137
Period size: 26 Copynumber: 3.2 Consensus size: 26
16268919 ATACAAATTT
* *
16268929 ATAATAGGTTAGGTAAATGTTCCATG
1 ATAATGGGTTAGGTAAATGTTTCATG
16268955 ATAATGGGTTAGGTAAATGTTTCATG
1 ATAATGGGTTAGGTAAATGTTTCATG
*
16268981 ATATTGGGTTAGGTAAATGTTTCATG
1 ATAATGGGTTAGGTAAATGTTTCATG
16269007 ATAA
1 ATAA
16269011 GATTTCATGT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 52 1.00
ACGTcount: A:0.33, C:0.05, G:0.24, T:0.38
Consensus pattern (26 bp):
ATAATGGGTTAGGTAAATGTTTCATG
Found at i:16282632 original size:17 final size:17
Alignment explanation
Indices: 16282598--16282652 Score: 78
Period size: 17 Copynumber: 3.4 Consensus size: 17
16282588 TGACATATAT
*
16282598 ATATGA-CTAG-TTTCA
1 ATATGATCTAGCTTTAA
16282613 ATATGATCTAGCTTTAA
1 ATATGATCTAGCTTTAA
*
16282630 ATATGATCTAACTTTAA
1 ATATGATCTAGCTTTAA
16282647 ATATGA
1 ATATGA
16282653 ATGCTTGATG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.17
16 4 0.11
17 26 0.72
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Consensus pattern (17 bp):
ATATGATCTAGCTTTAA
Found at i:16283712 original size:20 final size:20
Alignment explanation
Indices: 16283674--16283712 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
16283664 CTGAATTAGT
* *
16283674 CCCATTTCGTCTGTTTTTGG
1 CCCATTTCGTCTCTCTTTGG
16283694 CCCATTTCGTCTCTCTTTG
1 CCCATTTCGTCTCTCTTTG
16283713 CTTTCCTATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.05, C:0.31, G:0.15, T:0.49
Consensus pattern (20 bp):
CCCATTTCGTCTCTCTTTGG
Found at i:16290327 original size:10 final size:10
Alignment explanation
Indices: 16290312--16290341 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
16290302 AACCTACCCT
16290312 ACCCAATACA
1 ACCCAATACA
16290322 ACCCAAATACA
1 ACCC-AATACA
16290333 ACCCAATAC
1 ACCCAATAC
16290342 CCGATTGCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.50, C:0.40, G:0.00, T:0.10
Consensus pattern (10 bp):
ACCCAATACA
Found at i:16291574 original size:8 final size:7
Alignment explanation
Indices: 16291544--16291602 Score: 52
Period size: 6 Copynumber: 8.6 Consensus size: 7
16291534 TTGCTAAATT
16291544 TATTAT-
1 TATTATA
16291550 TATTAT-
1 TATTATA
16291556 TATTATA
1 TATTATA
16291563 TATTAGTA
1 TATTA-TA
* *
16291571 TATTTTT
1 TATTATA
16291578 TATTATA
1 TATTATA
16291585 TATGTATA
1 TAT-TATA
*
16291593 T-GTATA
1 TATTATA
16291599 TATT
1 TATT
16291603 TTTATACATA
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
6 17 0.40
7 15 0.35
8 11 0.26
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (7 bp):
TATTATA
Found at i:16291737 original size:3 final size:3
Alignment explanation
Indices: 16291686--16291720 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
16291676 ATATTATTGC
16291686 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
16291721 GTGTGTATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:16291837 original size:3 final size:3
Alignment explanation
Indices: 16291822--16291862 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
16291812 TAGATTTCAA
* *
16291822 TAT TAT TAC TAT TAT TAT TAT TAT TAT TAT TAT TAA TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
16291863 GTGTATATTT
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:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:16291878 original size:142 final size:145
Alignment explanation
Indices: 16291543--16291912 Score: 436
Period size: 145 Copynumber: 2.5 Consensus size: 145
16291533 TTTGCTAAAT
*
16291543 TTATTATTATTATTATTATATATTAGTATAT-TTTTTATTATATATGTATATGTATATATTTTTA
1 TTATTATTATTATTATTATATATTAGTGTATATTTTTATTATATATGTATATGTATATATTTTTA
* *
16291607 TACATAGTATTATTTTTTTATTACTTTATTTTAATATTTTTTTATACTACATTTGCTTTTCGTAT
66 TACATAGTATTATTTCTTTATTACTTTATTTT-ATA-----TTATACTA-ATTTGCTTTTAGTAT
*
16291672 TTCAATATTATTGCTATTATTA
124 TTCAATATTATTACTATTATTA
* *
16291694 TTATTATTATTATTATTATTATTATTAGTGTGTATTTTTATTATATATGTGTATGTATATGTATA
1 TTATTATTATTATTATTA-TA-TATTAGTGTATATTTTTATTATATATGTATATGTATA--TAT-
*
16291759 TGTTTATATATAGTATTA-TTCTTTATTACTTTATTTT-TA-T-TA-T-ATTTGCTTTTTAG-AT
61 T-TTTATACATAGTATTATTTCTTTATTACTTTATTTTATATTATACTAATTTGC-TTTTAGTAT
16291817 TTCAATATTATTACTATTATTA
124 TTCAATATTATTACTATTATTA
* * * *
16291839 TTATTATTATTATTATTA-ATATTAGTGTATATTTTTATTATATATGCATATATATGTATTTATA
1 TTATTATTATTATTATTATATATTAGTGTATATTTTTATTATATATGTATATGTATATATTTTTA
*
16291903 TA-TTAGTATT
66 TACATAGTATT
16291913 TTTAATTACC
Statistics
Matches: 197, Mismatches: 14, Indels: 30
0.82 0.06 0.12
Matches are distributed among these distances:
137 7 0.04
138 5 0.03
139 1 0.01
140 3 0.02
142 32 0.16
143 1 0.01
145 47 0.24
146 5 0.03
147 1 0.01
148 2 0.01
149 1 0.01
151 18 0.09
152 2 0.01
153 9 0.05
154 24 0.12
155 2 0.01
156 3 0.02
157 19 0.10
158 15 0.08
ACGTcount: A:0.30, C:0.04, G:0.06, T:0.60
Consensus pattern (145 bp):
TTATTATTATTATTATTATATATTAGTGTATATTTTTATTATATATGTATATGTATATATTTTTA
TACATAGTATTATTTCTTTATTACTTTATTTTATATTATACTAATTTGCTTTTAGTATTTCAATA
TTATTACTATTATTA
Found at i:16291980 original size:142 final size:141
Alignment explanation
Indices: 16291670--16291955 Score: 337
Period size: 145 Copynumber: 2.0 Consensus size: 141
16291660 TGCTTTTCGT
* *
16291670 ATTTCAATATTATTGCTATTATTATTATTATTATTATTATTATTATTATTAGTGTGTATTTTTAT
1 ATTTCAATATTATTACTATTATTATTATTATTATTATTATTA--A-TATTAGTGTATATTTTTAT
* * * **
16291735 TATATATGTGTATGTATATGTATATGTTTATATATAGTATTATTCTTTATTACTTTATTTTTATT
63 TATATA-GTGCATATATATGTATATGTATATATATAGTATTATTAATTATTACTTTATTTTTATT
* ** *
16291800 ATATTTGCTTTTTAG
127 ATATTTACACTTTAC
16291815 ATTTCAATATTATTACTATTATTATTATTATTATTATTATTAATATTAGTGTATATTTTTATTAT
1 ATTTCAATATTATTACTATTATTATTATTATTATTATTATTAATATTAGTGTATATTTTTATTAT
* *
16291880 ATA-TGCATATATATGTAT-T-TATATAT-TAGTATTTTTAATTACCTTATTTTAATATTATTAT
66 ATAGTGCATATATATGTATATGTATATATATAGTATTATTAATTA--TTACTTT-AT-TT-TTAT
16291941 TATATTATACACTTT
126 TATATT-TACACTTT
16291956 CCTTTTTATG
Statistics
Matches: 123, Mismatches: 12, Indels: 14
0.83 0.08 0.09
Matches are distributed among these distances:
137 12 0.10
138 6 0.05
139 7 0.06
140 15 0.12
141 2 0.02
142 34 0.28
143 6 0.05
145 41 0.33
ACGTcount: A:0.31, C:0.04, G:0.06, T:0.59
Consensus pattern (141 bp):
ATTTCAATATTATTACTATTATTATTATTATTATTATTATTAATATTAGTGTATATTTTTATTAT
ATAGTGCATATATATGTATATGTATATATATAGTATTATTAATTATTACTTTATTTTTATTATAT
TTACACTTTAC
Found at i:16292017 original size:3 final size:3
Alignment explanation
Indices: 16292003--16292222 Score: 51
Period size: 3 Copynumber: 72.3 Consensus size: 3
16291993 TTAATTTAAC
* * * * * *
16292003 TTA TTAA TTA TTA TTA TCA TTA TCA CTA TTG TTA TTA CT- TTA CTA
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
16292048 TCGTA ATA TAA TATA TTA TTA ATA TTA CTT- TTA TT- TTCA TTA TTA
1 T--TA TTA TTA T-TA TTA TTA TTA TTA -TTA TTA TTA TT-A TTA TTA
* * * * ** *
16292093 TTA TTA TTA CTA TTA TTCT TTA TTG TCA TGG TTA TT- TTA TTTA TTT
1 TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA -TTA TTA
* * * * * * * *
16292139 TTA -TA GCTA TTA TT- TTT TTA TCA CTA ATA TTA CTA CTG TTA -TA
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
16292182 TTTA TTA TTA TTA CTT- TTA TTA TAA TTA CTA TTA TTA TTA T
1 -TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA T
16292223 AGTTTTTCTT
Statistics
Matches: 152, Mismatches: 46, Indels: 38
0.64 0.19 0.16
Matches are distributed among these distances:
2 15 0.10
3 115 0.76
4 20 0.13
5 2 0.01
ACGTcount: A:0.30, C:0.08, G:0.03, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:16292202 original size:15 final size:15
Alignment explanation
Indices: 16292182--16292222 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
16292172 TACTGTTATA
16292182 TTTATTATTATTACT
1 TTTATTATTATTACT
*
16292197 TTTATTATAATTACT
1 TTTATTATTATTACT
*
16292212 ATTATTATTAT
1 TTTATTATTAT
16292223 AGTTTTTCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTATTATTATTACT
Found at i:16304373 original size:3 final size:3
Alignment explanation
Indices: 16304365--16304420 Score: 73
Period size: 3 Copynumber: 19.3 Consensus size: 3
16304355 TTTGCTAAAT
*
16304365 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TATA TTA GTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA
16304410 TT- TT- TTA TTA T
1 TTA TTA TTA TTA T
16304421 ATATGTATAT
Statistics
Matches: 49, Mismatches: 1, Indels: 6
0.88 0.02 0.11
Matches are distributed among these distances:
2 6 0.12
3 40 0.82
4 3 0.06
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:16304411 original size:8 final size:7
Alignment explanation
Indices: 16304365--16304439 Score: 63
Period size: 6 Copynumber: 11.3 Consensus size: 7
16304355 TTTGCTAAAT
16304365 TTAT-TA
1 TTATATA
16304371 TTAT-TA
1 TTATATA
16304377 TTAT-TA
1 TTATATA
16304383 TTAT-TA
1 TTATATA
16304389 TTAT-TA
1 TTATATA
16304395 TTATATA
1 TTATATA
16304402 TTAGTATA
1 TTA-TATA
* *
16304410 TTTTTTA
1 TTATATA
16304417 TTATATA
1 TTATATA
16304424 TGTATAT-
1 T-TATATA
*
16304431 GTATATA
1 TTATATA
16304438 TT
1 TT
16304440 TTTATACATA
Statistics
Matches: 59, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
6 33 0.56
7 15 0.25
8 11 0.19
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (7 bp):
TTATATA
Found at i:16304559 original size:17 final size:18
Alignment explanation
Indices: 16304539--16304572 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16304529 TTATTATTAG
*
16304539 TGTATAT-TTTTTATATA
1 TGTATATGTATTTATATA
16304556 TGTATATGTATTTATAT
1 TGTATATGTATTTATAT
16304573 TTATACATAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.29, C:0.00, G:0.09, T:0.62
Consensus pattern (18 bp):
TGTATATGTATTTATATA
Found at i:16304681 original size:19 final size:19
Alignment explanation
Indices: 16304654--16304708 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 19
16304644 CTATTATTAT
16304654 TATTATTATTAT-TAGTGTG
1 TATTATTATTATATA-TGTG
*
16304673 TATTTTTATTATATATGTG
1 TATTATTATTATATATGTG
16304692 TATGTA-TATGTATATAT
