Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 37 of 171
Found at i:16691535 original size:18 final size:19
Alignment explanation
Indices: 16691512--16691554 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
16691502 AAATATATAA
16691512 TTTAAACAAA-TA-ACATTT
1 TTTAAA-AAATTATACATTT
*
16691530 TTTAAAAAATTATATATTT
1 TTTAAAAAATTATACATTT
16691549 TTTAAA
1 TTTAAA
16691555 TAGTTAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 3 0.14
18 8 0.36
19 11 0.50
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (19 bp):
TTTAAAAAATTATACATTT
Found at i:16699341 original size:9 final size:9
Alignment explanation
Indices: 16699327--16699371 Score: 54
Period size: 9 Copynumber: 5.0 Consensus size: 9
16699317 AATTGATTTT
16699327 TTAATTAAA
1 TTAATTAAA
*
16699336 TTAATTGAA
1 TTAATTAAA
*
16699345 TTAATTGAA
1 TTAATTAAA
**
16699354 TTTTTTAAA
1 TTAATTAAA
16699363 TTAATTAAA
1 TTAATTAAA
16699372 AGAAATTTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (9 bp):
TTAATTAAA
Found at i:16701520 original size:3 final size:3
Alignment explanation
Indices: 16701512--16701547 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
16701502 CATTTAACCC
16701512 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
16701548 AAAACAACTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:16704009 original size:26 final size:26
Alignment explanation
Indices: 16703979--16704057 Score: 63
Period size: 26 Copynumber: 3.0 Consensus size: 26
16703969 TAAATTTGAG
16703979 ATTTAATTCTTATATTTTAATTTCAT
1 ATTTAATTCTTATATTTTAATTTCAT
* * * *
16704005 TTTTAGTTC-TACTATGCTTAAATTTGAT
1 ATTTAATTCTTA-TAT--TTTAATTTCAT
*
16704033 ATTTAATAT-TTATACTTTAATTTCA
1 ATTTAAT-TCTTATATTTTAATTTCA
16704058 AACATAATTT
Statistics
Matches: 39, Mismatches: 9, Indels: 10
0.67 0.16 0.17
Matches are distributed among these distances:
25 2 0.05
26 18 0.46
28 16 0.41
29 3 0.08
ACGTcount: A:0.30, C:0.09, G:0.04, T:0.57
Consensus pattern (26 bp):
ATTTAATTCTTATATTTTAATTTCAT
Found at i:16704037 original size:28 final size:27
Alignment explanation
Indices: 16703962--16704039 Score: 70
Period size: 26 Copynumber: 2.9 Consensus size: 27
16703952 AGCCCTTTTA
*
16703962 ATATGATTAAATTTGAGATTTAATTCTT
1 ATATG-TTAAATTTGATATTTAATTCTT
* * * *
16703990 ATAT-TTTAATTTCATTTTTAGTTC-T
1 ATATGTTAAATTTGATATTTAATTCTT
16704015 ACTATGCTTAAATTTGATATTTAAT
1 A-TATG-TTAAATTTGATATTTAAT
16704040 ATTTATACTT
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
25 2 0.05
26 18 0.47
28 18 0.47
ACGTcount: A:0.32, C:0.06, G:0.08, T:0.54
Consensus pattern (27 bp):
ATATGTTAAATTTGATATTTAATTCTT
Found at i:16706237 original size:16 final size:16
Alignment explanation
Indices: 16706216--16706270 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
16706206 CATTTTTAAT
16706216 AATAATGTTTAACAAA
1 AATAATGTTTAACAAA
* **
16706232 AATAATTATTTTATACAGT
1 AATAA-T-GTTTA-ACAAA
16706251 AATAATGTTTAACAAA
1 AATAATGTTTAACAAA
16706267 AATA
1 AATA
16706271 GTTTTGTTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
16 12 0.40
17 5 0.17
18 5 0.17
19 8 0.27
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.36
Consensus pattern (16 bp):
AATAATGTTTAACAAA
Found at i:16706237 original size:19 final size:19
Alignment explanation
Indices: 16706213--16706270 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
16706203 AACCATTTTT
16706213 AATAATAATGTTTAACAAA
1 AATAATAATGTTTAACAAA
*
16706232 AATAATTAT-TTTATAC---
1 AATAATAATGTTTA-ACAAA
*
16706248 AGTAATAATGTTTAACAAA
1 AATAATAATGTTTAACAAA
16706267 AATA
1 AATA
16706271 GTTTTGTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 10
0.68 0.09 0.23
Matches are distributed among these distances:
16 9 0.30
17 4 0.13
18 4 0.13
19 13 0.43
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.36
Consensus pattern (19 bp):
AATAATAATGTTTAACAAA
Found at i:16707010 original size:23 final size:23
Alignment explanation
Indices: 16706984--16707031 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
16706974 ACAAACAATC
* *
16706984 TAATT-ATATTTTAAAATTAATTT
1 TAATTAATATATT-AAATAAATTT
16707007 TAATTAATATATTAAATAAATTT
1 TAATTAATATATTAAATAAATTT
16707030 TA
1 TA
16707032 TAATTTGAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 16 0.73
24 6 0.27
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TAATTAATATATTAAATAAATTT
Found at i:16720202 original size:35 final size:33
Alignment explanation
Indices: 16720155--16720227 Score: 80
Period size: 34 Copynumber: 2.2 Consensus size: 33
16720145 AATTTATAAA
*
16720155 AAAAAT-AATATTA-AAAAACTTATTAAA-ATTGAT
1 AAAAATCATTATTATAAAAA-TTA-TAAATATT-AT
16720188 ATAAAATCATTATTATAAAAATTATAAATATTAT
1 A-AAAATCATTATTATAAAAATTATAAATATTAT
16720222 AAAAAT
1 AAAAAT
16720228 ATTTAAAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
33 6 0.17
34 12 0.34
35 12 0.34
36 5 0.14
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.36
Consensus pattern (33 bp):
AAAAATCATTATTATAAAAATTATAAATATTAT
Found at i:16720213 original size:9 final size:9
Alignment explanation
Indices: 16720199--16720244 Score: 51
Period size: 9 Copynumber: 5.2 Consensus size: 9
16720189 TAAAATCATT
16720199 ATTATAAAA
1 ATTATAAAA
*
16720208 ATTATAAAT
1 ATTATAAAA
16720217 ATTATAAAA
1 ATTATAAAA
*
16720226 A-TATTTAAA
1 ATTA-TAAAA
16720235 ATTA-AAAA
1 ATTATAAAA
16720243 AT
1 AT
16720245 GTATTACAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
8 7 0.23
9 22 0.71
10 2 0.06
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (9 bp):
ATTATAAAA
Found at i:16720221 original size:18 final size:19
Alignment explanation
Indices: 16720198--16720244 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
16720188 ATAAAATCAT
16720198 TATTATAAAAAT-TATAAA
1 TATTATAAAAATATATAAA
*
16720216 TATTATAAAAATATTTAAA
1 TATTATAAAAATATATAAA
16720235 -ATTA-AAAAAT
1 TATTATAAAAAT
16720245 GTATTACAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 6 0.22
18 16 0.59
19 5 0.19
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TATTATAAAAATATATAAA
Found at i:16720802 original size:9 final size:9
Alignment explanation
Indices: 16720783--16721036 Score: 171
Period size: 9 Copynumber: 27.3 Consensus size: 9
16720773 TAACTTCAAT
16720783 ATTTTTAATA
1 ATTTTT-ATA
*
16720793 ACTTTTATA
1 ATTTTTATA
16720802 ATTTTTTATA
1 A-TTTTTATA
*
16720812 ATTTTTATG
1 ATTTTTATA
16720821 ATTTTTATA
1 ATTTTTATA
* *
16720830 GAATTTAATA
1 -ATTTTTATA
16720840 TATTTTTATA
1 -ATTTTTATA
*
16720850 AATTTTA-A
1 ATTTTTATA
**
16720858 ATGTTTTACG
1 AT-TTTTATA
*
16720868 ACTTTTATA
1 ATTTTTATA
16720877 ATTTTTTATA
1 A-TTTTTATA
*
16720887 ATTTATTAGA
1 ATTT-TTATA
16720897 ATTTATTAT-
1 ATTT-TTATA
16720906 ATTTTTATA
1 ATTTTTATA
* *
16720915 ATATTTATG
1 ATTTTTATA
16720924 ATTTTT-TA
1 ATTTTTATA
16720932 TATATTTTATA
1 -AT-TTTTATA
16720943 ATTTTTATA
1 ATTTTTATA
*
16720952 AGTTTATATCA
1 A-TTTTTAT-A
*
16720963 ATTTTCAT-
1 ATTTTTATA
16720971 A-TTTT-TA
1 ATTTTTATA
**
16720978 ATATTCAATA
1 AT-TTTTATA
16720988 ATTTTTATA
1 ATTTTTATA
*
16720997 ATTTTTATT
1 ATTTTTATA
16721006 ATTTTTAAATA
1 ATTTTT--ATA
*
16721017 ATTTTTATG
1 ATTTTTATA
16721026 ATTTTTA-A
1 ATTTTTATA
16721034 ATT
1 ATT
16721037 ATTTTTATGG
Statistics
Matches: 192, Mismatches: 34, Indels: 38
0.73 0.13 0.14
Matches are distributed among these distances:
6 1 0.01
7 4 0.02
8 11 0.06
9 95 0.49
10 69 0.36
11 12 0.06
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (9 bp):
ATTTTTATA
Found at i:16720942 original size:7 final size:8
Alignment explanation
Indices: 16720785--16721001 Score: 55
Period size: 10 Copynumber: 23.5 Consensus size: 8
16720775 ACTTCAATAT
16720785 TTTTAATAA
1 TTTT-ATAA
16720794 CTTTTATAA
1 -TTTTATAA
16720803 TTTTTTATAA
1 --TTTTATAA
*
16720813 TTTTTATGAT
1 -TTTTAT-AA
16720823 TTTTATAGAA
1 TTTTAT--AA
*
16720833 TTTAATATAT
1 TTT--TATAA
16720843 TTTTATAAA
1 TTTTAT-AA
16720852 TTTTA-AA
1 TTTTATAA
16720859 TGTTT-TACGA
1 T-TTTATA--A
16720869 CTTTTATAA
1 -TTTTATAA
16720878 TTTTTTATAA
1 --TTTTATAA
*
16720888 TTTATTAGAA
1 -TT-TTATAA
*
16720898 TTTATTATAT
1 -TT-TTATAA
16720908 TTTTATAA
1 TTTTATAA
*
16720916 TATTTATGATT
1 T-TTTAT-A-A
16720927 TTTTATATA
1 TTTTATA-A
16720936 TTTTATAA
1 TTTTATAA
16720944 TTTTTATAA
1 -TTTTATAA
16720953 GTTTATATCAA
1 -TTT-TAT-AA
16720964 TTTTCAT-A
1 TTTT-ATAA
16720972 TTTT-TAA
1 TTTTATAA
*
16720979 TATTCAATAA
1 T-TT-TATAA
16720989 TTTTTATAA
1 -TTTTATAA
16720998 TTTT
1 TTTT
16721002 TATTATTTTT
Statistics
Matches: 166, Mismatches: 15, Indels: 54
0.71 0.06 0.23
Matches are distributed among these distances:
6 1 0.01
7 5 0.03
8 25 0.15
9 59 0.36
10 66 0.40
11 7 0.04
12 3 0.02
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (8 bp):
TTTTATAA
Found at i:16720948 original size:65 final size:65
Alignment explanation
Indices: 16720795--16720960 Score: 185
Period size: 65 Copynumber: 2.5 Consensus size: 65
16720785 TTTTAATAAC
* * *
16720795 TTTTATAATTTTTTATAATTTTTATGATTTTTATAGAATTTAATATATTTTTATAAATTTTAAAT
1 TTTTAT-ATATTTTATAATTTTTATAATTTATATAGAATTTAATATATTTTTATAAATTTTAAAT
16720860 G
65 G
* * *
16720861 TTTTACGA-CTTTTATAATTTTTTATAATTTAT-TAGAATTTATTATATTTTTAT-AATATTTAT
1 TTTTA-TATATTTTATAA-TTTTTATAATTTATATAGAATTTAATATATTTTTATAAAT-TTTA-
* *
16720923 GATT
62 AATG
16720927 TTTTATATATTTTATAATTTTTATAAGTTTATAT
1 TTTTATATATTTTATAATTTTTATAA-TTTATAT
16720961 CAATTTTCAT
Statistics
Matches: 84, Mismatches: 9, Indels: 13
0.79 0.08 0.12
Matches are distributed among these distances:
64 3 0.04
65 42 0.50
66 38 0.45
67 1 0.01
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.61
Consensus pattern (65 bp):
TTTTATATATTTTATAATTTTTATAATTTATATAGAATTTAATATATTTTTATAAATTTTAAATG
Found at i:16721019 original size:20 final size:20
Alignment explanation
Indices: 16720994--16721045 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
16720984 AATAATTTTT
*
16720994 ATAATTTTTATTATTTTTAA
1 ATAATTTTTATGATTTTTAA
16721014 ATAATTTTTATGATTTTTAA
1 ATAATTTTTATGATTTTTAA
*
16721034 ATTATTTTTATG
1 ATAATTTTTATG
16721046 GAAAAGATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (20 bp):
ATAATTTTTATGATTTTTAA
Found at i:16721032 original size:29 final size:30
Alignment explanation
Indices: 16720984--16721043 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
16720974 TTTAATATTC
16720984 AATAATTTTTATAATTTTT-ATTATTTTTA
1 AATAATTTTTATAATTTTTAATTATTTTTA
*
16721013 AATAATTTTTATGATTTTTAAATTATTTTTA
1 AATAATTTTTATAATTTTT-AATTATTTTTA
16721044 TGGAAAAGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 18 0.64
31 10 0.36
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (30 bp):
AATAATTTTTATAATTTTTAATTATTTTTA
Found at i:16721195 original size:116 final size:116
Alignment explanation
Indices: 16721074--16721307 Score: 423
Period size: 116 Copynumber: 2.0 Consensus size: 116
16721064 ACCATAAGCT
* *
16721074 ATCACTTATTACTATATGATTATTCTATCAATTTATTTTAATGGTCAACATAGTCAATGACAAAA
1 ATCACTTATTACTATATGATTATTCTACCAATTTATTTTAATGGTCAACATAGTCAATAACAAAA
*
16721139 ATCGTTAATGAATGGGTTTAATTAATTATTTTAATTAACGAAAAAAATTTA
66 ATCGTTAATGAATAGGTTTAATTAATTATTTTAATTAACGAAAAAAATTTA
* *
16721190 ATCACTTATTACTATATGATTATTCTGCCAATTTATTTTAATGGTCAACATGGTCAATAACAAAA
1 ATCACTTATTACTATATGATTATTCTACCAATTTATTTTAATGGTCAACATAGTCAATAACAAAA
16721255 ATCGTTAATGAATAGGTTTAATTAATTATTTTAATTAACGAAAAAAATTTA
66 ATCGTTAATGAATAGGTTTAATTAATTATTTTAATTAACGAAAAAAATTTA
16721306 AT
1 AT
16721308 TGGATACAAA
Statistics
Matches: 113, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
116 113 1.00
ACGTcount: A:0.41, C:0.10, G:0.09, T:0.40
Consensus pattern (116 bp):
ATCACTTATTACTATATGATTATTCTACCAATTTATTTTAATGGTCAACATAGTCAATAACAAAA
ATCGTTAATGAATAGGTTTAATTAATTATTTTAATTAACGAAAAAAATTTA
Found at i:16722052 original size:25 final size:25
Alignment explanation
Indices: 16722024--16722073 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
16722014 AATATGTTTG
*
16722024 AAATTTAATT-TTTATATTTTTTAAA
1 AAATTTAATTCATT-TATTTTTTAAA
*
16722049 AAATTTAGTTCATTTATTTTTTAAA
1 AAATTTAATTCATTTATTTTTTAAA
16722074 TTTAAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 20 0.91
26 2 0.09
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (25 bp):
AAATTTAATTCATTTATTTTTTAAA
Found at i:16731706 original size:14 final size:15
Alignment explanation
Indices: 16731687--16731715 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
16731677 CCCCTTCACG
16731687 CACGTG-CCATTTCA
1 CACGTGACCATTTCA
16731701 CACGTGACCATTTCA
1 CACGTGACCATTTCA
16731716 TCTTGGCATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.24, C:0.34, G:0.14, T:0.28
Consensus pattern (15 bp):
CACGTGACCATTTCA
Found at i:16734216 original size:29 final size:31
Alignment explanation
Indices: 16734184--16734253 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
16734174 AATCAAGATG
16734184 TCATATATAAAA-T-TACACAAAATAAAAAT
1 TCATATATAAAATTATACACAAAATAAAAAT
* * *
16734213 TCATGTATAAAATTATACACTAAATTAAAAT
1 TCATATATAAAATTATACACAAAATAAAAAT
16734244 TCATATATAA
1 TCATATATAA
16734254 TTTTGAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 11 0.31
30 1 0.03
31 23 0.66
ACGTcount: A:0.56, C:0.10, G:0.01, T:0.33
Consensus pattern (31 bp):
TCATATATAAAATTATACACAAAATAAAAAT
Found at i:16748136 original size:18 final size:17
Alignment explanation
Indices: 16748098--16748136 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
16748088 AATGCTTTTT
*
16748098 AAAAATATTTTTGGACCA
1 AAAAATATTTTT-GAACA
*
16748116 AAAAGTATTTTTGAACA
1 AAAAATATTTTTGAACA
16748133 AAAA
1 AAAA
16748137 TTTAATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.51, C:0.08, G:0.10, T:0.31
Consensus pattern (17 bp):
AAAAATATTTTTGAACA
Found at i:16753000 original size:1 final size:1
Alignment explanation
Indices: 16752994--16753019 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
16752984 ACATGTCATG
16752994 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
16753020 ATGGGTAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:16753636 original size:13 final size:13
Alignment explanation
Indices: 16753606--16753635 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
16753596 GGTGATCTCC
16753606 TTTTTCTTTTCTT
1 TTTTTCTTTTCTT
16753619 TTTTTCTTTT-TT
1 TTTTTCTTTTCTT
16753631 TTTTT
1 TTTTT
16753636 TGAAAAAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (13 bp):
TTTTTCTTTTCTT
Found at i:16754050 original size:46 final size:47
Alignment explanation
Indices: 16753983--16754090 Score: 191
Period size: 47 Copynumber: 2.3 Consensus size: 47
16753973 AAATAATTTT
*
16753983 TTAAAAATGGAAAATAT-AAAAAATAATTTAAAAAAACATGTTTATC
1 TTAAAAATGAAAAATATAAAAAAATAATTTAAAAAAACATGTTTATC
*
16754029 TTAAAAATGAAAAATGTAAAAAAATAATTTAAAAAAACATGTTTATC
1 TTAAAAATGAAAAATATAAAAAAATAATTTAAAAAAACATGTTTATC
16754076 TTAAAAATGAAAAAT
1 TTAAAAATGAAAAAT
16754091 TAAGTGACTT
Statistics
Matches: 59, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
46 15 0.25
47 44 0.75
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.30
Consensus pattern (47 bp):
TTAAAAATGAAAAATATAAAAAAATAATTTAAAAAAACATGTTTATC
Found at i:16762444 original size:2 final size:2
Alignment explanation
Indices: 16762437--16762478 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
16762427 ATCTAGACAG
16762437 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16762479 GGATAACCAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16762982 original size:30 final size:30
Alignment explanation
Indices: 16762940--16762998 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
16762930 TGGGGTGGGA
16762940 TGAGAGGGGAGTAAAAGTTTTAGGGGGAAAG
1 TGAGAGGGGAGTAAAAGTTTT-GGGGGAAAG
16762971 TGAGA-GGGAGTAAAAGTTTTGGGGGAAA
1 TGAGAGGGGAGTAAAAGTTTTGGGGGAAA
16762999 ATAAAAAGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 8 0.29
30 15 0.54
31 5 0.18
ACGTcount: A:0.36, C:0.00, G:0.44, T:0.20
Consensus pattern (30 bp):
TGAGAGGGGAGTAAAAGTTTTGGGGGAAAG
Found at i:16764566 original size:16 final size:16
Alignment explanation
Indices: 16764545--16764579 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
16764535 ATGAAAATAC
16764545 TAAAAA-ATTTGAAAAA
1 TAAAAAGATTT-AAAAA
16764561 TAAAAAGATTTAAAAA
1 TAAAAAGATTTAAAAA
16764577 TAA
1 TAA
16764580 TTTTATCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.26
Consensus pattern (16 bp):
TAAAAAGATTTAAAAA
Found at i:16764676 original size:15 final size:15
Alignment explanation
Indices: 16764634--16764676 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 15
16764624 TTTTTTTTTC
16764634 ATTATTTAATTTTATT
1 ATTATTT-ATTTTATT
16764650 ATTATGTT-TTTTATT
1 ATTAT-TTATTTTATT
16764665 ATTATTTATTTT
1 ATTATTTATTTT
16764677 TTGAAACTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 2 0.08
15 16 0.64
16 5 0.20
17 2 0.08
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (15 bp):
ATTATTTATTTTATT
Found at i:16771192 original size:82 final size:82
Alignment explanation
Indices: 16771052--16771209 Score: 228
Period size: 82 Copynumber: 1.9 Consensus size: 82
16771042 ATCGTATAAA
* * * * * *
16771052 TCCGTCAATTCATGGCACCCGGTGCCTAGTAGATAAACTACAATAAGTGAGCCTAGCTCTAATTG
1 TCCGTCAATTCATAGCACCCAGTGCCTAGCAGATAAACCACAATAAGTGAGCCCAGCTCTAATTA
16771117 GATTAACCAACGAAAAT
66 GATTAACCAACGAAAAT
* *
16771134 TCCGTCAACTTC-TAGCACCCAGTGCCTAGCGGATAAACCACAATAAGTGAGCCCAGCTCTAGTT
1 TCCGTCAA-TTCATAGCACCCAGTGCCTAGCAGATAAACCACAATAAGTGAGCCCAGCTCTAATT
16771198 AGATTAACCAAC
65 AGATTAACCAAC
16771210 AGGTTTGCGC
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
82 64 0.96
83 3 0.04
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.23
Consensus pattern (82 bp):
TCCGTCAATTCATAGCACCCAGTGCCTAGCAGATAAACCACAATAAGTGAGCCCAGCTCTAATTA
GATTAACCAACGAAAAT
Found at i:16775916 original size:18 final size:18
Alignment explanation
Indices: 16775876--16775916 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
16775866 TGAGTAATTT
*