1 TAT-TATTAT-TATATAT
16304709 TTATATATAC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 21 0.68
20 10 0.32
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (19 bp):
TATTATTATTATATATGTG
Found at i:16304684 original size:3 final size:3
Alignment explanation
Indices: 16304636--16304667 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
16304626 TGTATTTTAA
*
16304636 TAT TAT TAC TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
16304668 GTGTGTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:16304740 original size:14 final size:15
Alignment explanation
Indices: 16304706--16304750 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
16304696 TATATGTATA
*
16304706 TATTTATATATACTAT
1 TATTTTTAT-TACTAT
16304722 TATTTTTATTACT-T
1 TATTTTTATTACTAT
16304736 TATTTTTATTA-TAT
1 TATTTTTATTACTAT
16304750 T
1 T
16304751 TGCTTTTTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 1 0.04
14 14 0.52
15 4 0.15
16 8 0.30
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (15 bp):
TATTTTTATTACTAT
Found at i:16304808 original size:270 final size:263
Alignment explanation
Indices: 16304372--16304875 Score: 635
Period size: 271 Copynumber: 1.9 Consensus size: 263
16304362 AATTTATTAT
*
16304372 TATTATTATTATTATTATTATTATTATATATTAGTATATTTTTTATTATATATGTATATGTATAT
1 TATTATTACTATTATTATTATTATTATATATTAGTATATTTTTTATTATATATGTATATGTATAT
* * *
16304437 ATTTTTATACATAGTATTATTTTTTTATTACTTTATTTTAATGTTTTTATTATACTACATTTGCT
66 ATTTTTATACATACTATTA-TTTTTTATTACTTTATTTTAATATTTTTATTATACTACATAT-CT
* * *
16304502 TTTCGTATTTCAATATTATTATTATTATTATTATTAGTGTATATTTT-TTATATATGTATATGTA
129 ATTCGTATTTCAATATTATTATTATTATTATTATTAGTGTATATTTTATTATATATGCATATATA
* *
16304566 TTTATATTTATACA-TAGTATTTTTTAATTACTTTATTTTTATTATACTACATTTGTTTTTTGTA
194 TATATATTTATACAGTAGTA-TTTTTAATTACCTTATTTTTATTATACTACATTTGTTTTTTGTA
16304630 TTTTAA
258 TTTTAA
* * *
16304636 TATTATTACTATTATTATTATTATTAT-TATTAGTGTGTATTTTTATTATATATGTGTATGTATA
1 TATTATTACTATTATTATTATTATTATATATTAGTATAT-TTTTTATTATATATGTATATGTATA
* * *
16304700 TGTATATATTTATATATACTATTA-TTTTTATTACTTTATTTTTATTATATTTGCTTTTTGA-AT
65 --TAT-T-TTTATACATACTATTATTTTTTATTACTTTA-TTTTA--ATATTT--TTATT-ATAC
* * *
16304763 TTCAATAT-TATTC-TATTATTATTATTATTATTATTATTATTATTAGTGTATATTTTATTATAT
120 TAC-ATATCTATTCGTATT-TCAATATTATTATTATTATTATTATTAGTGTATATTTTATTATAT
* *
16304826 ATGCATATATATATGTATTTATATAGTAGTATTTTTAATTACCTTATTTT
183 ATGCATATATATATATATTTATACAGTAGTATTTTTAATTACCTTATTTT
16304876 AATATTATTA
Statistics
Matches: 205, Mismatches: 20, Indels: 23
0.83 0.08 0.09
Matches are distributed among these distances:
263 9 0.04
264 50 0.24
266 17 0.08
267 6 0.03
268 14 0.07
269 9 0.04
270 40 0.20
271 51 0.25
272 9 0.04
ACGTcount: A:0.30, C:0.04, G:0.06, T:0.61
Consensus pattern (263 bp):
TATTATTACTATTATTATTATTATTATATATTAGTATATTTTTTATTATATATGTATATGTATAT
ATTTTTATACATACTATTATTTTTTATTACTTTATTTTAATATTTTTATTATACTACATATCTAT
TCGTATTTCAATATTATTATTATTATTATTATTAGTGTATATTTTATTATATATGCATATATATA
TATATTTATACAGTAGTATTTTTAATTACCTTATTTTTATTATACTACATTTGTTTTTTGTATTT
TAA
Found at i:16304823 original size:3 final size:3
Alignment explanation
Indices: 16304776--16304807 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
16304766 AATATTATTC
16304776 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
16304808 GTGTATATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:16304833 original size:18 final size:19
Alignment explanation
Indices: 16304776--16304833 Score: 52
Period size: 18 Copynumber: 3.2 Consensus size: 19
16304766 AATATTATTC
*
16304776 TATTATTATTATTA-T-TA
1 TATTATTATTATTAGTGCA
*
16304793 TTATTATTATTATTAGTGTA
1 -TATTATTATTATTAGTGCA
16304813 TATT-TTATTATATA-TGCA
1 TATTATTATTAT-TAGTGCA
16304831 TAT
1 TAT
16304834 ATATATGTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
18 27 0.75
19 7 0.19
20 2 0.06
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (19 bp):
TATTATTATTATTAGTGCA
Found at i:16305101 original size:17 final size:17
Alignment explanation
Indices: 16305079--16305112 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
16305069 ATTATGTTTA
*
16305079 TTTTTATAACTATTATT
1 TTTTTATAACTAATATT
*
16305096 TTTTTATCACTAATATT
1 TTTTTATAACTAATATT
16305113 ACTACTGTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.09, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTTATAACTAATATT
Found at i:16305145 original size:15 final size:15
Alignment explanation
Indices: 16305125--16305163 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
16305115 TACTGTTATA
* *
16305125 TTTATTATTATTTCT
1 TTTATTATAATTACT
16305140 TTTATTATAATTACT
1 TTTATTATAATTACT
*
16305155 ATTATTATA
1 TTTATTATA
16305164 GCTTTTCTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTATTATAATTACT
Found at i:16305152 original size:21 final size:21
Alignment explanation
Indices: 16305082--16305157 Score: 52
Period size: 21 Copynumber: 3.7 Consensus size: 21
16305072 ATGTTTATTT
*
16305082 TTATAACTATTATTT-TTTTA
1 TTATAATTATTATTTCTTTTA
* * *
16305102 TCACTAA-TATTACTACTGTTATA
1 TTA-TAATTATTATTTCT-TT-TA
16305125 TT-T-ATTATTATTTCTTTTA
1 TTATAATTATTATTTCTTTTA
*
16305144 TTATAATTACTATT
1 TTATAATTATTATT
16305158 ATTATAGCTT
Statistics
Matches: 42, Mismatches: 7, Indels: 13
0.68 0.11 0.21
Matches are distributed among these distances:
19 4 0.10
20 12 0.29
21 21 0.50
22 2 0.05
23 3 0.07
ACGTcount: A:0.30, C:0.09, G:0.01, T:0.59
Consensus pattern (21 bp):
TTATAATTATTATTTCTTTTA
Found at i:16313258 original size:29 final size:29
Alignment explanation
Indices: 16313215--16313281 Score: 125
Period size: 29 Copynumber: 2.3 Consensus size: 29
16313205 CTCTAGTTTT
16313215 CACACGGCCTAAGACACGCCCGTGTGGCC
1 CACACGGCCTAAGACACGCCCGTGTGGCC
*
16313244 TACACGGCCTAAGACACGCCCGTGTGGCC
1 CACACGGCCTAAGACACGCCCGTGTGGCC
16313273 CACACGGCC
1 CACACGGCC
16313282 ATACCGCACA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.21, C:0.42, G:0.27, T:0.10
Consensus pattern (29 bp):
CACACGGCCTAAGACACGCCCGTGTGGCC
Found at i:16320905 original size:44 final size:44
Alignment explanation
Indices: 16320842--16320953 Score: 127
Period size: 44 Copynumber: 2.5 Consensus size: 44
16320832 ACGGCGAATC
16320842 TTATCTCTCTGAAA-TTGCAGTGGAGCAGACTGAAGATACCAATA
1 TTATCTCTCT-AAAGTTGCAGTGGAGCAGACTGAAGATACCAATA
* * * * * *
16320886 TTATCTCTCTAAAGTTGCAGCGGAGTAGAGTGAAGCTACTAATC
1 TTATCTCTCTAAAGTTGCAGTGGAGCAGACTGAAGATACCAATA
* * *
16320930 CTATCTCCCTAAAGTTGCAATGGA
1 TTATCTCTCTAAAGTTGCAGTGGA
16320954 TCGGATTAAA
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
43 3 0.05
44 54 0.95
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.29
Consensus pattern (44 bp):
TTATCTCTCTAAAGTTGCAGTGGAGCAGACTGAAGATACCAATA
Found at i:16322626 original size:3 final size:3
Alignment explanation
Indices: 16322618--16322785 Score: 78
Period size: 3 Copynumber: 55.3 Consensus size: 3
16322608 ATTAGTTAAT
* *
16322618 TTA TTA TTA TTAA TGTA -TA TTA TTA TTA TTA TTC TTA TTAA TGTA TTC
1 TTA TTA TTA TT-A T-TA TTA TTA TTA TTA TTA TTA TTA TT-A T-TA TTA
* * * * * * *
16322666 TTA TTA TT- GTA TTA TTG CTA TTA TTT TTA TTA TTA TCA CTA TTA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
** ** *
16322713 TTA -TA TT- TCC TT- TCTA TGC TTA TTTA TTTA TTA TTA -TA TTT TGTA
1 TTA TTA TTA TTA TTA T-TA TTA TTA -TTA -TTA TTA TTA TTA TTA T-TA
* *
16322758 TTA TTA TTA CTA TTA TTA CTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
16322786 ATCTCTATTT
Statistics
Matches: 122, Mismatches: 30, Indels: 26
0.69 0.17 0.15
Matches are distributed among these distances:
2 9 0.07
3 94 0.77
4 17 0.14
5 2 0.02
ACGTcount: A:0.29, C:0.07, G:0.04, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:16322649 original size:28 final size:28
Alignment explanation
Indices: 16322608--16322681 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 28
16322598 TATTAGTAAA
*
16322608 ATTAGTTAATTTATTATTATTAATGTA-T
1 ATTA-TTATTTTATTATTATTAATGTATT
*
16322636 ATTATTATTATTATTCTTATTAATGTATT
1 ATTATTATT-TTATTATTATTAATGTATT
* *
16322665 CTTATTATTGTATTATT
1 ATTATTATTTTATTATT
16322682 GCTATTATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
27 4 0.10
28 26 0.67
29 9 0.23
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.61
Consensus pattern (28 bp):
ATTATTATTTTATTATTATTAATGTATT
Found at i:16322666 original size:14 final size:14
Alignment explanation
Indices: 16322608--16322681 Score: 71
Period size: 14 Copynumber: 5.2 Consensus size: 14
16322598 TATTAGTAAA
*
16322608 ATTAGTTAATTTATT
1 ATTA-TTAATGTATT
16322623 ATTATTAATGTA-T
1 ATTATTAATGTATT
16322636 ATTATTATTAT-TATT
1 ATTATTA--ATGTATT
*
16322651 CTTATTAATGTATT
1 ATTATTAATGTATT
* *
16322665 CTTATTATTGTATT
1 ATTATTAATGTATT
16322679 ATT
1 ATT
16322682 GCTATTATTT
Statistics
Matches: 51, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
13 10 0.20
14 28 0.55
15 13 0.25
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.61
Consensus pattern (14 bp):
ATTATTAATGTATT
Found at i:16325341 original size:34 final size:34
Alignment explanation
Indices: 16325298--16325366 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
16325288 CCCTCACAAG
16325298 TATTATGAATATTCAATTCAGTACAATATATCTC
1 TATTATGAATATTCAATTCAGTACAATATATCTC
16325332 TATTATGAATATTCAATTCAGTACAATATATCTC
1 TATTATGAATATTCAATTCAGTACAATATATCTC
16325366 T
1 T
16325367 TTAGGAGAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.38, C:0.14, G:0.06, T:0.42
Consensus pattern (34 bp):
TATTATGAATATTCAATTCAGTACAATATATCTC
Found at i:16328948 original size:15 final size:15
Alignment explanation
Indices: 16328925--16328954 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
16328915 AAAACAATCT
*
16328925 CTATGTTGAGAACAA
1 CTATATTGAGAACAA
16328940 CTATATTGAGAACAA
1 CTATATTGAGAACAA
16328955 TTCGTGTTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (15 bp):
CTATATTGAGAACAA
Found at i:16329713 original size:14 final size:14