16775876 TAAATTTTACAAATTTAA
1 TAAATGTTACAAATTTAA
* *
16775894 GAAATGTTACAAATTTTA
1 TAAATGTTACAAATTTAA
16775912 TAAAT
1 TAAAT
16775917 CATCTTTGCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (18 bp):
TAAATGTTACAAATTTAA
Found at i:16779323 original size:28 final size:28
Alignment explanation
Indices: 16779286--16779357 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 28
16779276 CACTGCTATC
* *
16779286 AACTGACCAGCTAACTGCTAACTGACTCT
1 AACTAACCAGCTAACTGCTAACAGACT-T
*
16779315 AAC-AACCAGCTAACTGTTAACAGACTT
1 AACTAACCAGCTAACTGCTAACAGACTT
*
16779342 AACTAACCAACTAACT
1 AACTAACCAGCTAACT
16779358 ACTAGTTACT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
27 4 0.11
28 31 0.82
29 3 0.08
ACGTcount: A:0.39, C:0.29, G:0.10, T:0.22
Consensus pattern (28 bp):
AACTAACCAGCTAACTGCTAACAGACTT
Found at i:16782769 original size:20 final size:22
Alignment explanation
Indices: 16782740--16782782 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
16782730 AAAAACTTTT
16782740 GGGGAGAAAAAT-AGAATAAGG
1 GGGGAGAAAAATCAGAATAAGG
*
16782761 GGGGA-AAAAATCAGCATAAGG
1 GGGGAGAAAAATCAGAATAAGG
16782782 G
1 G
16782783 TGGTTGATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.49, C:0.05, G:0.37, T:0.09
Consensus pattern (22 bp):
GGGGAGAAAAATCAGAATAAGG
Found at i:16788064 original size:10 final size:9
Alignment explanation
Indices: 16788049--16788073 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
16788039 TATGAATTCA
16788049 TTTTTTTAT
1 TTTTTTTAT
16788058 TTTTTTTAT
1 TTTTTTTAT
16788067 TTTTTTT
1 TTTTTTT
16788074 CATTAAAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:16789008 original size:2 final size:2
Alignment explanation
Indices: 16789001--16789036 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
16788991 AATAATAATA
16789001 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16789037 CAAAGAATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16795684 original size:58 final size:57
Alignment explanation
Indices: 16795618--16795795 Score: 277
Period size: 58 Copynumber: 3.1 Consensus size: 57
16795608 ACTCATCAAC
*
16795618 AAACTAAACCCAAATATTTTTAAATCCACATATAATTTTATTCTTCAAAAACACTCAT
1 AAACTAAACCCAAATATTTTTAAA-CCAAATATAATTTTATTCTTCAAAAACACTCAT
*
16795676 AAACTAAACCCAAATATTTTTAAACTCAAATATAATTTCATTCTTCAAAAACACTCAT
1 AAACTAAACCCAAATATTTTTAAAC-CAAATATAATTTTATTCTTCAAAAACACTCAT
* *
16795734 AAATTAAACCCAAATATTTTTAAACCCAAATATAATTTTATTCCT-AAATAACACTCAT
1 AAACTAAACCCAAATATTTTTAAA-CCAAATATAATTTTATTCTTCAAA-AACACTCAT
16795792 AAAC
1 AAAC
16795796 AACTCCTTTT
Statistics
Matches: 111, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
57 4 0.04
58 106 0.95
59 1 0.01
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (57 bp):
AAACTAAACCCAAATATTTTTAAACCAAATATAATTTTATTCTTCAAAAACACTCAT
Found at i:16796361 original size:5 final size:5
Alignment explanation
Indices: 16796351--16796376 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
16796341 GAATAAATAT
16796351 ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG A
16796377 ATTCTATCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (5 bp):
ATTCG
Found at i:16796686 original size:17 final size:17
Alignment explanation
Indices: 16796666--16796698 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
16796656 ATAAAATTTC
16796666 AAAAAA-TATATTTTTTA
1 AAAAAATTA-ATTTTTTA
16796683 AAAAAATTAATTTTTT
1 AAAAAATTAATTTTTT
16796699 CTAAAGAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
AAAAAATTAATTTTTTA
Found at i:16797433 original size:17 final size:15
Alignment explanation
Indices: 16797391--16797435 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 15
16797381 ATATTATTCT
*
16797391 ATAAAAAATTTAATAA
1 ATAAAAAATAT-ATAA
16797407 ATAAAAAATATATAA
1 ATAAAAAATATATAA
16797422 ATTAAAATAATATA
1 A-TAAAA-AATATA
16797436 ACTATTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 5 0.19
16 15 0.58
17 6 0.23
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
ATAAAAAATATATAA
Found at i:16798653 original size:23 final size:22
Alignment explanation
Indices: 16798623--16798719 Score: 106
Period size: 22 Copynumber: 4.3 Consensus size: 22
16798613 GTTGGGGAAA
*
16798623 CAGTAAGCAAACACAGTGCAAT
1 CAGTAAGCACACACAGTGCAAT
16798645 CCAGTAAGCACACACAGTGCAAT
1 -CAGTAAGCACACACAGTGCAAT
* * *
16798668 CAGTAGGCGCACATAGTGCAAT
1 CAGTAAGCACACACAGTGCAAT
* *
16798690 CAGTAGGCACACGA-AGTGCGAAA
1 CAGTAAGCACAC-ACAGTGC-AAT
16798713 CAGTAAG
1 CAGTAAG
16798720 AGCGCTAGCG
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
22 35 0.54
23 30 0.46
ACGTcount: A:0.39, C:0.24, G:0.24, T:0.13
Consensus pattern (22 bp):
CAGTAAGCACACACAGTGCAAT
Found at i:16798717 original size:45 final size:46
Alignment explanation
Indices: 16798619--16798719 Score: 118
Period size: 45 Copynumber: 2.2 Consensus size: 46
16798609 AAGTGTTGGG
16798619 GAAACAGTAAGCAAACACAGTGCAATCCAGTAAGCACACACAGTGC
1 GAAACAGTAAGCAAACACAGTGCAATCCAGTAAGCACACACAGTGC
* * ** * *
16798665 -AATCAGTAGGCGCACATAGTGCAAT-CAGTAGGCACACGA-AGTGC
1 GAAACAGTAAGCAAACACAGTGCAATCCAGTAAGCACAC-ACAGTGC
16798709 GAAACAGTAAG
1 GAAACAGTAAG
16798720 AGCGCTAGCG
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
44 16 0.36
45 29 0.64
ACGTcount: A:0.41, C:0.23, G:0.24, T:0.13
Consensus pattern (46 bp):
GAAACAGTAAGCAAACACAGTGCAATCCAGTAAGCACACACAGTGC
Found at i:16807796 original size:3 final size:3
Alignment explanation
Indices: 16807788--16807818 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
16807778 AGGTACCCTT
16807788 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
16807819 ATTTCCTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:16817894 original size:18 final size:18
Alignment explanation
Indices: 16817871--16817906 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
16817861 TGCCGATCTA
16817871 TTTATGATGCAACAGCGC
1 TTTATGATGCAACAGCGC
16817889 TTTATGATGCAACAGCGC
1 TTTATGATGCAACAGCGC
16817907 ATGCAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (18 bp):
TTTATGATGCAACAGCGC
Found at i:16820022 original size:21 final size:21
Alignment explanation
Indices: 16819996--16820038 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
16819986 TTAGCTCAAA
16819996 TTACATTTCTTTATTCTTTTG
1 TTACATTTCTTTATTCTTTTG
16820017 TTACATTTCTTTATTCTTTTG
1 TTACATTTCTTTATTCTTTTG
16820038 T
1 T
16820039 AGTTCTACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.14, G:0.05, T:0.67
Consensus pattern (21 bp):
TTACATTTCTTTATTCTTTTG
Found at i:16826599 original size:3 final size:3
Alignment explanation
Indices: 16826591--16826623 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
16826581 GCTCCTAAGC
16826591 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
16826624 ATGATAAGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:16827687 original size:22 final size:23
Alignment explanation
Indices: 16827633--16827688 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 23
16827623 CTTAGGTTAA
16827633 TTATTTTTGTAGTCTTCATACATT
1 TTATTTTT-TAGTCTTCATACATT
* ** *
16827657 TAAAATTTT-GTCTTCATACTTT
1 TTATTTTTTAGTCTTCATACATT
16827679 TTATTTTTTA
1 TTATTTTTTA
16827689 AACCCGTCAG
Statistics
Matches: 24, Mismatches: 7, Indels: 3
0.71 0.21 0.09
Matches are distributed among these distances:
22 18 0.75
23 1 0.04
24 5 0.21
ACGTcount: A:0.23, C:0.11, G:0.05, T:0.61
Consensus pattern (23 bp):
TTATTTTTTAGTCTTCATACATT
Found at i:16827762 original size:18 final size:19
Alignment explanation
Indices: 16827739--16827778 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
16827729 ACATGATAAT
**
16827739 TATTTTTATTTTAAAAA-A
1 TATTTTTAAATTAAAAATA
16827757 TATTTTTAAATTAAAAATA
1 TATTTTTAAATTAAAAATA
16827776 TAT
1 TAT
16827779 ATGTAGCATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TATTTTTAAATTAAAAATA
Found at i:16833497 original size:18 final size:21
Alignment explanation
Indices: 16833458--16833510 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 21
16833448 ATCTTGATTG
16833458 AAAAATAA--ATATTTCACAT
1 AAAAATAATTATATTTCACAT
16833477 AAAGAA-AA-TATATTT-AC-T
1 AAA-AATAATTATATTTCACAT
16833495 AAAAATAATTATATTT
1 AAAAATAATTATATTT
16833511 GAAATAATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 2 0.07
18 6 0.20
19 14 0.47
20 8 0.27
ACGTcount: A:0.57, C:0.06, G:0.02, T:0.36
Consensus pattern (21 bp):
AAAAATAATTATATTTCACAT
Found at i:16835020 original size:13 final size:13
Alignment explanation
Indices: 16835002--16835026 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16834992 AAATATATTT
16835002 ATTAATTAAAAAC
1 ATTAATTAAAAAC
16835015 ATTAATTAAAAA
1 ATTAATTAAAAA
16835027 TAAAAAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
ATTAATTAAAAAC
Found at i:16835144 original size:14 final size:15
Alignment explanation
Indices: 16835125--16835158 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
16835115 GTGAAATATA
16835125 TTTTTCTAAAAACG-
1 TTTTTCTAAAAACGC