Alignment explanation
Indices: 16329696--16329722 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
16329686 AACATAAAAA
16329696 TTAAAAAAAATCTT
1 TTAAAAAAAATCTT
16329710 TTAAAAAAAATCT
1 TTAAAAAAAATCT
16329723 AAAACTATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.33
Consensus pattern (14 bp):
TTAAAAAAAATCTT
Found at i:16329757 original size:24 final size:26
Alignment explanation
Indices: 16329713--16329763 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
16329703 AAATCTTTTA
*
16329713 AAAAAAATCTAAAACTATGAAAAAAT
1 AAAAAAATATAAAACTATGAAAAAAT
16329739 AAAAAAATATAAAA-T-TGAAAAAAT
1 AAAAAAATATAAAACTATGAAAAAAT
16329763 A
1 A
16329764 TCATTTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 10 0.42
25 1 0.04
26 13 0.54
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.20
Consensus pattern (26 bp):
AAAAAAATATAAAACTATGAAAAAAT
Found at i:16329991 original size:29 final size:32
Alignment explanation
Indices: 16329957--16330021 Score: 82
Period size: 29 Copynumber: 2.1 Consensus size: 32
16329947 ATAAAAATTG
*
16329957 AAAATTTTTATATAATATTTT-G-ATTTT-TT
1 AAAATTTATATATAATATTTTAGAATTTTATT
* *
16329986 AAAATTTATATTTTATATTTTAGAATTTTATT
1 AAAATTTATATATAATATTTTAGAATTTTATT
16330018 AAAA
1 AAAA
16330022 AATAATTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 18 0.60
30 1 0.03
31 5 0.17
32 6 0.20
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (32 bp):
AAAATTTATATATAATATTTTAGAATTTTATT
Found at i:16329996 original size:22 final size:21
Alignment explanation
Indices: 16329971--16330017 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
16329961 TTTTTATATA
*
16329971 ATATTTTGATTTTTTAAAATTT
1 ATATTTT-ATATTTTAAAATTT
*
16329993 ATATTTTATATTTTAGAATTT
1 ATATTTTATATTTTAAAATTT
16330014 -TATT
1 ATATT
16330018 AAAAAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 4 0.17
21 12 0.52
22 7 0.30
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (21 bp):
ATATTTTATATTTTAAAATTT
Found at i:16331107 original size:36 final size:36
Alignment explanation
Indices: 16331039--16331109 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
16331029 TAATTTTACA
* *
16331039 ATTTTTTATGATTTTTATAAAAGGTTACAATTTTTT
1 ATTTTTTACGATTTTTATAAAAGATTACAATTTTTT
*
16331075 ATTTTTTACGATTTTTATAAAA-ATTTCTAATTTTT
1 ATTTTTTACGATTTTTATAAAAGATTAC-AATTTTT
16331110 AATAAATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
35 3 0.10
36 28 0.90
ACGTcount: A:0.31, C:0.04, G:0.06, T:0.59
Consensus pattern (36 bp):
ATTTTTTACGATTTTTATAAAAGATTACAATTTTTT
Found at i:16331124 original size:17 final size:19
Alignment explanation
Indices: 16331085--16331126 Score: 61
Period size: 17 Copynumber: 2.3 Consensus size: 19
16331075 ATTTTTTACG
16331085 ATTTTTATAAAAATTTCTA
1 ATTTTTATAAAAATTTCTA
*
16331104 ATTTTTA-ATAAATTT-TA
1 ATTTTTATAAAAATTTCTA
16331121 ATTTTT
1 ATTTTT
16331127 TATATTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.36
18 7 0.32
19 7 0.32
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
ATTTTTATAAAAATTTCTA
Found at i:16331125 original size:46 final size:44
Alignment explanation
Indices: 16331071--16331205 Score: 137
Period size: 45 Copynumber: 3.0 Consensus size: 44
16331061 GGTTACAATT
*
16331071 TTTTATTTTTTACGATTTTTATAAAAATTTCTAATTTTTAATAAA
1 TTTTATTTTTTA-TATTTTTATAAAAATTTCTAATTTTTAATAAA
* * *
16331116 TTTTAATTTTTTATATTTTTATTAAAATTTAATAATTTTT-GTAAA
1 TTTT-ATTTTTTATATTTTTATAAAAATTT-CTAATTTTTAATAAA
* * ***
16331161 ATTTATTATTTATTATTTTTTATAATTTTTTCTAATTTTTAATAA
1 TTTTATTTTTTA-TA-TTTTTATAAAAATTTCTAATTTTTAATAA
16331206 GAGTAGGGGC
Statistics
Matches: 73, Mismatches: 12, Indels: 9
0.78 0.13 0.10
Matches are distributed among these distances:
44 7 0.10
45 36 0.49
46 30 0.41
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.62
Consensus pattern (44 bp):
TTTTATTTTTTATATTTTTATAAAAATTTCTAATTTTTAATAAA
Found at i:16331126 original size:18 final size:18
Alignment explanation
Indices: 16331085--16331128 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
16331075 ATTTTTTACG
16331085 ATTTTTATAAAAATTTCTA
1 ATTTTT-TAAAAATTTCTA
16331104 A-TTTTTAATAAATTT-TA
1 ATTTTTTAA-AAATTTCTA
16331121 ATTTTTTA
1 ATTTTTTA
16331129 TATTTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 6 0.26
18 16 0.70
19 1 0.04
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (18 bp):
ATTTTTTAAAAATTTCTA
Found at i:16331386 original size:90 final size:90
Alignment explanation
Indices: 16331207--16331430 Score: 235
Period size: 90 Copynumber: 2.5 Consensus size: 90
16331197 TTTTAATAAG
* *
16331207 AGTAGGGGCTTAATTGCTTTTTTGAAAAATTTTGAGAGTCTTTTTTATGCATTTTGAAAGTTCAA
1 AGTAGGGGCTTAATTGCTTTTTTGAAAAAGTTTGAGAGCCTTTTTTATGCATTTTGAAAGTTCAA
* *
16331272 TTGTACCCAATTGAGTGAAAAAAAAA
66 -TGTACCCAATTAAATGAAAAAAAAA
16331298 AGTAGGGGCTTAATTG-TTTTTTGAAAAAGTTTGAG-GACCTTTTTGT-TGCATTTTGAAAGTTT
1 AGTAGGGGCTTAATTGCTTTTTTGAAAAAGTTTGAGAG-CCTTTTT-TATGCATTTTGAAAG-TT
* * * * *
16331360 TAA-GTGCTCAATTAAATG-CAAGAAAA
63 CAATGTACCCAATTAAATGAAAAAAAAA
* * * * *
16331386 AGGAGAGACTTAATTACTTTTTTTAAAAAAGTTTGAGAG-CTTTTT
1 AGTAGGGGCTTAATTGC-TTTTTTGAAAAAGTTTGAGAGCCTTTTT
16331431 ACATCCCTAA
Statistics
Matches: 113, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
88 18 0.16
89 18 0.16
90 55 0.49
91 22 0.19
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (90 bp):
AGTAGGGGCTTAATTGCTTTTTTGAAAAAGTTTGAGAGCCTTTTTTATGCATTTTGAAAGTTCAA
TGTACCCAATTAAATGAAAAAAAAA
Found at i:16334929 original size:23 final size:22
Alignment explanation
Indices: 16334892--16334934 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
16334882 TGTGACTTTT
*
16334892 GTACATACATGCATCTTAGATAA
1 GTACATACATACATC-TAGATAA
*
16334915 GTACATTCATACATCTAGAT
1 GTACATACATACATCTAGAT
16334935 TTTTTAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.33
Consensus pattern (22 bp):
GTACATACATACATCTAGATAA
Found at i:16341897 original size:24 final size:24
Alignment explanation
Indices: 16341867--16341912 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
16341857 TTTAATTTTC
16341867 AAAATTTTAAAAAAATAAAAATAA
1 AAAATTTTAAAAAAATAAAAATAA
*
16341891 AAAATTTTCAAAAAATAAAAAT
1 AAAATTTTAAAAAAATAAAAAT
16341913 TGCATTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (24 bp):
AAAATTTTAAAAAAATAAAAATAA
Found at i:16341949 original size:30 final size:29
Alignment explanation
Indices: 16341909--16342028 Score: 120
Period size: 30 Copynumber: 4.1 Consensus size: 29
16341899 CAAAAAATAA
*
16341909 AAATTGCATTTTTACCCTTAAATTTTTCCT
1 AAATTGCATTTTAACCCTTAAATTTTT-CT
*
16341939 AAATTTCATTTTAACCCTTAAACTTTCTT-T
1 AAATTGCATTTTAACCCTTAAA-TTT-TTCT
* * * * *
16341969 AAATTTCACTTAAACCCCTAAACTTTTCTT
1 AAATTGCATTTTAACCCTTAAATTTTTC-T
16341999 AAATTGCATTTTAACCC-TAAA-TTTTCT
1 AAATTGCATTTTAACCCTTAAATTTTTCT
16342026 AAA
1 AAA
16342029 AATTACATTT
Statistics
Matches: 77, Mismatches: 9, Indels: 11
0.79 0.09 0.11
Matches are distributed among these distances:
27 4 0.05
28 7 0.09
29 6 0.08
30 55 0.71
31 3 0.04
32 2 0.03
ACGTcount: A:0.33, C:0.21, G:0.02, T:0.45
Consensus pattern (29 bp):
AAATTGCATTTTAACCCTTAAATTTTTCT
Found at i:16342271 original size:15 final size:16
Alignment explanation
Indices: 16342253--16342291 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
16342243 AAAAGAGCAA
16342253 AAAAAAAATTT-CAGC
1 AAAAAAAATTTCCAGC
*
16342268 AAAAAAATTTTCCAGC
1 AAAAAAAATTTCCAGC
16342284 AAAAAAAA
1 AAAAAAAA
16342292 AACAACAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.64, C:0.13, G:0.05, T:0.18
Consensus pattern (16 bp):
AAAAAAAATTTCCAGC
Found at i:16342271 original size:16 final size:17
Alignment explanation
Indices: 16342252--16342292 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
16342242 AAAAAGAGCA
16342252 AAAAAAAAATTT-CAGC
1 AAAAAAAAATTTCCAGC
*
16342268 -AAAAAAATTTTCCAGC
1 AAAAAAAAATTTCCAGC
16342284 AAAAAAAAA
1 AAAAAAAAA
16342293 ACAACAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 10 0.48
16 4 0.19
17 7 0.33
ACGTcount: A:0.66, C:0.12, G:0.05, T:0.17
Consensus pattern (17 bp):
AAAAAAAAATTTCCAGC
Found at i:16343087 original size:19 final size:19
Alignment explanation
Indices: 16343065--16343101 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
16343055 AACTATATTA
16343065 TGTACATAT-ATATATTTTT
1 TGTACATATCAT-TATTTTT
16343084 TGTACATATCATTATTTT
1 TGTACATATCATTATTTT
16343102 ATATTATTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.30, C:0.08, G:0.05, T:0.57
Consensus pattern (19 bp):
TGTACATATCATTATTTTT
Found at i:16355284 original size:79 final size:81
Alignment explanation
Indices: 16355136--16355781 Score: 397
Period size: 87 Copynumber: 7.8 Consensus size: 81
16355126 TTCTGTTTTC
* * * * * *
16355136 AAAATTCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTCAATTAC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTAC
16355201 TGTTTGTCAA-A-A-A
66 TGTTTGTCAATATATA
* * *
16355214 AAAAAGTCGACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAGTTT
1 AAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCA-ATT
* *
16355279 A-TGTTTTTCAATTTATATTTTGC
64 ACTGTTTGTCAA--TATA---T-A
* * * *
16355302 AAAAATCAATTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTAC
* * *
16355367 TATTCT-T-AATGACTGTTT
66 TGTT-TGTCAAT-A-T-ATA
** * * *
16355385 TTAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCACGACACGCTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTAC
* *
16355450 TGTTTTTTCCAATCTATATTTTTC
66 TG-TTTGT-CAA--TATA----TA
** * * * * * *
16355474 AAAAATCAACTCATATTGTTAGAGGTGAATTGAGCATCAGGACACGTTGAGGTATTTTCGATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTAC
* * * *
16355539 CGTTTTTCAATTTATGTTTTTC
66 TGTTTGTCAA--TA----TATA
* * *
16355561 AAAAATCAATTCATATTACGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTCC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATT--
* * * * *
16355626 TCTTTTTTTTAA-A-AAA
64 ACTGTTTGTCAATATATA
** * ** * *
16355642 AAAAAGTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGTATTTTCAATTT
1 AAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTA
16355707 CTGTCTT-TC-----A-A
65 CTGT-TTGTCAATATATA
* * *
16355718 AAAAATCAACTCATATTGCGAGAGGTGAGTT-AACCTCAGGTCACACACTGAGGTATTTTCAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG--ACACGCTGAGGTAATTTCAATT
16355782 TTTTGCTTTT
Statistics
Matches: 459, Mismatches: 73, Indels: 74
0.76 0.12 0.12
Matches are distributed among these distances:
74 7 0.02
75 24 0.05
76 27 0.06
77 1 0.00
78 4 0.01
79 57 0.12
80 8 0.02
81 7 0.02
82 50 0.11
83 63 0.14
84 5 0.01
85 1 0.00
86 9 0.02
87 116 0.25
88 12 0.03
89 67 0.15
91 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.34
Consensus pattern (81 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTAC
TGTTTGTCAATATATA
Found at i:16355507 original size:89 final size:87
Alignment explanation
Indices: 16355214--16355782 Score: 547
Period size: 87 Copynumber: 6.7 Consensus size: 87
16355204 TTGTCAAAAA
* * * *
16355214 AAAAAGTCGACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAGTTT
1 AAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTT
* *
16355279 ATGTTTTTCAATTTATATTTTGC
65 CTGTTTTTCAATTTATATTTTTC
* *
16355302 AAAAATCAATTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
* * * *
16355367 TATTCTT-AA-TGACTGTTTTT-
66 TGTTTTTCAATTTA-TATTTTTC
*
16355387 --AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCACGACACGCTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
*
16355450 TGTTTTTTCCAATCTATATTTTTC
66 TG-TTTTT-CAATTTATATTTTTC
** * * * *
16355474 AAAAATCAACTCATATTGTTAGAGGTGAATTGAGCATCAGGACACGTTGAGGTATTTTCGATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
* *
16355539 CGTTTTTCAATTTATGTTTTTC
66 TGTTTTTCAATTTATATTTTTC
* * * * *
16355561 AAAAATCAATTCATATTACGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTCC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
* ****
16355626 TCTTTTT---TTTA-A--AAAA
66 TGTTTTTCAATTTATATTTTTC
** * **
16355642 AAAAAGTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGTATTTTCAATTT
1 AAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTT
*
16355707 CTGTCTTTC-----A-A------
65 CTGTTTTTCAATTTATATTTTTC
* *
16355718 AAAAATCAACTCATATTGCGAGAGGTGAGTT-AACCTCAGGTCACACACTGAGGTATTTTCAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG--ACACGCTGAGGTATTTTCAATT
16355782 T
64 T
16355783 TTTGCTTTTT
Statistics
Matches: 404, Mismatches: 65, Indels: 36
0.80 0.13 0.07
Matches are distributed among these distances:
74 7 0.02
75 24 0.06
76 27 0.07
80 2 0.00
81 5 0.01
82 55 0.14
83 61 0.15
84 8 0.02
85 2 0.00
86 15 0.04
87 131 0.32
88 10 0.02
89 57 0.14
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (87 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
TGTTTTTCAATTTATATTTTTC
Found at i:16355527 original size:172 final size:173
Alignment explanation
Indices: 16355223--16355633 Score: 542
Period size: 172 Copynumber: 2.4 Consensus size: 173
16355213 AAAAAAGTCG
* * *
16355223 ACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAGTTTATG-TTTTT
1 ACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTTTTT
* * * *
16355287 CAATTTATATTTTGCAAAAATCAATTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGA
66 CAATCTATATTTTGCAAAAATCAACTCATATTGCGAGAGGTGAATTGAGCATCAGGACACGCTGA
* *
16355352 GGTATTTTTAATTTCTATTCTT-AA-TGACTGTTTTT-AAATCA
131 GGTATTTTCAATTTCCATTCTTCAATTGA-TGTTTTTAAAATCA
* *
16355393 ACTCATATTGCGAGAGGTGAGTTGAGCCTCACGACACGCTGAGGTATTTTCAATTTCTGTTTTTT
1 ACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTTTTT
* ** *
16355458 CCAATCTATATTTTTCAAAAATCAACTCATATTGTTAGAGGTGAATTGAGCATCAGGACACGTTG
66 -CAATCTATATTTTGCAAAAATCAACTCATATTGCGAGAGGTGAATTGAGCATCAGGACACGCTG
* * * *
16355523 AGGTATTTTCGATTTCCGTTTTTCAATTTATGTTTTTCAAAAATCA
130 AGGTATTTTCAATTTCCATTCTTCAATTGATGTTTTT--AAAATCA
* * * * *
16355569 ATTCATATTACGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTCCTCTTTTTT
1 ACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTTTTT
16355634 TTAAAAAAAA
Statistics
Matches: 208, Mismatches: 26, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
170 54 0.26
171 5 0.02
172 74 0.36
173 9 0.04
174 2 0.01
176 64 0.31
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.37
Consensus pattern (173 bp):
ACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTTTTT
CAATCTATATTTTGCAAAAATCAACTCATATTGCGAGAGGTGAATTGAGCATCAGGACACGCTGA
GGTATTTTCAATTTCCATTCTTCAATTGATGTTTTTAAAATCA
Found at i:16355722 original size:82 final size:75
Alignment explanation
Indices: 16355561--16355827 Score: 252
Period size: 82 Copynumber: 3.4 Consensus size: 75
16355551 TATGTTTTTC
* * * * *
16355561 AAAAATCAATTCATATTACGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTCC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTATTTTCAATT--
* * *
16355626 TCTTTTTTTTAAAAAA
64 TC-TCTCTTT---CAA
** * *
16355642 AAAAAGTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGTATTTTCAATTT
1 AAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTATTTTCAATTT
*
16355707 CTGTCTTTCAA
65 CTCTCTTTCAA
*
16355718 AAAAATCAACTCATATTGCGAGAGGTGAGTT-AACCTCAGGTCACACACTGAGGTATTTTCAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG--ACACACTGAGGTATTTTCAA-T
* *
16355782 TTTTGCTTTTTC-A
63 TTCT-CTCTTTCAA
*
16355795 AAAGATCAACTCATAATT-CGAGAGGTGAGTTGA
1 AAAAATCAACTCAT-ATTGCGAGAGGTGAGTTGA
16355828 ACTTCGGGTC
Statistics
Matches: 158, Mismatches: 21, Indels: 17
0.81 0.11 0.09
Matches are distributed among these distances:
74 7 0.04
75 24 0.15
76 26 0.16
77 31 0.20
78 9 0.06
79 5 0.03
80 2 0.01
81 5 0.03
82 49 0.31
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Consensus pattern (75 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTATTTTCAATTTC
TCTCTTTCAA
Found at i:16355823 original size:77 final size:78
Alignment explanation
Indices: 16355642--16355863 Score: 244
Period size: 78 Copynumber: 2.9 Consensus size: 78
16355632 TTTTAAAAAA
** * * *
16355642 AAAAAG-TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAG--ACACATTGAGGTATTTTCAA
1 AAAAAGATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAGGTCACACACTGAGGTATTTTCAA
*
16355704 -TTTCTGTCTTTC
66 TTTTTTGTCTTTC
*
16355716 AAAAAAATCAACTCATATTGCGAGAGGTGAGTT-AACCTCAGGTCACACACTGAGGTATTTTCAA
1 AAAAAGATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAGGTCACACACTGAGGTATTTTCAA
*
16355780 TTTTTTGCTTTTTC
66 TTTTTTG-TCTTTC
* * * * *
16355794 -AAAAGATCAACTCATAATT-CGAGAGGTGAGTTGAACTTCGGGTCGCATC-CCGAGCTATTTTC
1 AAAAAGATCAACTCAT-ATTGCGAGAGGTGAGTTGAACCTCAGGTCACA-CACTGAGGTATTTTC
16355856 AATTTTTT
64 AATTTTTT
16355864 TTTGTTTTTC
Statistics
Matches: 126, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
74 12 0.10
75 24 0.19
76 19 0.15
77 32 0.25
78 38 0.30
79 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (78 bp):
AAAAAGATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAGGTCACACACTGAGGTATTTTCAA
TTTTTTGTCTTTC
Found at i:16356045 original size:24 final size:24
Alignment explanation
Indices: 16356015--16356060 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
16356005 TTTAATTTTC
16356015 AAAATTTAAAAAAAATAAAAATAA
1 AAAATTTAAAAAAAATAAAAATAA
**
16356039 AAAATTTTCAAAAAATAAAAAT
1 AAAATTTAAAAAAAATAAAAAT
16356061 TGCTTTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (24 bp):
AAAATTTAAAAAAAATAAAAATAA
Found at i:16356104 original size:29 final size:29
Alignment explanation
Indices: 16356066--16356171 Score: 108
Period size: 29 Copynumber: 3.6 Consensus size: 29
16356056 AAAATTGCTT
*
16356066 TTTTACCCCTAAACTTTTCCTAAATTTCA
1 TTTTAACCCTAAACTTTTCCTAAATTTCA
* *
16356095 TTTTAACCCTTAAA-ATTTCTTTAAATTTCA
1 TTTTAACCC-TAAACTTTTC-CTAAATTTCA
* * *
16356125 CTTAAACCCTAAAC-TTTCCTTAAATTGCA
1 TTTTAACCCTAAACTTTTCC-TAAATTTCA
*
16356154 TTTTAACCCTAAATTTTT
1 TTTTAACCCTAAACTTTT
16356172 TAAAAATTAC
Statistics
Matches: 62, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
29 39 0.63
30 23 0.37
ACGTcount: A:0.31, C:0.23, G:0.01, T:0.45
Consensus pattern (29 bp):
TTTTAACCCTAAACTTTTCCTAAATTTCA
Found at i:16356120 original size:30 final size:29
Alignment explanation
Indices: 16356086--16356175 Score: 112
Period size: 29 Copynumber: 3.1 Consensus size: 29
16356076 AAACTTTTCC
16356086 TAAATTTCATTTTAACCCTTAAAATTTCTT
1 TAAATTTCATTTTAACCC-TAAAATTTCTT
* * * *
16356116 TAAATTTCACTTAAACCCTAAACTTTCCT
1 TAAATTTCATTTTAACCCTAAAATTTCTT
*
16356145 TAAATTGCATTTTAACCCT-AAATTT-TT
1 TAAATTTCATTTTAACCCTAAAATTTCTT
16356172 TAAA
1 TAAA
16356176 AATTACATTT
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
27 5 0.10
28 5 0.10
29 25 0.49
30 16 0.31
ACGTcount: A:0.36, C:0.19, G:0.01, T:0.44
Consensus pattern (29 bp):
TAAATTTCATTTTAACCCTAAAATTTCTT
Found at i:16356417 original size:15 final size:16
Alignment explanation
Indices: 16356399--16356436 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
16356389 AAAAGAGCAA
16356399 AAAAAAATTTT-CAGC
1 AAAAAAATTTTCCAGC
*
16356414 AAAACAATTTTCCAGC
1 AAAAAAATTTTCCAGC
16356430 AAAAAAA
1 AAAAAAA
16356437 AACAAAAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.58, C:0.16, G:0.05, T:0.21
Consensus pattern (16 bp):
AAAAAAATTTTCCAGC
Found at i:16357252 original size:17 final size:17
Alignment explanation
Indices: 16357213--16357254 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
16357203 TATTTATAAC
*
16357213 TATATTATGTACATATA
1 TATATTTTGTACATATA
16357230 TATATTTTGTACATATCA
1 TATATTTTGTACATAT-A
16357248 T-TATTTT
1 TATATTTT
16357255 ATATTATTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 21 0.91
18 2 0.09
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (17 bp):
TATATTTTGTACATATA
Found at i:16357386 original size:19 final size:18
Alignment explanation
Indices: 16357327--16357397 Score: 63
Period size: 19 Copynumber: 3.7 Consensus size: 18
16357317 TTTATTGTAG
16357327 ATATTATTATTAT-TACAT