*
16835139 TTTTTCTCAAAACGC
1 TTTTTCTAAAAACGC
16835154 TTTTT
1 TTTTT
16835159 TGTCACATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.26, C:0.18, G:0.06, T:0.50
Consensus pattern (15 bp):
TTTTTCTAAAAACGC
Found at i:16835998 original size:15 final size:15
Alignment explanation
Indices: 16835980--16836009 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
16835970 ATAATAAATA
*
16835980 ATAAATAATTATATT
1 ATAAATAATCATATT
16835995 ATAAATAATCATATT
1 ATAAATAATCATATT
16836010 TGTGATAAAT
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:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (15 bp):
ATAAATAATCATATT
Found at i:16837061 original size:17 final size:17
Alignment explanation
Indices: 16837036--16837074 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 17
16837026 GGATCTGTAC
16837036 ATAAATTT-AATTATAT
1 ATAAATTTAAATTATAT
16837052 ATAAAGTTTAGAATTATAT
1 ATAAA-TTTA-AATTATAT
16837071 ATAA
1 ATAA
16837075 TTTTTTTCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 5 0.25
17 3 0.15
19 12 0.60
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (17 bp):
ATAAATTTAAATTATAT
Found at i:16849175 original size:59 final size:58
Alignment explanation
Indices: 16849061--16849206 Score: 161
Period size: 59 Copynumber: 2.5 Consensus size: 58
16849051 ACTGACAGCT
* * * *
16849061 CTTTTTTGTCAGATAAAAAATATAATTTTTTTGTGTTGGCCATTATATTGTCGACACCCC
1 CTTTTTTATCAGATAAAAAATATAA-TTTTTTGTGTTGGCCATTAAATGGCCGACA-CCC
* *
16849121 CTTTTTTATCAGATAAAAAATTTAATTTTTTGTGTTGGCCA-TACAATGGCCGACATCC
1 CTTTTTTATCAGATAAAAAATATAATTTTTTGTGTTGGCCATTA-AATGGCCGACACCC
* * *
16849179 C-TATTTATCTGATAAAAAAATCTAATTT
1 CTTTTTTATCAGAT-AAAAAATATAATTT
16849207 GCATGGTCGA
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
57 10 0.13
58 18 0.24
59 24 0.32
60 23 0.31
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.42
Consensus pattern (58 bp):
CTTTTTTATCAGATAAAAAATATAATTTTTTGTGTTGGCCATTAAATGGCCGACACCC
Found at i:16849299 original size:100 final size:100
Alignment explanation
Indices: 16849110--16849297 Score: 247
Period size: 100 Copynumber: 1.9 Consensus size: 100
16849100 CCATTATATT
*
16849110 GTCGACACCCCCTTTTTTATCAGATAAAAAATTTAATTTTTTGTGTTGGCCATACAATGGCCGAC
1 GTCGACACCCCCTTTTTTATCAGAT--AAAATTCAATTTTTTGTGTTGGCCATACAATGGCCGAC
16849175 ATCCCTATTTATCTGATAAAAAAATCTAATTTGCATG
64 ATCCCTATTTATCTGATAAAAAAATCTAATTTGCATG
* * * * *
16849212 GTCGACACCCCCTTTTTTATTAGAT-AAATTCATTTTTTTTGTGTTGGTCATGCAATGGTCGACA
1 GTCGACACCCCCTTTTTTATCAGATAAAATTCA-ATTTTTTGTGTTGGCCATACAATGGCCGACA
* *
16849276 -CCCTCTTT-TCTCATATAAAAAA
65 TCCCTATTTATCTGATA-AAAAAA
16849298 ATTTCAAAAT
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
98 6 0.08
99 19 0.25
100 27 0.36
102 24 0.32
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (100 bp):
GTCGACACCCCCTTTTTTATCAGATAAAATTCAATTTTTTGTGTTGGCCATACAATGGCCGACAT
CCCTATTTATCTGATAAAAAAATCTAATTTGCATG
Found at i:16849366 original size:60 final size:59
Alignment explanation
Indices: 16849245--16849443 Score: 174
Period size: 61 Copynumber: 3.3 Consensus size: 59
16849235 ATAAATTCAT
* * *
16849245 TTTTTTTGTGTTGGTCATGCAATGGTCGACACCCTCTTTTCTCATATAAAAAAATTTCAAAA
1 TTTTTTGGTGTT-GCCATGCAATGGTCGACACCC-CTTTTTTCA-ATAAAAAAATTTCAAAA
* * *
16849307 -TTTTTGGTTTTGACCATGCCATGGTCAACACACCCTTTTTTCAGATAAAAAAA-TTCAAAA
1 TTTTTTGGTGTTG-CCATGCAATGGTCGACAC-CCCTTTTTTCA-ATAAAAAAATTTCAAAA
* * * *
16849367 TTTTTTTGTGTTGCCATGCTATGGCCGACACCCCCTTTTTGTCAAGT-AAAAAATTT--AAT
1 TTTTTTGGTGTTGCCATGCAATGGTCGACA-CCCCTTTTT-TCAA-TAAAAAAATTTCAAAA
*
16849426 TTTTTTTGTGTTGGCCAT
1 TTTTTTGGTGTT-GCCAT
16849444 ACCATGACCG
Statistics
Matches: 116, Mismatches: 13, Indels: 18
0.79 0.09 0.12
Matches are distributed among these distances:
59 14 0.12
60 42 0.36
61 58 0.50
62 2 0.02
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.41
Consensus pattern (59 bp):
TTTTTTGGTGTTGCCATGCAATGGTCGACACCCCTTTTTTCAATAAAAAAATTTCAAAA
Found at i:16849435 original size:59 final size:60
Alignment explanation
Indices: 16849208--16849517 Score: 217
Period size: 60 Copynumber: 5.2 Consensus size: 60
16849198 ATCTAATTTG
* * * * * *
16849208 CATGGTCGACACCCCCTTTTTT--ATTAGATAAA-TTCATTTTTTTTGTGTTGGTCATGC
1 CATGGCCGACACCCCCTTTTTTCAAGTAAAAAAATTTAATTTTTTTTGTGTTGGCCATGC
* * * * ** * * *
16849265 AATGGTCGACACCCTCTTTTCTCATA-TAAAAAAATTTCAAAATTTTTGGTTTTGACCATGC
1 CATGGCCGACACCCCCTTTTTTCA-AGTAAAAAAATTT-AATTTTTTTTGTGTTGGCCATGC
* * * * *
16849326 CATGGTCAACACACCCTTTTTTC-AGATAAAAAAATTCAAAATTTTTTTGTGTT-GCCATGC
1 CATGGCCGACACCCCCTTTTTTCAAG-TAAAAAAATT-TAATTTTTTTTGTGTTGGCCATGC
* *
16849386 TATGGCCGACACCCCCTTTTTGTCAAGT-AAAAAATTTAATTTTTTTTGTGTTGGCCATAC
1 CATGGCCGACACCCCCTTTTT-TCAAGTAAAAAAATTTAATTTTTTTTGTGTTGGCCATGC
* * * *** *
16849446 CATGACCGAGATCCCCTTTTTATTTGGT-AAAAAA-TT-ATTTTTTTTAGTGTTGGCCATGT
1 CATGGCCGACACCCCCTTTTT-TCAAGTAAAAAAATTTAATTTTTTTT-GTGTTGGCCATGC
*
16849505 AATGGCCGACACC
1 CATGGCCGACACC
16849518 AACTTCCCCT
Statistics
Matches: 198, Mismatches: 43, Indels: 22
0.75 0.16 0.08
Matches are distributed among these distances:
57 19 0.10
58 9 0.05
59 43 0.22
60 66 0.33
61 59 0.30
62 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (60 bp):
CATGGCCGACACCCCCTTTTTTCAAGTAAAAAAATTTAATTTTTTTTGTGTTGGCCATGC
Found at i:16853467 original size:83 final size:85
Alignment explanation
Indices: 16853352--16853935 Score: 826
Period size: 85 Copynumber: 6.9 Consensus size: 85
16853342 ATTTAAAATT
* * * *
16853352 AATTTAACATTATTTAAATAAAAAAATTATTATTATATTA-AATTTATATCAAATATTGTGTTCA
1 AATTTAA-A-TATTTAAATAAAAAAATTATTATTATATTACAATTTTTATCAAATAATATGTTGA
16853416 TTTGACAATACATTATTTA-TCA
64 TTTGACAATACATTATTTACT-A
** * * * * *
16853438 AATTTTCATATTTAAAT-TACAAATTATTATTATATAACAATTTTTATCAAATAATGTATTGATT
1 AATTTAAATATTTAAATAAAAAAATTATTATTATATTACAATTTTTATCAAATAATATGTTGATT
* *
16853502 TAATAATACATTATTTACTA
66 TGACAATACATTATTTACTA
* *
16853522 AATTTAAATATTTAAATAAAAAAGATTATTATTATTATATTACAATTTTTATCAAATAATTTATT
1 AATTTAAATATTTAAAT-AAAAA-A--ATTATTATTATATTACAATTTTTATCAAATAATATGTT
*
16853587 AATTTGACAATACATTATTTACTA
62 GATTTGACAATACATTATTTACTA
16853611 AATTTAAATATTTAAATAAAAAAATTATTATTATATTACAATTTTTATCAAATAATATGTTGATT
1 AATTTAAATATTTAAATAAAAAAATTATTATTATATTACAATTTTTATCAAATAATATGTTGATT
*
16853676 TGACAATACATTGTTTACTA
66 TGACAATACATTATTTACTA
* *
16853696 AATTTAAATATTTAAAT--AAAATTTATTATTATATTACAATTTTTATCAAATAATATATTGATT
1 AATTTAAATATTTAAATAAAAAAATTATTATTATATTACAATTTTTATCAAATAATATGTTGATT
* *
16853759 TGATAATACATTATTTATTA
66 TGACAATACATTATTTACTA
16853779 AATTTAAATATTTAAATAAAAAAGATTATTATTATATTACAATTTTTATCAAATAATATGTTGA-
1 AATTTAAATATTTAAATAAAAAA-ATTATTATTATATTACAATTTTTATCAAATAATATGTTGAT
*
16853843 TTGACAATATATTATTTACT-
65 TTGACAATACATTATTTACTA
*
16853863 AATTTAAATATTTAAAT--AAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATT
1 AATTTAAATATTTAAATAAAAAAATTATTATTATATTACAATTTTTATCAAATAATATGTTGATT
16853926 TGACAATACA
66 TGACAATACA
16853936 AATTTAGCAA
Statistics
Matches: 451, Mismatches: 36, Indels: 26
0.88 0.07 0.05
Matches are distributed among these distances:
81 39 0.09
82 14 0.03
83 95 0.21
84 79 0.18
85 98 0.22
86 45 0.10
87 2 0.00
88 5 0.01
89 74 0.16
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.46
Consensus pattern (85 bp):
AATTTAAATATTTAAATAAAAAAATTATTATTATATTACAATTTTTATCAAATAATATGTTGATT
TGACAATACATTATTTACTA
Found at i:16853724 original size:257 final size:253
Alignment explanation
Indices: 16853351--16853935 Score: 912
Period size: 257 Copynumber: 2.3 Consensus size: 253
16853341 CATTTAAAAT
* * *
16853351 TAATTTAACATTATTTAAATAAAAAAATTATTATTATATTA-AATTTATATCAAATATTGTGTTC
1 TAATTTAA-A-TATTTAAATAAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTG
**
16853415 ATTTGACAATACATTATTTATCAAATTTTCATATTTAAATTACAAATTATTATTATATAACAATT
64 ATTTGACAATACATTATTTATCAAATTTAAATATTTAAATTACAAATTATTATTATATAACAATT
*
16853480 TTTATCAAATAATGTATTGATTTAATAATACATTATTTACTAAATTTAAATATTTAAATAAAAAA
129 TTTATCAAATAATATATTGATTTAATAATACATTATTTACTAAATTTAAATATTTAAATAAAAAA
*
16853545 GATTATTATTATTATATTACAATTTTTATCAAATAATTTATTAATTTGACAATACATTATTTAC
194 G---ATTATTATTATATTACAATTTTTATCAAATAATATATTAA-TTGACAATACATTATTTAC
*
16853609 TAAATTTAAATATTTAAATAAAAAAATTATTATTATATTACAATTTTTATCAAATAATATGTTGA
1 T-AATTTAAATATTTAAATAAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGA
* *
16853674 TTTGACAATACATTGTTTA-CTAAATTTAAATATTTAAA-TA-AAATTTATTATTATATTACAAT
65 TTTGACAATACATTATTTATC-AAATTTAAATATTTAAATTACAAA-TTATTATTATATAACAAT
* *
16853736 TTTTATCAAATAATATATTGATTTGATAATACATTATTTATTAAATTTAAATATTTAAATAAAAA
128 TTTTATCAAATAATATATTGATTTAATAATACATTATTTACTAAATTTAAATATTTAAATAAAAA
* * *
16853801 AGATTATTATTATATTACAATTTTTATCAAATAATATGTTGATTGACAATATATTATTTAC
193 AGATTATTATTATATTACAATTTTTATCAAATAATATATTAATTGACAATACATTATTTAC
16853862 TAATTTAAATATTTAAAT--AAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGAT
1 TAATTTAAATATTTAAATAAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGAT
16853925 TTGACAATACA
66 TTGACAATACA
16853936 AATTTAGCAA
Statistics
Matches: 307, Mismatches: 16, Indels: 16
0.91 0.05 0.05
Matches are distributed among these distances:
250 55 0.18
252 17 0.06
253 19 0.06
254 37 0.12
256 3 0.01
257 114 0.37
258 55 0.18
259 7 0.02
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.46
Consensus pattern (253 bp):
TAATTTAAATATTTAAATAAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGAT
TTGACAATACATTATTTATCAAATTTAAATATTTAAATTACAAATTATTATTATATAACAATTTT
TATCAAATAATATATTGATTTAATAATACATTATTTACTAAATTTAAATATTTAAATAAAAAAGA
TTATTATTATATTACAATTTTTATCAAATAATATATTAATTGACAATACATTATTTAC
Found at i:16853849 original size:168 final size:169
Alignment explanation
Indices: 16853352--16853935 Score: 838
Period size: 168 Copynumber: 3.4 Consensus size: 169
16853342 ATTTAAAATT
* * * *
16853352 AATTTAACATTATTTAAATAAAAAAATTATTATTATATTA-AATTTATATCAAATATTGTGTTCA
1 AATTTAA-A-TATTTAAAT-AAAAAATTATTATTATATTACAATTTTTATCAAATAATGTATTGA
* ** * * *
16853416 TTTGACAATACATTATTTATCAAATTTTCATATTTAAAT-TACAAATTATTATTATATAACAATT
63 TTTGACAATACATTATTTATTAAATTTAAATATTTAAATAAAAAAATTATTATTATATTACAATT
* * * *
16853480 TTTATCAAATAATGTATTGATTTAATAATACATTATTTACTA
128 TTTATCAAATAATATGTTGATTTGACAATACATTATTTACTA
*
16853522 AATTTAAATATTTAAATAAAAAAGATTATTATTATTATATTACAATTTTTATCAAATAATTTATT
1 AATTTAAATATTTAAAT--AAAA-A--ATTATTATTATATTACAATTTTTATCAAATAATGTATT
* *
16853587 AATTTGACAATACATTATTTACTAAATTTAAATATTTAAATAAAAAAATTATTATTATATTACAA
61 GATTTGACAATACATTATTTATTAAATTTAAATATTTAAATAAAAAAATTATTATTATATTACAA
*
16853652 TTTTTATCAAATAATATGTTGATTTGACAATACATTGTTTACTA
126 TTTTTATCAAATAATATGTTGATTTGACAATACATTATTTACTA
* *
16853696 AATTTAAATATTTAAAT-AAAATTTATTATTATATTACAATTTTTATCAAATAATATATTGATTT
1 AATTTAAATATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTATTGATTT
*
16853760 GATAATACATTATTTATTAAATTTAAATATTTAAATAAAAAAGATTATTATTATATTACAATTTT
66 GACAATACATTATTTATTAAATTTAAATATTTAAATAAAAAA-ATTATTATTATATTACAATTTT
*
16853825 TATCAAATAATATGTTGA-TTGACAATATATTATTTACT-
130 TATCAAATAATATGTTGATTTGACAATACATTATTTACTA
*
16853863 AATTTAAATATTTAAAT-AAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTT
1 AATTTAAATATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTATTGATTT
16853927 GACAATACA
66 GACAATACA
16853936 AATTTAGCAA
Statistics
Matches: 379, Mismatches: 28, Indels: 17
0.89 0.07 0.04
Matches are distributed among these distances:
167 69 0.18
168 107 0.28
169 46 0.12
170 9 0.02
171 3 0.01
172 15 0.04
173 54 0.14
174 76 0.20
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.46
Consensus pattern (169 bp):
AATTTAAATATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTATTGATTT
GACAATACATTATTTATTAAATTTAAATATTTAAATAAAAAAATTATTATTATATTACAATTTTT
ATCAAATAATATGTTGATTTGACAATACATTATTTACTA
Found at i:16856375 original size:30 final size:30
Alignment explanation
Indices: 16856341--16856432 Score: 98
Period size: 30 Copynumber: 3.1 Consensus size: 30
16856331 TTGATTTTTT
*
16856341 TTTCGTTTACT-TTTTAAATTTAATTTGTAA
1 TTTCGTTT-CTATTTTAAATTTAATTTCTAA
*
16856371 TTTCGTTTTTATTTTAAATTTAATTTCTAA
1 TTTCGTTTCTATTTTAAATTTAATTTCTAA
* * * **
16856401 TTTCCTGTATATTTT-AATTTTTTTTCTAA
1 TTTCGTTTCTATTTTAAATTTAATTTCTAA
16856430 TTT
1 TTT
16856433 TCTGTATATT
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
29 16 0.30
30 38 0.70
ACGTcount: A:0.24, C:0.08, G:0.04, T:0.64
Consensus pattern (30 bp):
TTTCGTTTCTATTTTAAATTTAATTTCTAA
Found at i:16856429 original size:29 final size:29
Alignment explanation
Indices: 16856352--16856448 Score: 104
Period size: 30 Copynumber: 3.3 Consensus size: 29
16856342 TTCGTTTACT
* * * *
16856352 TTTTAAATTTAATTTGTAATTTCGTTTTTA
1 TTTT-AATTTAATTTCTAATTTCCTGTATA
16856382 TTTTAAATTTAATTTCTAATTTCCTGTATA
1 TTTT-AATTTAATTTCTAATTTCCTGTATA
** *
16856412 TTTTAATTTTTTTTCTAATTTTCTGTATA
1 TTTTAATTTAATTTCTAATTTCCTGTATA
*
16856441 TTCTAATT
1 TTTTAATT
16856449 ATTATTTTTT
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
29 29 0.49
30 30 0.51
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.63
Consensus pattern (29 bp):
TTTTAATTTAATTTCTAATTTCCTGTATA
Found at i:16856446 original size:17 final size:17
Alignment explanation
Indices: 16856395--16856448 Score: 55
Period size: 17 Copynumber: 3.5 Consensus size: 17
16856385 TAAATTTAAT
*
16856395 TTCTAATTTCCTGTATA
1 TTCTAATTTTCTGTATA
*
16856412 TTTTAA-TTT-T-T-T-
1 TTCTAATTTTCTGTATA
16856424 TTCTAATTTTCTGTATA
1 TTCTAATTTTCTGTATA
16856441 TTCTAATT
1 TTCTAATT
16856449 ATTATTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 10
0.69 0.07 0.24
Matches are distributed among these distances:
12 5 0.17
13 4 0.14
14 2 0.07
15 2 0.07
16 3 0.10
17 13 0.45
ACGTcount: A:0.22, C:0.11, G:0.04, T:0.63
Consensus pattern (17 bp):
TTCTAATTTTCTGTATA
Found at i:16857337 original size:59 final size:59
Alignment explanation
Indices: 16857262--16857874 Score: 440
Period size: 60 Copynumber: 10.3 Consensus size: 59
16857252 AGGGGAAGTT
* * * * **
16857262 GGTGTTGGCCATTACATGGCTAACACCAAAAAATTTAATTTTTTACCAAATAAAAAAGG
1 GGTGTCGGCCATTGCATGGCCAACACCAAAAAATTTAATTTTTTATCTGATAAAAAAGG
* * * ** ***
16857321 GGTGTCGACCATTACATGGCCAATACCAAAAAAATAAAAAAAATTTATCTG--AAAAAAGG
1 GGTGTCGGCCATTGCATGGCCAACACC-AAAAAAT-TTAATTTTTTATCTGATAAAAAAGG
* * * *
16857380 GGTGTCGACCATTACATGTG-CAACACCTAAAAATTTTAAAATTTTTTTATCTGA-CAAAAAGG
1 GGTGTCGGCCATTGCATG-GCCAACACC-AAAAAATTT--AA-TTTTTTATCTGATAAAAAAGG
*
16857442 GGATGTCGG----T--ATGGCCAACACCAAAAAAAATTGAAATTTTTTTATCTG---AAAAAGG
1 GG-TGTCGGCCATTGCATGGCCAACACC--AAAAAATT-TAA-TTTTTTATCTGATAAAAAAGG
* * * *
16857497 GGATGTCTGTCATTGCATGACCAATA-CAAAAAATTTGAATTTTTTTTATCT-A-AAAAAAGG
1 GG-TGTCGGCCATTGCATGGCCAACACCAAAAAATTT-AA--TTTTTTATCTGATAAAAAAGG
* * * *
16857557 AAGTGTCGGCCATTGCATGACCAACACCAAAAAAATTTGAAATTTTTTATTTGA-GAAAAAGG
1 -GGTGTCGGCCATTGCATGGCCAACACC-AAAAAATTT--AATTTTTTATCTGATAAAAAAGG
* * * * * *
16857619 GGTGTCGGCTATTGCATGGCTAAGA-CAAAAAATTAAAATTATTATCTGATAAAAAAGG
1 GGTGTCGGCCATTGCATGGCCAACACCAAAAAATTTAATTTTTTATCTGATAAAAAAGG
* * * * *
16857677 GGTGTCCGCCATTGCATGGCCAACACCCAAAAATTTGATTTTTTTATCAGATTAAAAAGG
1 GGTGTCGGCCATTGCATGGCCAACACCAAAAAATTT-AATTTTTTATCTGATAAAAAAGG
* * * *
16857737 GGTGTCGGCCA-TGCAATGGCCAACACAAAAAAATTGT-A-TTTTTACCTGACAAAAAAAG
1 GGTGTCGGCCATTGC-ATGGCCAACACCAAAAAATT-TAATTTTTTATCTGATAAAAAAGG
* * * * *
16857795 GGTGTCGGTCATTGCATAGCCAACACTAAAAAATTTAATTTTTTTATCAGATTAAAAAGG
1 GGTGTCGGCCATTGCATGGCCAACACCAAAAAATTTAA-TTTTTTATCTGATAAAAAAGG
16857855 GGTGTCGGCCATTGCATGGC
1 GGTGTCGGCCATTGCATGGC
16857875 TTACACACAA
Statistics
Matches: 443, Mismatches: 76, Indels: 69
0.75 0.13 0.12
Matches are distributed among these distances:
55 15 0.03
56 1 0.00
57 36 0.08
58 89 0.20
59 96 0.22
60 118 0.27
61 55 0.12
62 26 0.06
63 7 0.02
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.28
Consensus pattern (59 bp):
GGTGTCGGCCATTGCATGGCCAACACCAAAAAATTTAATTTTTTATCTGATAAAAAAGG
Found at i:16857556 original size:60 final size:59
Alignment explanation
Indices: 16857262--16857872 Score: 361
Period size: 59 Copynumber: 10.3 Consensus size: 59
16857252 AGGGGAAGTT
* * * * * * *
16857262 GGTGTTGGCCATTACATGGCTAACACCAAAAAATTT-AA-TTTTTTACCAAATAAAAAAGG
1 GGTGTCGGCCATTGCATGACCAACA-CAAAAAATTTGAATTTTTTTATC-TAGAAAAAAGG
* * * * * ** ****
16857321 GGTGTCGACCATTACATGGCCAATACCAAAAAAATAAAAAAAATTTATCT-GAAAAAAGG
1 GGTGTCGGCCATTGCATGACCAACA-CAAAAAATTTGAATTTTTTTATCTAGAAAAAAGG
* * ** * *
16857380 GGTGTCGACCATTACATGTGCAACACCTAAAAATTTTAAAATTTTTTTATCT-GACAAAAAGG
1 GGTGTCGGCCATTGCATGACCAACA-C-AAAAAATTT-GAATTTTTTTATCTAGA-AAAAAGG
* *
16857442 GGATGTCGG----T--ATGGCCAACACCAAAAAAAATTGAAATTTTTTTATCT-G-AAAAAGG
1 GG-TGTCGGCCATTGCATGACCAACA-C-AAAAAATTTG-AATTTTTTTATCTAGAAAAAAGG
* * *
16857497 GGATGTCTGTCATTGCATGACCAATACAAAAAATTTGAATTTTTTTTATCTA-AAAAAAGG
1 GG-TGTCGGCCATTGCATGACCAACACAAAAAATTTGAA-TTTTTTTATCTAGAAAAAAGG
* * *
16857557 AAGTGTCGGCCATTGCATGACCAACACCAAAAAAATTTGAAATTTTTTAT-TTGAGAAAAAGG
1 -GGTGTCGGCCATTGCATGACCAACA-C-AAAAAATTTGAATTTTTTTATCTAGA-AAAAAGG
* * * * ** * *
16857619 GGTGTCGGCTATTGCATGGCTAAGACAAAAAA-TT-AAAATTATTATCTGATAAAAAAGG
1 GGTGTCGGCCATTGCATGACCAACACAAAAAATTTGAATTTTTTTATCT-AGAAAAAAGG
* * *
16857677 GGTGTCCGCCATTGCATGGCCAACACCCAAAAATTTG-ATTTTTTTATC-AGATTAAAAAGG
1 GGTGTCGGCCATTGCATGACCAACA-CAAAAAATTTGAATTTTTTTATCTAGA--AAAAAGG
* * * * * *
16857737 GGTGTCGGCCA-TGCAATGGCCAACACAAAAAAATTG--TATTTTTACCTGACAAAAAAAG
1 GGTGTCGGCCATTGC-ATGACCAACACAAAAAATTTGAATTTTTTTATCT-AGAAAAAAGG
*
16857795 GGTGTCGGTCATTGCAT-AGCCAACACTAAAAAATTT-AATTTTTTTATC-AGATTAAAAAGG
1 GGTGTCGGCCATTGCATGA-CCAACAC-AAAAAATTTGAATTTTTTTATCTAGA--AAAAAGG
16857855 GGTGTCGGCCATTGCATG
1 GGTGTCGGCCATTGCATG
16857873 GCTTACACAC
Statistics
Matches: 441, Mismatches: 72, Indels: 76
0.75 0.12 0.13
Matches are distributed among these distances:
55 15 0.03
57 40 0.09
58 70 0.16
59 120 0.27
60 107 0.24
61 56 0.13
62 28 0.06
63 5 0.01