1 ATATTATT-TTATGTACAT
* *
16357345 ATATTTATTATATGCATATAT
1 ATA-TTATTTTATG--TACAT
16357366 ATATGTATTTTATGTACAT
1 ATAT-TATTTTATGTACAT
16357385 ATTATTATTTTAT
1 A-TATTATTTTAT
16357398 ATTATTATTA
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
18 6 0.14
19 18 0.42
20 4 0.09
21 15 0.35
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.56
Consensus pattern (18 bp):
ATATTATTTTATGTACAT
Found at i:16357460 original size:6 final size:6
Alignment explanation
Indices: 16357449--16357475 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
16357439 TAGTACATGA
16357449 TTTATT TTTATT TTTATT TTTATT TTT
1 TTTATT TTTATT TTTATT TTTATT TTT
16357476 TTTGTAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:16362356 original size:38 final size:37
Alignment explanation
Indices: 16362285--16362357 Score: 94
Period size: 37 Copynumber: 1.9 Consensus size: 37
16362275 TAATTATACA
*
16362285 TTTAAAAATTGTTAGAATTTAAATTATAATTATTAAT
1 TTTAAAAATTGTTAGAATTTAAAATATAATTATTAAT
**
16362322 TTTAAAAATTGTTCTAATTTTAAAATA-AAGTTATTA
1 TTTAAAAATTGTTAGAA-TTTAAAATATAA-TTATTA
16362358 GTTGAATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
37 17 0.55
38 14 0.45
ACGTcount: A:0.45, C:0.01, G:0.05, T:0.48
Consensus pattern (37 bp):
TTTAAAAATTGTTAGAATTTAAAATATAATTATTAAT
Found at i:16364028 original size:26 final size:26
Alignment explanation
Indices: 16363997--16364046 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
16363987 AAACATAATT
16363997 TCAAATGAGAGACTTTTGAGTTTTCA
1 TCAAATGAGAGACTTTTGAGTTTTCA
* *
16364023 TCAAATGAGGGATTTTTGAGTTTT
1 TCAAATGAGAGACTTTTGAGTTTT
16364047 AGGTGAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.28, C:0.08, G:0.22, T:0.42
Consensus pattern (26 bp):
TCAAATGAGAGACTTTTGAGTTTTCA
Found at i:16365934 original size:25 final size:25
Alignment explanation
Indices: 16365903--16365953 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
16365893 TAAGAGTTTG
16365903 TACTCATCCTCAATTTCATTGTAGT
1 TACTCATCCTCAATTTCATTGTAGT
16365928 TACTCATCCTCAATTTCATTGTAGT
1 TACTCATCCTCAATTTCATTGTAGT
16365953 T
1 T
16365954 TTAGCATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.24, C:0.24, G:0.08, T:0.45
Consensus pattern (25 bp):
TACTCATCCTCAATTTCATTGTAGT
Found at i:16367467 original size:3 final size:3
Alignment explanation
Indices: 16367459--16367486 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
16367449 AACTAATTCC
16367459 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
16367487 TGTAAAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:16368707 original size:14 final size:17
Alignment explanation
Indices: 16368676--16368716 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
16368666 TACCTAAAGG
16368676 TTATTTTATCTTCTTTA
1 TTATTTTATCTTCTTTA
*
16368693 TTATTTTACTCTTATTT-
1 TTATTTTA-TCTTCTTTA
16368710 TTATTTT
1 TTATTTT
16368717 TATTTTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.73
Consensus pattern (17 bp):
TTATTTTATCTTCTTTA
Found at i:16369418 original size:3 final size:3
Alignment explanation
Indices: 16369410--16369440 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
16369400 TGTATTTCAA
*
16369410 TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
16369441 GTACATTAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:16369543 original size:3 final size:3
Alignment explanation
Indices: 16369535--16369574 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
16369525 TTTGTATTTC
*
16369535 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATC ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
16369575 ACATTACTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:16378404 original size:73 final size:74
Alignment explanation
Indices: 16378212--16378430 Score: 253
Period size: 77 Copynumber: 2.9 Consensus size: 74
16378202 TTTTTATTTC
* * *
16378212 TGTTCCAAAGATCAACTCATATGGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAAGTATTGTC
1 TGTT-CAAAAATCAACTCATAT-GCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTC
**
16378277 AATTTTTTGGAT
64 AA-TTACTGGAT
* * * *
16378289 TGTTCAAAAAATCAACTCATATTACGAGAGGTGAGTTAAGCCTCGGGGCACGCTGTGGTATTTTC
1 TGTTC-AAAAATCAACTCATA-TGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTC
*
16378354 AATTACT-GTT
64 AATTACTGGAT
* * *
16378364 TG-TCAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACATGCTGAGGTAATTTCA
1 TGTTCAAAAATCAACTCATA-TGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCA
16378428 ATT
65 ATT
16378431 TTTGTTTTCT
Statistics
Matches: 122, Mismatches: 18, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
73 55 0.45
74 2 0.02
75 4 0.03
76 4 0.03
77 56 0.46
78 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (74 bp):
TGTTCAAAAATCAACTCATATGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAA
TTACTGGAT
Found at i:16378437 original size:73 final size:73
Alignment explanation
Indices: 16378212--16378437 Score: 258
Period size: 73 Copynumber: 3.0 Consensus size: 73
16378202 TTTTTATTTC
* *
16378212 TGTTCCAAAGATCAACTCATATGGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAAGT-ATTGT
1 TGTT-CAAAAATCAACTCATAT-GCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATT-T
*
16378276 CAATTTTTTGGAT
63 CAA-TTTTT-GTT
* * * * *
16378289 TGTTCAAAAAATCAACTCATATTACGAGAGGTGAGTTAAGCCTCGGGGCACGCTGTGGTATTTTC
1 TGTTC-AAAAATCAACTCATA-TGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTC
**
16378354 AATTACTGTT
64 AATTTTTGTT
* *
16378364 TG-TCAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACATGCTGAGGTAATTTCA
1 TGTTCAAAAATCAACTCATA-TGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCA
16378428 ATTTTTGTT
65 ATTTTTGTT
16378437 T
1 T
16378438 TCTCCAATTT
Statistics
Matches: 126, Mismatches: 20, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
73 60 0.48
74 2 0.02
75 4 0.03
76 4 0.03
77 53 0.42
78 3 0.02
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.31
Consensus pattern (73 bp):
TGTTCAAAAATCAACTCATATGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAA
TTTTTGTT
Found at i:16378517 original size:88 final size:85
Alignment explanation
Indices: 16378349--16378836 Score: 331
Period size: 88 Copynumber: 5.7 Consensus size: 85
16378339 CGCTGTGGTA
* *
16378349 TTTTCAA-TTACTGTTTGTCAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACAT
1 TTTTCAATTTA-TGTTT-TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
*
16378413 GCTGAGGTAATTTCAATTTTTGT
64 GCTGAGGTATTTTCAA-TTTTGT
*
16378436 TTTCTCCAATTTATGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACAC
1 TTT-T-CAATTTATGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
* * *
16378501 GCCGAGATATTGTCAA---T-T
64 GCTGAGGTATTTTCAATTTTGT
* * * * *
16378519 TTTT--A--TATG-TTTCAAAAATCAACTCATATTGCGAGA--G-GTGAGTTGA---G-C-CTCA
1 TTTTCAATTTATGTTTTC--AAA--AA-TCA-ACT-C-ATATTGCGAGAGGTGAGTTGAGCCTCA
16378571 GGACACGCTGAGGTATTTTCAATTTCTGT
58 GGACACGCTGAGGTATTTTCAATTT-TGT
* *
16378600 TTTTCAATTTCTGTCCTTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
1 TTTTCAATTTATGT--TTT-CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
* *
16378665 CGCTGAGGTATTTTCAATTGATGA
63 CGCTGAGGTATTTTCAATT-TTGT
* * * *
16378689 TTTGCAAATTT-TGTTTTCAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT--TGACT
1 TTTTC-AATTTATGTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
*
16378751 CGCGTGCTGCGCTATTTTCAATTTCTG-
63 CGC-TG-AG-G-TATTTTCAATTT-TGT
* * * * *
16378778 TTTT-AATGTATGTTTTTAAAGAGTCAACTCATATTGCAAGAAGTGAGTTGAG-CTCAGGA
1 TTTTCAATTTATGTTTTCAAA-AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGA
16378837 TCACACACCA
Statistics
Matches: 318, Mismatches: 38, Indels: 89
0.71 0.09 0.20
Matches are distributed among these distances:
76 26 0.08
77 4 0.01
78 4 0.01
79 1 0.00
80 3 0.01
81 17 0.05
82 5 0.02
83 9 0.03
84 13 0.04
85 5 0.02
86 11 0.03
87 45 0.14
88 105 0.33
89 49 0.15
90 21 0.07
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.35
Consensus pattern (85 bp):
TTTTCAATTTATGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
TGAGGTATTTTCAATTTTGT
Found at i:16378569 original size:164 final size:161
Alignment explanation
Indices: 16378294--16378683 Score: 552
Period size: 164 Copynumber: 2.4 Consensus size: 161
16378284 TGGATTGTTC
* * * *
16378294 AAAAAATCAACTCATATTACGAGAGGTGAGTTAAGCCTCGGGGCACGCTGTGGTATTTTCAATTA
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATTA
*
16378359 CTGTTTGTCAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACATGCTGAGGTAAT
66 CTGTTTGTCAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAAT
*
16378424 TTCAATTTTTGTTTTCTCCAATTTATGT-TTT-
131 TTCAATTTCTGTTTT-T-CAATTTATGTCTTTA
* * * *
16378455 CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCCGAGATATTGTCAATT-
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATTA
* * *
16378519 TTTTATATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGG
66 CTGT-T-TG--TCAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGG
* *
16378584 TATTTTCAATTTCTGTTTTTCAATTTCTGTCCTTTA
127 TAATTTCAATTTCTGTTTTTCAATTTATGT-CTTTA
*
16378620 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATT
16378684 GATGATTTGC
Statistics
Matches: 202, Mismatches: 20, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
160 2 0.01
161 57 0.28
162 11 0.05
163 1 0.00
164 72 0.36
165 59 0.29
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.33
Consensus pattern (161 bp):
AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATTA
CTGTTTGTCAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAAT
TTCAATTTCTGTTTTTCAATTTATGTCTTTA
Found at i:16378578 original size:76 final size:79
Alignment explanation
Indices: 16378366--16378745 Score: 370
Period size: 88 Copynumber: 4.5 Consensus size: 79
16378356 TTACTGTTTG
* * *
16378366 TCAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACATGCTGAGGTAATTTCAATT
1 TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAA--
*
16378431 TTTGTTTTCTCCAATTTATGTTT
64 --T-TTTT-T--AA-TTATGCTT
* * * *
16378454 TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCCGAGATATTGTCAATT
1 TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATT
16378519 TTTT-A-TATG-TT
66 TTTTAATTATGCTT
16378530 TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATT
1 TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAA--
*
16378595 TCTGTTTTTCAATTTCTGTCCTT
64 --T-TTTTT-AA-TTATG--CTT
*
16378618 TAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAAT
1 T-CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAAT
* *
16378683 TGATGATTTGCAAATTTTGTTT
65 T--T--TTT---AATTATGCTT
*
16378705 TCAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT
1 TC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
16378746 TGACTCGCGT
Statistics
Matches: 253, Mismatches: 18, Indels: 42
0.81 0.06 0.13
Matches are distributed among these distances:
76 61 0.24
77 4 0.02
79 1 0.00
80 1 0.00
81 5 0.02
82 1 0.00
83 5 0.02
84 2 0.01
85 4 0.02
86 1 0.00
87 3 0.01
88 98 0.39
89 65 0.26
90 2 0.01
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (79 bp):
TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATT
TTTTAATTATGCTT
Found at i:16378605 original size:14 final size:14
Alignment explanation
Indices: 16378586--16378613 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
16378576 CGCTGAGGTA
16378586 TTTTCAATTTCTGT
1 TTTTCAATTTCTGT
16378600 TTTTCAATTTCTGT
1 TTTTCAATTTCTGT
16378614 CCTTTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.07, T:0.64
Consensus pattern (14 bp):
TTTTCAATTTCTGT
Found at i:16378683 original size:89 final size:85
Alignment explanation
Indices: 16378532--16378836 Score: 357
Period size: 89 Copynumber: 3.5 Consensus size: 85
16378522 TATATGTTTC
*
16378532 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
16378597 TGTTTTTCAATTTCTGTCCTTTAA
66 TG-TTTTCAATTT-TGT--TTTAA
* **
16378621 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTGA
1 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
*
16378686 TGATTTGCAAATTTTGTTTTCAA
66 TG-TTTTC-AATTTTGTTTT-AA
* * *
16378709 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT--TGACTCGCGTGCTGCGCTATTTTCAA
1 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACACGC-TG-AG-G-TATTTTCAA
* *
16378772 TTTCTGTTTT-AATGTATGTTTTTA
62 TTTCTGTTTTCAAT-TTTGTTTTAA
* * *
16378796 AAGAGTCAACTCATATTGCAAGAAGTGAGTTGAG-CTCAGGA
1 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGA
16378837 TCACACACCA
Statistics
Matches: 190, Mismatches: 17, Indels: 19
0.84 0.08 0.08
Matches are distributed among these distances:
86 8 0.04
87 40 0.21
88 48 0.25
89 76 0.40
90 18 0.09
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (85 bp):
AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
TGTTTTCAATTTTGTTTTAA
Found at i:16379896 original size:13 final size:13
Alignment explanation
Indices: 16379878--16379930 Score: 54
Period size: 13 Copynumber: 4.0 Consensus size: 13
16379868 TATATACATC
16379878 ATAATAAAAAAAT
1 ATAATAAAAAAAT
*
16379891 ATAATAAAAATAT
1 ATAATAAAAAAAT
*
16379904 ATATACAAAACAAAT
1 ATA-ATAAAA-AAAT
*
16379919 ATTA-AAAAAAAT
1 ATAATAAAAAAAT
16379931 TACCTTTTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
12 4 0.12
13 19 0.56
14 6 0.18
15 5 0.15
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.25
Consensus pattern (13 bp):
ATAATAAAAAAAT
Found at i:16380023 original size:11 final size:11
Alignment explanation
Indices: 16380007--16380041 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
16379997 CCCTTCCCCC
16380007 CTCCCTTCTCT
1 CTCCCTTCTCT
16380018 CTCCCTTCTCT
1 CTCCCTTCTCT
16380029 CTTCCC-TCTCT
1 C-TCCCTTCTCT
16380040 CT
1 CT
16380042 TCTTTTTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.04
11 18 0.78
12 4 0.17
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (11 bp):
CTCCCTTCTCT
Found at i:16380489 original size:3 final size:3
Alignment explanation
Indices: 16380481--16380511 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
16380471 TGTATTTCAA
*
16380481 TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
16380512 GTATATTAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:16380847 original size:25 final size:24
Alignment explanation
Indices: 16380791--16380847 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 24
16380781 TTAATAGTCA
16380791 ATAT-TTTTAATATATATTATATG
1 ATATATTTTAATATATATTATATG
* *
16380814 A-ATAATTT-ATATATAATATTATG
1 ATATATTTTAATATATATTA-TATG
16380837 TATATATTTTA
1 -ATATATTTTA
16380848 GTATTATCAG
Statistics
Matches: 26, Mismatches: 3, Indels: 7
0.72 0.08 0.19
Matches are distributed among these distances:
22 11 0.42
23 8 0.31
24 1 0.04
25 6 0.23
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (24 bp):
ATATATTTTAATATATATTATATG
Found at i:16392274 original size:27 final size:29
Alignment explanation
Indices: 16392244--16392303 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
16392234 TTTTTTACCT
* *
16392244 AAAAAAATAT-AAAAA-ATATTAATTATG
1 AAAAAAATATGAAAAATAAATTAATTACG
**
16392271 AAAAAGTTATGAAAAATAAATTAATTACG
1 AAAAAAATATGAAAAATAAATTAATTACG
16392300 AAAA
1 AAAA
16392304 TAGGCATTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 8 0.30
28 5 0.19
29 14 0.52
ACGTcount: A:0.65, C:0.02, G:0.07, T:0.27
Consensus pattern (29 bp):
AAAAAAATATGAAAAATAAATTAATTACG
Found at i:16392707 original size:18 final size:20
Alignment explanation
Indices: 16392674--16392710 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
16392664 TAGAAAAATC
16392674 TTATTATGTATAAATTATAA
1 TTATTATGTATAAATTATAA
16392694 TTATTA-GT-TAAATTATA
1 TTATTATGTATAAATTATA
16392711 GTTTCCAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 2 0.12
20 6 0.35
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.51
Consensus pattern (20 bp):
TTATTATGTATAAATTATAA
Found at i:16395388 original size:3 final size:3
Alignment explanation
Indices: 16395382--16395771 Score: 151
Period size: 3 Copynumber: 127.7 Consensus size: 3
16395372 AACAATGATG
* * * * * *
16395382 ATA ATA ATA ATA ATA ATA AGTA ATA AAA ATG ACA ACA ATG ATA ACA
1 ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA
* *
16395428 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AGCA GCTA A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA -ATA ATA
* * * * * * * *
16395474 AAA AGTA ATA AAA ATA ATA TTA ACA GTA ATG ATA ATG GTA ATA ATAA
1 ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A
* * * * * *
16395521 ATA ATA GTA AAA ATA ATA ATA TTA GTA ATA ATA AT- ATA TTA A-A TTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * *
16395567 GTTA AT- ATA ATA ATA ACGT- ATA AGTA A-A CAAA AAA ATA TATA ATA
1 -ATA ATA ATA ATA ATA A--TA ATA A-TA ATA -ATA ATA ATA -ATA ATA
* * * * *
16395612 ATAA ATA AAA AGA A-A GGTGA CA-A ATA TATA A-A ATA ATA GTA ACA
1 AT-A ATA ATA ATA ATA -AT-A -ATA ATA -ATA ATA ATA ATA ATA ATA
* * *
16395656 GTA ATA A-G ATA A-A TATA AT- ATA ATA A-A TATA ATA ATA AGA ATA
1 ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA
* * * *
16395699 AAA ATA ATA ACA CATTA CTA ATG ATA ATA ATA ATA ATA ATA ATA TATA
1 ATA ATA ATA ATA -A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA
*
16395747 ATA ATA ACA ATA ATA A-A ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
16395772 CTTAAAATAG
Statistics
Matches: 287, Mismatches: 66, Indels: 68
0.68 0.16 0.16
Matches are distributed among these distances:
2 20 0.07
3 231 0.80
4 33 0.11
5 3 0.01
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:16395408 original size:43 final size:42
Alignment explanation
Indices: 16395360--16395449 Score: 153
Period size: 43 Copynumber: 2.1 Consensus size: 42
16395350 AATATAACAA
* *
16395360 AATAAAAATGACAACAATGATGATAATAATAATAATAATAAGT
1 AATAAAAATGACAACAATGATAACAATAATAATAATAATAA-T
16395403 AATAAAAATGACAACAATGATAACAATAATAATAATAATAAT
1 AATAAAAATGACAACAATGATAACAATAATAATAATAATAAT
16395445 AATAA
1 AATAA
16395450 TAATAATAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
42 6 0.13
43 39 0.87
ACGTcount: A:0.63, C:0.06, G:0.07, T:0.24
Consensus pattern (42 bp):
AATAAAAATGACAACAATGATAACAATAATAATAATAATAAT
Found at i:16395780 original size:22 final size:25
Alignment explanation
Indices: 16395722--16395771 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
16395712 ATTACTAATG
*
16395722 ATAATAATAATAATAATAATATATA
1 ATAATAACAATAATAATAATATATA
16395747 ATAATAACAATAATAA-AATA-ATA
1 ATAATAACAATAATAATAATATATA
16395770 AT
1 AT
16395772 CTTAAAATAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 5 0.21
24 4 0.17
25 15 0.62
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (25 bp):
ATAATAACAATAATAATAATATATA
Found at i:16400144 original size:33 final size:33
Alignment explanation
Indices: 16400075--16400172 Score: 108
Period size: 33 Copynumber: 2.9 Consensus size: 33
16400065 CTATACCCAT
* * *
16400075 CTATGCCGAATGCATAGATACATACACTTATTTTCAC
1 CTATGCCGAATGCAT--ACACATA-A-ATATATTCAC
16400112 CTATGCCGAATGCATACACATAAATATATTCAC
1 CTATGCCGAATGCATACACATAAATATATTCAC
* *
16400145 CTATGCCGAATGCA-ACATATATATATAT
1 CTATGCCGAATGCATACACATAAATATAT
16400173 ATATACATAT
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
32 12 0.21
33 22 0.39
34 1 0.02
35 6 0.11
37 15 0.27
ACGTcount: A:0.37, C:0.22, G:0.10, T:0.31
Consensus pattern (33 bp):
CTATGCCGAATGCATACACATAAATATATTCAC
Found at i:16400436 original size:41 final size:41
Alignment explanation
Indices: 16400391--16400546 Score: 226
Period size: 41 Copynumber: 3.8 Consensus size: 41
16400381 ACCGGCTCTT
*
16400391 AGCCTGCTAGACTTATAGTCCGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
16400432 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
*
16400473 AGCCTGCTAGACTTATAGTCTGAATAAT-T-TCACCGGCGTTA
1 AGCCTGCTAGACTTATAGTCTG-A-AATGTGTCACCGGCATTA
* * * *
16400514 AGCCTGCTAGACGTAAAGTCTGAATTATGTCAC
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCAC
16400547 TAACGATAAA
Statistics
Matches: 106, Mismatches: 5, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
39 2 0.02
40 2 0.02
41 97 0.92
42 2 0.02
43 3 0.03
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (41 bp):
AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
Found at i:16407785 original size:33 final size:33
Alignment explanation
Indices: 16407716--16407813 Score: 108
Period size: 33 Copynumber: 2.9 Consensus size: 33
16407706 CTATACCCAT
* * *
16407716 CTATGCCGAATGCATAGATACATACACTTATTTTCAC
1 CTATGCCGAATGCAT--ACACATA-A-ATATATTCAC
16407753 CTATGCCGAATGCATACACATAAATATATTCAC
1 CTATGCCGAATGCATACACATAAATATATTCAC
* *
16407786 CTATGCCGAATGCA-ACATATATATATAT
1 CTATGCCGAATGCATACACATAAATATAT
16407814 ATACATATCT
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
32 12 0.21
33 22 0.39
34 1 0.02
35 6 0.11
37 15 0.27
ACGTcount: A:0.37, C:0.22, G:0.10, T:0.31
Consensus pattern (33 bp):
CTATGCCGAATGCATACACATAAATATATTCAC
Found at i:16408075 original size:41 final size:41
Alignment explanation
Indices: 16408030--16408226 Score: 308
Period size: 41 Copynumber: 4.8 Consensus size: 41
16408020 ACCGGCTCTT
*
16408030 AGCCTGCTAGACTTATAGTCCGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
16408071 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
16408112 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
*
16408153 AGCCTGCTAGACTTATAGTCTGAATAAT-T-TCACCGGCGTTA
1 AGCCTGCTAGACTTATAGTCTG-A-AATGTGTCACCGGCATTA
* * * *
16408194 AGCCTGCTAGACGTAAAGTCTGAATTATGTCAC
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCAC
16408227 TAACGATAAA
Statistics
Matches: 147, Mismatches: 5, Indels: 8
0.92 0.03 0.05
Matches are distributed among these distances:
39 2 0.01
40 2 0.01
41 138 0.94
42 2 0.01
43 3 0.02
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.29
Consensus pattern (41 bp):
AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
Found at i:16412487 original size:16 final size:15
Alignment explanation
Indices: 16412452--16412487 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
16412442 AAATAAGAGG
16412452 GGAAAAAAATAAAAA
1 GGAAAAAAATAAAAA
*
16412467 TGAAAAAAATAAACAA
1 GGAAAAAAATAAA-AA
16412483 GGAAA
1 GGAAA
16412488 TACCCTTTCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.75, C:0.03, G:0.14, T:0.08
Consensus pattern (15 bp):
GGAAAAAAATAAAAA
Found at i:16414953 original size:50 final size:50
Alignment explanation
Indices: 16414877--16415054 Score: 232
Period size: 50 Copynumber: 3.5 Consensus size: 50
16414867 ACCATGGAAA
16414877 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
* * * * * *
16414927 AAAGTGATAAGTAATAACTTCTGCTACACTTATCTGATTAAAGACAAGTG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
16414977 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAATGG-CAAATG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAA-GGACAAATG
* * * * *
16415027 ACAACTGAAAATTGGTAGCTTCAGCTAC
1 A-AAGTGATAAGTGATAGCTTCGGCTAC
16415055 CTGATCAGTG
Statistics
Matches: 109, Mismatches: 17, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
50 87 0.80
51 22 0.20
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.28
Consensus pattern (50 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
Found at i:16415074 original size:31 final size:31
Alignment explanation
Indices: 16415032--16415233 Score: 298
Period size: 31 Copynumber: 6.5 Consensus size: 31
16415022 AAATGACAAC
*
16415032 TGAAAATTGGTAGCTTCAGCTACCTGATCAG
1 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
*
16415063 TGAAAAGTGGTAGTTTCAGCTACCTGATCAG
1 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
* *
16415094 TGAAAAGTGGTAGCTTCTGCTACCTAATCAG
1 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
*
16415125 TGAAAAGTGGTAGCTTCGGCTACCTGATCAG
1 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
*
16415156 TGAAAAGTGGTAGC-TCTGGCTACCTGATCAG
1 TGAAAAGTGGTAGCTTC-AGCTACCTGATCAG
* **
16415187 TGAAAAATGGTAGCACCAGCTACCTGATCAG
1 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
*
16415218 TGAATAGTGGTAGCTT
1 TGAAAAGTGGTAGCTT
16415234 TGGCTACAAG
Statistics
Matches: 155, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
30 2 0.01
31 152 0.98
32 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (31 bp):
TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
Found at i:16415334 original size:47 final size:49
Alignment explanation
Indices: 16415265--16415389 Score: 159
Period size: 47 Copynumber: 2.6 Consensus size: 49
16415255 AAGTGATTTT
* *
16415265 TGTATAAGACCATATCTGGGATATGGCATCGGTGTGATATATG-CTAC-
1 TGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGACTACG
* * *
16415312 TGTATAAGACCATATCTGGGATATGACATCAGTGAGATATGTGATTACG
1 TGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGACTACG
* *
16415361 TGTA-AA-ACCATAGCTGGGCTATGGCATCA
1 TGTATAAGACCATATCTGGGATATGGCATCA
16415390 TTATGTAAAG
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
47 59 0.87
48 5 0.07
49 4 0.06
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (49 bp):
TGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGACTACG
Found at i:16423153 original size:13 final size:13
Alignment explanation
Indices: 16423137--16423170 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
16423127 AGGGATACGG
* *
16423137 CCGTGTGATATGC
1 CCGTGTGACACGC
16423150 CCGTGTGACACGC
1 CCGTGTGACACGC
16423163 CCGTGTGA
1 CCGTGTGA
16423171 GGAAGTCCAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.15, C:0.29, G:0.32, T:0.24
Consensus pattern (13 bp):
CCGTGTGACACGC
Found at i:16425023 original size:13 final size:13
Alignment explanation
Indices: 16425005--16425035 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
16424995 TTCCTGAAAC
16425005 TTTCACTCTACTT
1 TTTCACTCTACTT
16425018 TTTCACTCTACTT
1 TTTCACTCTACTT
16425031 TTTCA
1 TTTCA
16425036 GTCACATGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.16, C:0.29, G:0.00, T:0.55
Consensus pattern (13 bp):
TTTCACTCTACTT
Found at i:16432869 original size:24 final size:25
Alignment explanation
Indices: 16432842--16432890 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
16432832 CTTTTTTTAT
*
16432842 TAAATAAAAAAC-TTTAAAATATAA
1 TAAATAAAAAACATTTAAAACATAA
* *
16432866 TAAATCAAATACATTTAAAACATAA
1 TAAATAAAAAACATTTAAAACATAA
16432891 AAACAAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (25 bp):
TAAATAAAAAACATTTAAAACATAA
Found at i:16432883 original size:25 final size:23
Alignment explanation
Indices: 16432854--16432899 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
16432844 AATAAAAAAC
*
16432854 TTTAAAATATAATAAATCAAATACA
1 TTTAAAACATAA-AAA-CAAATACA
16432879 TTTAAAACATAAAAACAAATA
1 TTTAAAACATAAAAACAAATA
16432900 TTAAAACAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 3 0.15
25 11 0.55
ACGTcount: A:0.63, C:0.09, G:0.00, T:0.28
Consensus pattern (23 bp):
TTTAAAACATAAAAACAAATACA
Found at i:16439763 original size:42 final size:43
Alignment explanation
Indices: 16439695--16439811 Score: 139
Period size: 42 Copynumber: 2.7 Consensus size: 43
16439685 TCCTAGACGT
* * *
16439695 GGTCTTACATGTAATCAAATATCGATGCCACTGTCCCAAATAA
1 GGTCTTACACGAAATCAAATATCGATGCCAATGTCCCAAATAA
* *
16439738 GGTCTTACACGAAATCAAATA-CGATGCCAATGTCCCAGATAT
1 GGTCTTACACGAAATCAAATATCGATGCCAATGTCCCAAATAA
* *
16439780 GGTCTTACACATAAATCATAA-GTCGATGCCAA
1 GGTCTTACAC-GAAATCA-AATATCGATGCCAA
16439812 CATCCCAGAC
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
42 28 0.44
43 25 0.39
44 11 0.17
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (43 bp):
GGTCTTACACGAAATCAAATATCGATGCCAATGTCCCAAATAA
Found at i:16439818 original size:44 final size:42
Alignment explanation
Indices: 16439694--16439835 Score: 135
Period size: 44 Copynumber: 3.3 Consensus size: 42
16439684 GTCCTAGACG
* * * *
16439694 TGGTCTTACATGTAATCAAATATCGATGCC-ACTGTCCCAAATA
1 TGGTCTTACACGAAATCAAATA-CGATGCCAAC-ATCCCAGATA
* **
16439737 AGGTCTTACACGAAATCAAATACGATGCCAATGTCCCAGATA
1 TGGTCTTACACGAAATCAAATACGATGCCAACATCCCAGATA
* **
16439779 TGGTCTTACACATAAATCATAAGT-CGATGCCAACATCCCAGACG
1 TGGTCTTACAC-GAAATCA-AA-TACGATGCCAACATCCCAGATA
16439823 TGGTCTTACACGA
1 TGGTCTTACACGA
16439836 GAACACATAT
Statistics
Matches: 83, Mismatches: 12, Indels: 8
0.81 0.12 0.08
Matches are distributed among these distances:
42 26 0.31
43 27 0.33
44 29 0.35
45 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (42 bp):
TGGTCTTACACGAAATCAAATACGATGCCAACATCCCAGATA
Found at i:16442335 original size:22 final size:22
Alignment explanation
Indices: 16442310--16442352 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
16442300 TTTTCTTCTC
*
16442310 CTTTCCCCTTTTCTTTATTTTT
1 CTTTCCCATTTTCTTTATTTTT
*
16442332 CTTTCTCATTTTCTTTATTTT
1 CTTTCCCATTTTCTTTATTTT
16442353 ATATTCTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.07, C:0.23, G:0.00, T:0.70
Consensus pattern (22 bp):
CTTTCCCATTTTCTTTATTTTT
Found at i:16442364 original size:3 final size:3
Alignment explanation
Indices: 16442356--16442393 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
16442346 TTATTTTATA
16442356 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
16442394 TTCCTCCTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:16448796 original size:17 final size:18
Alignment explanation
Indices: 16448776--16448809 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
16448766 CAATTCATAA
*
16448776 ATTATTCATAC-ATAAAC
1 ATTAATCATACAATAAAC
16448793 ATTAATCATACAATAAA
1 ATTAATCATACAATAAA
16448810 TCAATTCATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.32
Consensus pattern (18 bp):
ATTAATCATACAATAAAC
Found at i:16454440 original size:21 final size:19
Alignment explanation
Indices: 16454406--16454467 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 19
16454396 TAAGTTATGT
16454406 ATAATAATATAATATGAATAAA
1 ATAATAA-A-AATAT-AATAAA
16454428 AT-ATAAGGAAATATAATATAAA