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (59 bp):
GGTGTCGGCCATTGCATGACCAACACAAAAAATTTGAATTTTTTTATCTAGAAAAAAGG
Found at i:16857742 original size:118 final size:117
Alignment explanation
Indices: 16857262--16857881 Score: 408
Period size: 118 Copynumber: 5.2 Consensus size: 117
16857252 AGGGGAAGTT
* * * * * * **
16857262 GGTGTTGGCCATTACATGGCTAACACCAAAAAATTTAATTTTTTACCAAATAAAAAAGGGGTGTC
1 GGTGTCGGCCATTGCATGGCTAACA-CAAAAAAATTAAATTATTATCTGA-AAAAAAGGGGTGTC
* * * *** **** *
16857327 GACCATTACATGGCCAATACCAAAAAAATAAAAAAAATTTATCTGA--AAAAAGG
64 GGCCATTGCATGGCCAACACC-AAAAAATTTGATTTTTTTATCAGATTAAAAAGG
* * ** * *
16857380 GGTGTCGACCATTACATGTGC-AACACCTAAAAATTTTAAAATTTTTTTATCTGACAAAAAGGGG
1 GGTGTCGGCCATTGCATG-GCTAACA-C-AAAAAAATT-AAA--TTATTATCTGAAAAAAAGGGG
* *
16857444 ATGTCGG----T--ATGGCCAACACCAAAAAAAATTGAAATTTTTTTATC---TGAAAAAGG
60 -TGTCGGCCATTGCATGGCCAACACC-AAAAAATTTG--ATTTTTTTATCAGATTAAAAAGG
* * * * * * * * *
16857497 GGATGTCTGTCATTGCATGACCAATACAAAAAATTTGAATTTTTTTTATCT-AAAAAAAGGAAGT
1 GG-TGTCGGCCATTGCATGGCTAACACAAAAAAATT-AA--ATTATTATCTGAAAAAAAGG-GGT
* * ** *
16857561 GTCGGCCATTGCATGACCAACACCAAAAAAATTTGAAATTTTTTATTTGA-GAAAAAGG
61 GTCGGCCATTGCATGGCCAACACC-AAAAAATTTG-ATTTTTTTATCAGATTAAAAAGG
* *
16857619 GGTGTCGGCTATTGCATGGCTAAGAC-AAAAAATTAAAATTATTATCTGATAAAAAAGGGGTGTC
1 GGTGTCGGCCATTGCATGGCTAACACAAAAAAATT-AAATTATTATCTGA-AAAAAAGGGGTGTC
* *
16857683 CGCCATTGCATGGCCAACACCCAAAAATTTGATTTTTTTATCAGATTAAAAAGG
64 GGCCATTGCATGGCCAACACCAAAAAATTTGATTTTTTTATCAGATTAAAAAGG
* ** * * *
16857737 GGTGTCGGCCA-TGCAATGGCCAACACAAAAAAATTGTATTTTTACCTGACAAAAAAAGGGTGTC
1 GGTGTCGGCCATTGC-ATGGCTAACACAAAAAAATTAAATTATTATCTGA-AAAAAAGGGGTGTC
* * * *
16857801 GGTCATTGCATAGCCAACACTAAAAAATTTAATTTTTTTATCAGATTAAAAAGG
64 GGCCATTGCATGGCCAACACCAAAAAATTTGATTTTTTTATCAGATTAAAAAGG
*
16857855 GGTGTCGGCCATTGCATGGCTTACACA
1 GGTGTCGGCCATTGCATGGCTAACACA
16857882 CAATTTTTTT
Statistics
Matches: 404, Mismatches: 68, Indels: 60
0.76 0.13 0.11
Matches are distributed among these distances:
115 14 0.03
116 38 0.09
117 25 0.06
118 180 0.45
119 47 0.12
120 29 0.07
121 48 0.12
122 23 0.06
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (117 bp):
GGTGTCGGCCATTGCATGGCTAACACAAAAAAATTAAATTATTATCTGAAAAAAAGGGGTGTCGG
CCATTGCATGGCCAACACCAAAAAATTTGATTTTTTTATCAGATTAAAAAGG
Found at i:16859295 original size:58 final size:58
Alignment explanation
Indices: 16859230--16859347 Score: 218
Period size: 58 Copynumber: 2.0 Consensus size: 58
16859220 AAGTCATCTT
*
16859230 TTGTTCTTAGGGAGAAAACGTATTCACTACAAGTAGTGATACATGCAGTATATTTGTC
1 TTGTTCTTAGGGAGAAAACGTATTCACTACAAGTAGTGATACATGCAATATATTTGTC
*
16859288 TTGTTCTTTGGGAGAAAACGTATTCACTACAAGTAGTGATACATGCAATATATTTGTC
1 TTGTTCTTAGGGAGAAAACGTATTCACTACAAGTAGTGATACATGCAATATATTTGTC
16859346 TT
1 TT
16859348 ACTTATCGCT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (58 bp):
TTGTTCTTAGGGAGAAAACGTATTCACTACAAGTAGTGATACATGCAATATATTTGTC
Found at i:16870277 original size:21 final size:20
Alignment explanation
Indices: 16870249--16870306 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 20
16870239 TAACTTGACT
16870249 TTTGGGTTTAGATTTCAAGG
1 TTTGGGTTTAGATTTCAAGG
*
16870269 TTTGAGGTTTAGAATTCAAGG
1 TTTG-GGTTTAGATTTCAAGG
16870290 TTTCGGGTTTAAGATTT
1 TTT-GGGTTT-AGATTT
16870307 GAGGTTCAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.12
21 23 0.70
22 6 0.18
ACGTcount: A:0.22, C:0.05, G:0.28, T:0.45
Consensus pattern (20 bp):
TTTGGGTTTAGATTTCAAGG
Found at i:16876800 original size:14 final size:13
Alignment explanation
Indices: 16876769--16876832 Score: 51
Period size: 13 Copynumber: 4.9 Consensus size: 13
16876759 TAAACCAAAC
16876769 TTTTCAAAAGTAT
1 TTTTCAAAAGTAT
16876782 TTTTCAAAA-TCACT
1 TTTTCAAAAGT-A-T
*
16876796 TTTTC-AAAGCAT
1 TTTTCAAAAGTAT
* * *
16876808 TTTTTAAAAGCAC
1 TTTTCAAAAGTAT
*
16876821 TTCTCAAAAGTA
1 TTTTCAAAAGTA
16876833 ATGCTAAACT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
12 6 0.15
13 29 0.71
14 6 0.15
ACGTcount: A:0.38, C:0.16, G:0.06, T:0.41
Consensus pattern (13 bp):
TTTTCAAAAGTAT
Found at i:16876804 original size:26 final size:27
Alignment explanation
Indices: 16876769--16876830 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 27
16876759 TAAACCAAAC
* *
16876769 TTTTCAAAAGTATTTTTCAAAATCACT
1 TTTTCAAAAGCATTTTTCAAAAGCACT
*
16876796 TTTTC-AAAGCATTTTTTAAAAGCAC-
1 TTTTCAAAAGCATTTTTCAAAAGCACT
*
16876821 TTCTCAAAAG
1 TTTTCAAAAG
16876831 TAATGCTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 4 0.13
26 21 0.70
27 5 0.17
ACGTcount: A:0.37, C:0.16, G:0.06, T:0.40
Consensus pattern (27 bp):
TTTTCAAAAGCATTTTTCAAAAGCACT
Found at i:16881966 original size:31 final size:31
Alignment explanation
Indices: 16881928--16882017 Score: 144
Period size: 31 Copynumber: 2.9 Consensus size: 31
16881918 AAATGGTCAT
16881928 TGAACTATTTGAAAGTTTTAATTTAAGTTAC
1 TGAACTATTTGAAAGTTTTAATTTAAGTTAC
* *
16881959 TGAACTATTTGAAGGTTTTAATTTAAATTAC
1 TGAACTATTTGAAAGTTTTAATTTAAGTTAC
* *
16881990 TGAACTATTTGAAAATTTTTATTTAAGT
1 TGAACTATTTGAAAGTTTTAATTTAAGT
16882018 CACTAATTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 53 1.00
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.47
Consensus pattern (31 bp):
TGAACTATTTGAAAGTTTTAATTTAAGTTAC
Found at i:16885898 original size:17 final size:17
Alignment explanation
Indices: 16885876--16885914 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
16885866 CTCCACCTTG
* *
16885876 ACAAGAATTCTCTACGA
1 ACAAGAACTCTCAACGA
16885893 ACAAGAACTCTCAACGA
1 ACAAGAACTCTCAACGA
16885910 ACAAG
1 ACAAG
16885915 TTCTCCACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.26, G:0.13, T:0.15
Consensus pattern (17 bp):
ACAAGAACTCTCAACGA
Found at i:16887856 original size:15 final size:15
Alignment explanation
Indices: 16887836--16887872 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
16887826 TTGTAGCACT
16887836 CTTTCTTAATGTGTC
1 CTTTCTTAATGTGTC
16887851 CTTTCTTAATGTGTC
1 CTTTCTTAATGTGTC
16887866 CTTTCTT
1 CTTTCTT
16887873 CTTGCAGAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.11, C:0.22, G:0.11, T:0.57
Consensus pattern (15 bp):
CTTTCTTAATGTGTC
Found at i:16894632 original size:2 final size:2
Alignment explanation
Indices: 16894627--16894656 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
16894617 TATTGCTCAT
16894627 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
16894657 ATCCTGTGCA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:16902831 original size:2 final size:2
Alignment explanation
Indices: 16902813--16902848 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
16902803 AGATGCTTAA
* *
16902813 AT AT AA AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16902849 CAGCTAAAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:16903505 original size:2 final size:2
Alignment explanation
Indices: 16903498--16903523 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
16903488 TTCTTCTAGT
16903498 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
16903524 ACTATACCTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:16903832 original size:2 final size:2
Alignment explanation
Indices: 16903825--16903851 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
16903815 TTCTCTTTTC
16903825 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
16903852 TCAAATGGAT
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:16909172 original size:38 final size:39
Alignment explanation
Indices: 16909083--16909229 Score: 131
Period size: 39 Copynumber: 3.8 Consensus size: 39
16909073 CCAAAAGCAA
* *
16909083 AGAATCTATAAC-AAGGTTAGATCTCGTTATATTATCC-T
1 AGAATCTACAACAAAGGCTAGATCTCGTTATATTA-CCTT
*
16909121 AGAATCTAAAAC-AAGGCTAGATCTCGTTATATTA-CTT
1 AGAATCTACAACAAAGGCTAGATCTCGTTATATTACCTT
* ** * **
16909158 GAGAATCTGCAACAAATTCTAGACCTCACTATATTACCTT
1 -AGAATCTACAACAAAGGCTAGATCTCGTTATATTACCTT
* * **
16909198 AGAATCTGCTACAAATTCTAGATCTCGTTATA
1 AGAATCTACAACAAAGGCTAGATCTCGTTATA
16909230 ATCTGTAATA
Statistics
Matches: 92, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
36 1 0.01
37 1 0.01
38 42 0.46
39 45 0.49
40 3 0.03
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.33
Consensus pattern (39 bp):
AGAATCTACAACAAAGGCTAGATCTCGTTATATTACCTT
Found at i:16918187 original size:17 final size:18
Alignment explanation
Indices: 16918149--16918187 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
16918139 CCAATTGCCG
*
16918149 CAGTGAGGCGGCTAGCAAC
1 CAGTGAGGCAGCTA-CAAC
16918168 CAGTGAGGCAGCTA-AAC
1 CAGTGAGGCAGCTACAAC
16918185 CAG
1 CAG
16918188 CAACGTACAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
19 13 0.68
ACGTcount: A:0.31, C:0.26, G:0.33, T:0.10
Consensus pattern (18 bp):
CAGTGAGGCAGCTACAAC
Found at i:16930009 original size:31 final size:31
Alignment explanation
Indices: 16929967--16930041 Score: 114
Period size: 31 Copynumber: 2.4 Consensus size: 31
16929957 CATAACATTT
* *