1 ATAATAA--AAATAT-A-ATAAA
16454450 ATAATAAAAATATAATAA
1 ATAATAAAAATATAATAA
16454468 GTATTTTGCA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
19 4 0.11
20 1 0.03
21 16 0.46
22 10 0.29
23 4 0.11
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (19 bp):
ATAATAAAAATATAATAAA
Found at i:16454519 original size:22 final size:23
Alignment explanation
Indices: 16454491--16454535 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
16454481 AAAAATATGG
* *
16454491 TAAAATAATTACTATAA-AAAAA
1 TAAAATAAATAATATAATAAAAA
16454513 TAAAATAAATAATATAATAAAAA
1 TAAAATAAATAATATAATAAAAA
16454536 AATATATGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (23 bp):
TAAAATAAATAATATAATAAAAA
Found at i:16454539 original size:13 final size:13
Alignment explanation
Indices: 16454504--16454541 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
16454494 AATAATTACT
*
16454504 ATAAAAAAATAAA
1 ATAAAAAAATATA
*
16454517 AT-AAATAATATA
1 ATAAAAAAATATA
16454529 ATAAAAAAATATA
1 ATAAAAAAATATA
16454542 TGTGAAAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
ATAAAAAAATATA
Found at i:16454946 original size:20 final size:21
Alignment explanation
Indices: 16454912--16454951 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
16454902 ATTTGCCATT
*
16454912 TACAAATTTAGTAAATAATAA
1 TACAAATTTAGTAAAAAATAA
*
16454933 TACAATTTTA-TAAAAAATA
1 TACAAATTTAGTAAAAAATA
16454952 TATAAAGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (21 bp):
TACAAATTTAGTAAAAAATAA
Found at i:16454964 original size:12 final size:11
Alignment explanation
Indices: 16454941--16454970 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
16454931 AATACAATTT
16454941 TATAAAAAATA
1 TATAAAAAATA
16454952 TATAAAGAAATA
1 TATAAA-AAATA
16454964 TATAAAA
1 TATAAAA
16454971 TAAAATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (11 bp):
TATAAAAAATA
Found at i:16454976 original size:14 final size:14
Alignment explanation
Indices: 16454946--16454993 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
16454936 AATTTTATAA
16454946 AAAATATAT-AAA-
1 AAAATATATAAAAT
*
16454958 GAAATATATAAAAT
1 AAAATATATAAAAT
*
16454972 AAAATATATATAAT
1 AAAATATATAAAAT
*
16454986 ATAATATA
1 AAAATATA
16454994 ATTTATAGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
12 8 0.27
13 3 0.10
14 19 0.63
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (14 bp):
AAAATATATAAAAT
Found at i:16454982 original size:16 final size:16
Alignment explanation
Indices: 16454961--16455026 Score: 55
Period size: 16 Copynumber: 4.1 Consensus size: 16
16454951 ATATAAAGAA
16454961 ATATATAAAATAAAAT
1 ATATATAAAATAAAAT
* *
16454977 ATATATAATATAATAT
1 ATATATAAAATAAAAT
* *
16454993 A-ATTTATAGATAAAAT
1 ATATATA-AAATAAAAT
16455009 ATATGATAATAA-AAAAT
1 ATAT-ATAA-AATAAAAT
16455026 A
1 A
16455027 ATGGATAATA
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
15 4 0.10
16 23 0.59
17 9 0.23
18 3 0.08
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (16 bp):
ATATATAAAATAAAAT
Found at i:16455026 original size:17 final size:17
Alignment explanation
Indices: 16455004--16455037 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
16454994 ATTTATAGAT
16455004 AAAATATAT-GATAATAA
1 AAAATA-ATGGATAATAA
16455021 AAAATAATGGATAATAA
1 AAAATAATGGATAATAA
16455038 TAGTAATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 14 0.88
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.26
Consensus pattern (17 bp):
AAAATAATGGATAATAA
Found at i:16456993 original size:206 final size:206
Alignment explanation
Indices: 16456639--16457400 Score: 1256
Period size: 206 Copynumber: 3.7 Consensus size: 206
16456629 AAATCTGCTT
* *
16456639 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCAC
1 CTTCGATCTGCTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCAC
* * * * * *
16456704 GCAAAAACCAAATCAACTATGTCTTCGATTTGCTCCTTGTAAACACAAGGATACCAAACCATCTT
66 GTAAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAATCATCTT
*
16456769 GGATCTGCTTCAGTCTAATCATCTAAAGGTTAGATCTGCTATGTGTCTGCCCTCCGTCGAATATG
131 GGATCTGCTTCAGTCTAATCATCTGAAGGTTAGATCTGCTATGTGTCTGCCCTCCGTCGAATATG
*
16456834 GAGACGCAAAA
196 GAGACGCCAAA
* *
16456845 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCAC
1 CTTCGATCTGCTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCAC
*
16456910 GTAAAAGCTAAATCAGCTATGAT-TTCGATTTGTTCCTTGTAAACACAAGGATGCCAAATCATCT
66 GTAAAAGCCAAATCAGCTATG-TCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAATCATCT
16456974 TGGATCTGCTTCAGTCTAATCATCTGAAGGTTAGATCTGCTATGTGTCTGCCCTCCGTCGAATAT
130 TGGATCTGCTTCAGTCTAATCATCTGAAGGTTAGATCTGCTATGTGTCTGCCCTCCGTCGAATAT
16457039 GGAGACGCCAAA
195 GGAGACGCCAAA
* * *
16457051 CTTCGATCTGCTCTCTGACAATACAGAGATGCCAAATTATCTTAGATTTGTTTCATCGTAAGCAC
1 CTTCGATCTGCTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCAC
*
16457116 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAATCATCTT
66 GTAAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAATCATCTT
* *
16457181 GGATCTGCTTCAGTCTAATCATCTGAAGGTTAGATCTGTTATGTGTCTGCCCTCCATCGAATATG
131 GGATCTGCTTCAGTCTAATCATCTGAAGGTTAGATCTGCTATGTGTCTGCCCTCCGTCGAATATG
*
16457246 GAGAAGCCAAA
196 GAGACGCCAAA
* *
16457257 CTTCGATCTGCTCTCTGACAATACAGAGATGCCAAATCGTCTTAGATTTGCTTCATCGTAAGCAC
1 CTTCGATCTGCTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCAC
* * * * *
16457322 ATGAAAGCTAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCAGAAGGATGCCAAATCATCTT
66 GTAAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAATCATCTT
16457387 GGATCTTGCTTCAG
131 GGATC-TGCTTCAG
16457401 CCAGATCTGC
Statistics
Matches: 527, Mismatches: 26, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
205 1 0.00
206 517 0.98
207 9 0.02
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.31
Consensus pattern (206 bp):
CTTCGATCTGCTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCAC
GTAAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCCAAATCATCTT
GGATCTGCTTCAGTCTAATCATCTGAAGGTTAGATCTGCTATGTGTCTGCCCTCCGTCGAATATG
GAGACGCCAAA
Found at i:16462210 original size:31 final size:31
Alignment explanation
Indices: 16462172--16462235 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
16462162 TGTTATCAGT
16462172 TCCCACTCGACTTCTCCTTCGTTCAAACGCG
1 TCCCACTCGACTTCTCCTTCGTTCAAACGCG
16462203 TCCCACTCGACTTCTCCTTCGTTCAAACGCG
1 TCCCACTCGACTTCTCCTTCGTTCAAACGCG
16462234 TC
1 TC
16462236 TTTCTTCTCG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.16, C:0.42, G:0.12, T:0.30
Consensus pattern (31 bp):
TCCCACTCGACTTCTCCTTCGTTCAAACGCG
Found at i:16465251 original size:24 final size:23
Alignment explanation
Indices: 16465235--16465283 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 23
16465225 TTTGCTCCCT
16465235 CATGTCATTCTGGATTTTGGCCAA
1 CATGTCATTCTGGA-TTTGGCCAA
16465259 CATGTCATTCTGGATTTTGGCCAA
1 CATGTCATTCTGGA-TTTGGCCAA
16465283 C
1 C
16465284 TGCTCTTACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.37
Consensus pattern (23 bp):
CATGTCATTCTGGATTTGGCCAA
Found at i:16469253 original size:5 final size:5
Alignment explanation
Indices: 16469243--16469299 Score: 53
Period size: 5 Copynumber: 11.2 Consensus size: 5
16469233 GTTATGTATA
* * * *
16469243 ATAAT ATAAT ATGAAT AAAAT ATAAGG A-AAT ATAAT ATAAA ATAAT AAAAT
1 ATAAT ATAAT AT-AAT ATAAT ATAA-T ATAAT ATAAT ATAAT ATAAT ATAAT
16469294 ATAAT A
1 ATAAT A
16469300 AGTATTTTGC
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
4 1 0.02
5 35 0.85
6 5 0.12
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (5 bp):
ATAAT
Found at i:16469287 original size:10 final size:10
Alignment explanation
Indices: 16469243--16469300 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
16469233 GTTATGTATA
*
16469243 ATAATATAAT
1 ATAATAAAAT
16469253 ATGAATAAAAT
1 AT-AATAAAAT
**
16469264 ATAAGGAAAT
1 ATAATAAAAT
16469274 ATAATATAAA-
1 ATAATA-AAAT
16469284 ATAATAAAAT
1 ATAATAAAAT
16469294 ATAATAA
1 ATAATAA
16469301 GTATTTTGCA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
9 3 0.08
10 25 0.62
11 12 0.30
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (10 bp):
ATAATAAAAT
Found at i:16469430 original size:18 final size:18
Alignment explanation
Indices: 16469407--16469461 Score: 74
Period size: 18 Copynumber: 2.9 Consensus size: 18
16469397 GAATATTGAA
16469407 TAATAAAAATATAGTATG
1 TAATAAAAATATAGTATG
16469425 TAATAAAAATATAGTATG
1 TAATAAAAATATAGTATG
* *
16469443 AAATATATAATATACGTAT
1 TAATA-AAAATATA-GTAT
16469462 AATAATAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
18 22 0.67
19 7 0.21
20 4 0.12
ACGTcount: A:0.55, C:0.02, G:0.09, T:0.35
Consensus pattern (18 bp):
TAATAAAAATATAGTATG
Found at i:16469820 original size:12 final size:13
Alignment explanation
Indices: 16469788--16469834 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
16469778 AATTTTATAA
16469788 AAAATATATAAA-
1 AAAATATATAAAT
*
16469800 GAAATATATAAAAT
1 AAAATATAT-AAAT
*
16469814 AAAATATATATAT
1 AAAATATATAAAT
*
16469827 ATAATATA
1 AAAATATA
16469835 ATATAATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
12 8 0.28
13 13 0.45
14 8 0.28
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (13 bp):
AAAATATATAAAT
Found at i:16469838 original size:14 final size:13
Alignment explanation
Indices: 16469783--16469867 Score: 54
Period size: 12 Copynumber: 6.7 Consensus size: 13
16469773 AATTAAATTT
*
16469783 TATAAAAAATATA
1 TATAATAAATATA
*
16469796 TA-AAGAAATATA
1 TATAATAAATATA
*
16469808 TAAAATAAA-ATA
1 TATAATAAATATA
*
16469820 TAT-ATATATA-A
1 TATAATAAATATA
* *
16469831 TATAATATAATTTT
1 TATAATA-AATATA
16469845 TAT-ATAAAATATA
1 TATAAT-AAATATA
16469858 TGATAATAAA
1 T-ATAATAAA
16469868 AAATAATGGA
Statistics
Matches: 55, Mismatches: 9, Indels: 15
0.70 0.11 0.19
Matches are distributed among these distances:
11 8 0.15
12 20 0.36
13 16 0.29
14 9 0.16
15 2 0.04
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (13 bp):
TATAATAAATATA
Done.