16929967 CAAACATAAGTGATTAAAATGTAATCTGAGG
1 CAAACAAAAGTGATTAAAATGTAATCTGAGA
* *
16929998 CAAACAAAAGTGTTTAAAATGTAATTTGAGA
1 CAAACAAAAGTGATTAAAATGTAATCTGAGA
16930029 CAAACAAAAGTGA
1 CAAACAAAAGTGA
16930042 CTATTTTGGT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.49, C:0.09, G:0.17, T:0.24
Consensus pattern (31 bp):
CAAACAAAAGTGATTAAAATGTAATCTGAGA
Found at i:16941732 original size:13 final size:13
Alignment explanation
Indices: 16941714--16941752 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
16941704 ATATGAGAAT
16941714 GGAGAAAAATAAA
1 GGAGAAAAATAAA
*
16941727 GGAGAAGAATAAA
1 GGAGAAAAATAAA
*
16941740 AG-GAAAAATAAA
1 GGAGAAAAATAAA
16941752 G
1 G
16941753 AAATAAAAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
12 9 0.41
13 13 0.59
ACGTcount: A:0.67, C:0.00, G:0.26, T:0.08
Consensus pattern (13 bp):
GGAGAAAAATAAA
Found at i:16971626 original size:30 final size:30
Alignment explanation
Indices: 16971592--16971653 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
16971582 AAACTCCAAA
* *
16971592 CCTTTTTACTTTTCCTC-AAAAACTTTTACT
1 CCTTTCTAATTTT-CTCTAAAAACTTTTACT
*
16971622 CCTTTCTAATTTTCTCTTAAAACTTTTACT
1 CCTTTCTAATTTTCTCTAAAAACTTTTACT
16971652 CC
1 CC
16971654 CCTCCCATCT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 3 0.11
30 25 0.89
ACGTcount: A:0.23, C:0.27, G:0.00, T:0.50
Consensus pattern (30 bp):
CCTTTCTAATTTTCTCTAAAAACTTTTACT
Found at i:16976461 original size:4 final size:4
Alignment explanation
Indices: 16976454--16976485 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
16976444 GTGAGAGGGT
16976454 GATG GATG GATG GATG GATG GATG GATG GATG
1 GATG GATG GATG GATG GATG GATG GATG GATG
16976486 AAAGGAAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.50, T:0.25
Consensus pattern (4 bp):
GATG
Found at i:16979766 original size:25 final size:26
Alignment explanation
Indices: 16979731--16979787 Score: 89
Period size: 25 Copynumber: 2.2 Consensus size: 26
16979721 TGAGTCGAGA
16979731 TGGGTCAGAGGTTCCTTG-GTTTGAG
1 TGGGTCAGAGGTTCCTTGAGTTTGAG
*
16979756 TGGGTCCGAGGTTCCTTGAGTTTGAG
1 TGGGTCAGAGGTTCCTTGAGTTTGAG
*
16979782 TTGGTC
1 TGGGTC
16979788 GAAGGACCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 17 0.59
26 12 0.41
ACGTcount: A:0.11, C:0.14, G:0.39, T:0.37
Consensus pattern (26 bp):
TGGGTCAGAGGTTCCTTGAGTTTGAG
Found at i:16980825 original size:19 final size:18
Alignment explanation
Indices: 16980801--16980853 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 18
16980791 TAATAAGAAA
16980801 AGTATTTTACTTAAATTTT
1 AGTATTTTA-TTAAATTTT
*
16980820 AGTATTAGTTATAAAATTTT
1 AGTATT--TTATTAAATTTT
*
16980840 TGTATTTTAATTAA
1 AGTATTTT-ATTAA
16980854 TCATAATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 2 0.07
19 10 0.36
20 13 0.46
21 3 0.11
ACGTcount: A:0.36, C:0.02, G:0.08, T:0.55
Consensus pattern (18 bp):
AGTATTTTATTAAATTTT
Found at i:16985352 original size:141 final size:140
Alignment explanation
Indices: 16985086--16985400 Score: 384
Period size: 141 Copynumber: 2.2 Consensus size: 140
16985076 TTTTAAGACT
* ** * *
16985086 ACACTTTTGGTGCAACACTTTTTTAAGTGTTGAGATAAATTTCTCAACATACGTTTTGGCCAACT
1 ACACTTTTGGGGCAACACTTTCCTAAGTGTTGGGATAAACTTCTCAACATACGTTTTGGCCAACT
* * * * **
16985151 TTTTGTATAAGGGTTGAGATATGCATGCCTAAGACAACGCTTAAATAAGAGTTGGTTTTGTCCAA
66 TTTTCTATAAGGGTTGAGATATGCATGCATAAGACAACGCTTAAATAAAAGTCGACTTTGTCCAA
16985216 CACTAT-GTCG
131 CACTATGGT-G
* * * *
16985226 ATACTTTTGGGGCAACACTTTCCTAAGTGTTGGGATAGACTTGTCGACATACGCTTTT-GCCAAC
1 ACACTTTTGGGGCAACACTTTCCTAAGTGTTGGGATAAACTTCTCAACATACG-TTTTGGCCAAC
* **
16985290 TCTTTTCTATAAGGGTTGAGATATGCATGTATAAGGTAACGCTTAAATAAAAGTCGACTTTGTCC
65 T-TTTTCTATAAGGGTTGAGATATGCATGCATAAGACAACGCTTAAATAAAAGTCGACTTTGTCC
*
16985355 AATACTATGGTG
129 AACACTATGGTG
*
16985367 ACACTTTT-GGGCTGACACTTTCCTAAAGTGTTGG
1 ACACTTTTGGGGC-AACACTTTCCT-AAGTGTTGG
16985401 TGTCGGCATA
Statistics
Matches: 149, Mismatches: 21, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
140 55 0.37
141 83 0.56
142 11 0.07
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (140 bp):
ACACTTTTGGGGCAACACTTTCCTAAGTGTTGGGATAAACTTCTCAACATACGTTTTGGCCAACT
TTTTCTATAAGGGTTGAGATATGCATGCATAAGACAACGCTTAAATAAAAGTCGACTTTGTCCAA
CACTATGGTG
Found at i:16985495 original size:133 final size:134
Alignment explanation
Indices: 16985132--16985506 Score: 409
Period size: 141 Copynumber: 2.7 Consensus size: 134
16985122 AAATTTCTCA
* * *
16985132 ACATACGTTTTGGCCAACTTTTTGTATAAGGGTTGAGATATGCATGCCTAAGACAACGCTTAAAT
1 ACATACGCTTTGGCCAACTCTTTGTATAAGGGTTGAGATATGCATGCCTAAGGCAACGCTTAAAT
* *
16985197 AAGAGTTGGTTTTGTCCAACACTAT-GTCGATACTTTTGGGGCAACACTTTCCTAAGTGTTGGGA
66 AAGAGTTGATTTT-TCCAACACTATGGT-GACACTTTTGGGGCAACACTTTCCTAAGTGTT-GG-
16985261 TAGACTTGTCG
127 -AGA--TGTCG
* * ** *
16985272 ACATACGCTTTTGCCAACTCTTTTCTATAAGGGTTGAGATATGCATGTATAAGGTAACGCTTAAA
1 ACATACGCTTTGGCCAACTC-TTTGTATAAGGGTTGAGATATGCATGCCTAAGGCAACGCTTAAA
* * * * *
16985337 TAAAAGTCGACTTTGTCCAATACTATGGTGACACTTTT-GGGCTGACACTTTCCTAAAGTGTT-G
65 TAAGAGTTGA-TTTTTCCAACACTATGGTGACACTTTTGGGGC-AACACTTTCCT-AAGTGTTGG
16985400 -G-TGTCG
127 AGATGTCG
* * * * *
16985406 GCATACGCTTTGGTCAACTCTTTGTATAATGGTTGGGATATGTATGCCTAAGGCAACGCTTAAAT
1 ACATACGCTTTGGCCAACTCTTTGTATAAGGGTTGAGATATGCATGCCTAAGGCAACGCTTAAAT
* *
16985471 AAGAGTTAGATTTTTTCAACACTATGCTGACACTTT
66 AAGAGTT-GATTTTTCCAACACTATGGTGACACTTT
16985507 CGTAAGTGTT
Statistics
Matches: 198, Mismatches: 31, Indels: 19
0.80 0.12 0.08
Matches are distributed among these distances:
133 65 0.33
134 24 0.12
137 1 0.01
140 22 0.11
141 74 0.37
142 12 0.06
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.34
Consensus pattern (134 bp):
ACATACGCTTTGGCCAACTCTTTGTATAAGGGTTGAGATATGCATGCCTAAGGCAACGCTTAAAT
AAGAGTTGATTTTTCCAACACTATGGTGACACTTTTGGGGCAACACTTTCCTAAGTGTTGGAGAT
GTCG
Found at i:16985941 original size:7 final size:7
Alignment explanation
Indices: 16985931--16985991 Score: 54
Period size: 7 Copynumber: 8.7 Consensus size: 7
16985921 TTTTTTACCG
16985931 TAAACCT
1 TAAACCT
16985938 TAAA-CT
1 TAAACCT
16985944 TAGAACCT
1 TA-AACCT
*
16985952 CAAACCT
1 TAAACCT
*
16985959 TAAACCA
1 TAAACCT
16985966 TAAA-CT
1 TAAACCT
*
16985972 TAAAACCC
1 T-AAACCT
*
16985980 TAAACCC
1 TAAACCT
16985987 TAAAC
1 TAAAC
16985992 ATGAACCTCA
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
6 6 0.13
7 34 0.76
8 5 0.11
ACGTcount: A:0.48, C:0.30, G:0.02, T:0.21
Consensus pattern (7 bp):
TAAACCT
Found at i:16985971 original size:28 final size:28
Alignment explanation
Indices: 16985931--16985991 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
16985921 TTTTTTACCG
* * *
16985931 TAAACCTTAAACTTAGAA-CCTCAAACCT
1 TAAACCATAAACTTAAAACCCT-AAACCC
16985959 TAAACCATAAACTTAAAACCCTAAACCC
1 TAAACCATAAACTTAAAACCCTAAACCC
16985987 TAAAC
1 TAAAC
16985992 ATGAACCTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 26 0.90
29 3 0.10
ACGTcount: A:0.48, C:0.30, G:0.02, T:0.21
Consensus pattern (28 bp):
TAAACCATAAACTTAAAACCCTAAACCC
Found at i:17002475 original size:24 final size:24
Alignment explanation
Indices: 17002438--17002498 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
17002428 AACTAATAAG
* *
17002438 AGTTTGACTCAAACAAATAAACAA
1 AGTTTAACTGAAACAAATAAACAA
* * *
17002462 AGTTTAATTGAAACAATTAAACAG
1 AGTTTAACTGAAACAAATAAACAA
17002486 AGTTTAACTGAAA
1 AGTTTAACTGAAA
17002499 GATTATTTCT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.51, C:0.11, G:0.11, T:0.26
Consensus pattern (24 bp):
AGTTTAACTGAAACAAATAAACAA
Found at i:17005448 original size:17 final size:17
Alignment explanation
Indices: 17005426--17005464 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
17005416 AGATGGAGAA
* * *
17005426 CTTGTTCGTTGAGAGTT
1 CTTGTTAGTAGAGAATT
17005443 CTTGTTAGTAGAGAATT
1 CTTGTTAGTAGAGAATT
17005460 CTTGT
1 CTTGT
17005465 CAAGGTGGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.18, C:0.10, G:0.26, T:0.46
Consensus pattern (17 bp):
CTTGTTAGTAGAGAATT
Found at i:17005533 original size:5 final size:5
Alignment explanation
Indices: 17005525--17005552 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
17005515 ATTCAGTGGC
17005525 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
17005553 GTCCAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:17006337 original size:6 final size:6
Alignment explanation
Indices: 17006326--17006382 Score: 78
Period size: 6 Copynumber: 9.3 Consensus size: 6
17006316 CCATTAAAAA
* * *
17006326 TCCATG TCCATG TCCATG TCCATG TCCATG TCTATTG TCTATG TCTATG
1 TCCATG TCCATG TCCATG TCCATG TCCATG TCCA-TG TCCATG TCCATG
17006375 TCCATG TC
1 TCCATG TC
17006383 TTGTTAAAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
6 42 0.88
7 6 0.12
ACGTcount: A:0.16, C:0.28, G:0.16, T:0.40
Consensus pattern (6 bp):
TCCATG
Found at i:17006364 original size:25 final size:24
Alignment explanation
Indices: 17006326--17006383 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 24
17006316 CCATTAAAAA
*
17006326 TCCATGTCCATGTCCATGTCCATG
1 TCCATGTCTATGTCCATGTCCATG
* *
17006350 TCCATGTCTATTGTCTATGTCTATG
1 TCCATGTCTA-TGTCCATGTCCATG
17006375 TCCATGTCT
1 TCCATGTCT
17006384 TGTTAAAATG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 9 0.30
25 21 0.70
ACGTcount: A:0.16, C:0.28, G:0.16, T:0.41
Consensus pattern (24 bp):
TCCATGTCTATGTCCATGTCCATG
Found at i:17022506 original size:25 final size:26
Alignment explanation
Indices: 17022465--17022524 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 26
17022455 ACCACAAAAT
*
17022465 ATTTTTTAAATTTTTTC-CTTTCATTTG
1 ATTTTTTAAA-TTTTTCGATTT-ATTTG
17022492 ATTTTTTAAA-TTTTCGATTTATTTG
1 ATTTTTTAAATTTTTCGATTTATTTG
17022517 ACTTTTTT
1 A-TTTTTT
17022525 TTTGCGAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 11 0.37
26 9 0.30
27 10 0.33
ACGTcount: A:0.20, C:0.08, G:0.05, T:0.67
Consensus pattern (26 bp):
ATTTTTTAAATTTTTCGATTTATTTG
Found at i:17027427 original size:21 final size:22
Alignment explanation
Indices: 17027379--17027428 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
17027369 ATTTTTTTAA
*
17027379 AATTTAAAAATTAAAAAAATAT
1 AATTAAAAAATTAAAAAAATAT
** *
17027401 TTTTAAAAAATTTAAAAAAT-T
1 AATTAAAAAATTAAAAAAATAT
17027422 AATTAAA
1 AATTAAA
17027429 TATTTACGTG
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
AATTAAAAAATTAAAAAAATAT
Found at i:17029781 original size:19 final size:20
Alignment explanation
Indices: 17029757--17029795 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
17029747 GCCCCATCCC
*
17029757 CATCCCCG-CTACCCCGCAT
1 CATCCCCGCCCACCCCGCAT
*
17029776 CATCCCGGCCCACCCCGCAT
1 CATCCCCGCCCACCCCGCAT
17029796 AATATAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.15, C:0.59, G:0.13, T:0.13
Consensus pattern (20 bp):
CATCCCCGCCCACCCCGCAT
Found at i:17043259 original size:18 final size:18
Alignment explanation
Indices: 17043236--17043295 Score: 61
Period size: 18 Copynumber: 3.2 Consensus size: 18
17043226 TGTGTTTCGG
17043236 AAGAAGAGAAGGAAAGGT
1 AAGAAGAGAAGGAAAGGT
17043254 AAGAAGTAGAAGG-AAGAG-
1 AAGAAG-AGAAGGAAAG-GT
17043272 AAGAAGAGGAAGAGAAAGGGT
1 AAGAAGA-GAAG-GAAA-GGT
17043293 AAG
1 AAG
17043296 GGTAAGGGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
17 1 0.03
18 19 0.54
19 8 0.23
20 3 0.09
21 4 0.11
ACGTcount: A:0.55, C:0.00, G:0.40, T:0.05
Consensus pattern (18 bp):
AAGAAGAGAAGGAAAGGT
Found at i:17063191 original size:17 final size:17
Alignment explanation
Indices: 17063169--17063204 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
17063159 AAGAAGGTAC
*
17063169 ATGAGTCGTATAAATTA
1 ATGAGTCGCATAAATTA
17063186 ATGAGTCGCATAAATTA
1 ATGAGTCGCATAAATTA
17063203 AT
1 AT
17063205 TATTGAAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.33
Consensus pattern (17 bp):
ATGAGTCGCATAAATTA
Found at i:17071040 original size:26 final size:26
Alignment explanation
Indices: 17071011--17071070 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
17071001 ACACCAAACT
17071011 TTTCAAAAATACTTCTTAAAAATACG
1 TTTCAAAAATACTTCTTAAAAATACG
* * * * *
17071037 TTTCCACAATACTTTTTAAAAGTACT
1 TTTCAAAAATACTTCTTAAAAATACG
17071063 TTTCAAAA
1 TTTCAAAA
17071071 GCAATGCTAA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.42, C:0.17, G:0.03, T:0.38
Consensus pattern (26 bp):
TTTCAAAAATACTTCTTAAAAATACG
Found at i:17071071 original size:13 final size:13
Alignment explanation
Indices: 17071008--17071070 Score: 65
Period size: 13 Copynumber: 4.8 Consensus size: 13
17070998 TTTACACCAA
17071008 ACTTTTCAAAAAT
1 ACTTTTCAAAAAT
17071021 ACTTCTT-AAAAAT
1 ACTT-TTCAAAAAT
* * *
17071034 ACGTTTCCACAAT
1 ACTTTTCAAAAAT
* *
17071047 ACTTTTTAAAAGT
1 ACTTTTCAAAAAT
17071060 ACTTTTCAAAA
1 ACTTTTCAAAA
17071071 GCAATGCTAA
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
12 2 0.05
13 35 0.90
14 2 0.05
ACGTcount: A:0.41, C:0.17, G:0.03, T:0.38
Consensus pattern (13 bp):
ACTTTTCAAAAAT
Found at i:17073287 original size:37 final size:34
Alignment explanation
Indices: 17073207--17073289 Score: 89
Period size: 33 Copynumber: 2.4 Consensus size: 34
17073197 CTGGGATAAT
*
17073207 ATGAAGCAAATAATCGCAAATTTTTTAAGGTAAA
1 ATGAAGCAATTAATCGCAAATTTTTTAAGGTAAA
* *
17073241 A-AAACCAATTAATCGCAAATTTTAAAATTAAGG-AAA
1 ATGAAGCAATTAATCGCAAATTTT----TTAAGGTAAA
17073277 ATGAAGCAATTAA
1 ATGAAGCAATTAA
17073290 ACAAAAACAA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
33 19 0.49
34 1 0.03
36 4 0.10
37 15 0.38
ACGTcount: A:0.52, C:0.10, G:0.12, T:0.27
Consensus pattern (34 bp):
ATGAAGCAATTAATCGCAAATTTTTTAAGGTAAA
Found at i:17088675 original size:23 final size:23
Alignment explanation
Indices: 17088645--17088889 Score: 248
Period size: 23 Copynumber: 10.5 Consensus size: 23
17088635 ACACTAGCGC
*
17088645 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGTTTAGCACTGTGT-GT
17088668 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG-T-TTAGCACTGTGTGT
*
17088693 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
*
17088716 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGTTTAGCACTGTGT-GT
17088739 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG-T-TTAGCACTGTGTGT
* *
17088764 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
* * *
17088787 GCTCTCTGATTAGTACTTTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
*
17088810 ACTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
* *
17088833 GCTCTCTGTTGCCCAGCACT-TATGT
1 GCTCTCTGTT---TAGCACTGTGTGT
* *
17088858 GCTCTCTG-TTAGTACTTTG-GT
1 GCTCTCTGTTTAGCACTGTGTGT
*
17088879 ACTCTCTGTTT
1 GCTCTCTGTTT
17088890 GTTCCGCATA
Statistics
Matches: 191, Mismatches: 19, Indels: 25
0.81 0.08 0.11
Matches are distributed among these distances:
21 14 0.07
22 6 0.03
23 110 0.58
24 3 0.02
25 46 0.24
26 12 0.06
ACGTcount: A:0.11, C:0.24, G:0.22, T:0.43
Consensus pattern (23 bp):
GCTCTCTGTTTAGCACTGTGTGT
Found at i:17088718 original size:48 final size:46
Alignment explanation
Indices: 17088645--17088840 Score: 252
Period size: 48 Copynumber: 4.2 Consensus size: 46
17088635 ACACTAGCGC
* *
17088645 GCTCTCTGTTTAGCAC-GTCTCGTGCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGT-GTGCTCTCTG-T-TTAGCACTGTGTGT
*
17088693 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACTGTGT-GT
* *
17088739 GCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTG--ATTAGCACTGTGTGTGCTCTCTGTTTAGCACTGTGTGT
* * *
17088787 GCTCTCTGATTAGTACTTTGTGTACTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACTGTGTGT
17088833 GCTCTCTG
1 GCTCTCTG
17088841 TTGCCCAGCA
Statistics
Matches: 132, Mismatches: 11, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
45 3 0.02
46 58 0.44
47 1 0.01
48 65 0.49
49 5 0.04
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.42
Consensus pattern (46 bp):
GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACTGTGTGT
Found at i:17088733 original size:71 final size:71
Alignment explanation
Indices: 17088645--17088840 Score: 310
Period size: 71 Copynumber: 2.8 Consensus size: 71
17088635 ACACTAGCGC
17088645 GCTCTCTGTTTAGCACGTCTCGTGCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACT
1 GCTCTCTGTTTAGCACGTCTCGTGCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACT
17088710 GTGTGT
66 GTGTGT
17088716 GCTCTCTGTTTAGCACGTCTCGTGCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACT
1 GCTCTCTGTTTAGCACGTCTCGTGCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACT
*
17088781 TTGTGT
66 GTGTGT
* * *
17088787 GCTCTCTGATTAGTAC-T-TTGTGTACTCTCTG-T-TTAGCACTGTGTGTGCTCTCTG
1 GCTCTCTGTTTAGCACGTCTCGTG--CTCTCTGTTATTAGCACTGTGTGTGCTCTCTG
17088841 TTGCCCAGCA
Statistics
Matches: 119, Mismatches: 4, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
69 26 0.22
70 2 0.02
71 91 0.76
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.42
Consensus pattern (71 bp):
GCTCTCTGTTTAGCACGTCTCGTGCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACT
GTGTGT
Found at i:17088859 original size:71 final size:69
Alignment explanation
Indices: 17088669--17088888 Score: 281
Period size: 71 Copynumber: 3.1 Consensus size: 69
17088659 ACGTCTCGTG
*
17088669 CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACGT
1 CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACT-TGTGTGCTCTCTG-TTAGTAC-T
*
17088734 CTCGTG--
63 -TTGTGTA
17088740 CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGTACTT
1 CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCAC-TTGTGTGCTCTCTG-TTAGTACTT
17088805 TGTGTA
64 TGTGTA
*
17088811 CTCTCTG-T-TTAGCACTGTGTGTGCTCTCTG-TTGCCCAGCACTTATGTGCTCTCTGTTAGTAC
1 CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATT----AGCACTTGTGTGCTCTCTGTTAGTAC
17088873 TTTG-GTA
62 TTTGTGTA
17088880 CTCTCTGTT
1 CTCTCTGTT
17088889 TGTTCCGCAT
Statistics
Matches: 137, Mismatches: 4, Indels: 17
0.87 0.03 0.11
Matches are distributed among these distances:
68 2 0.01
69 36 0.26
70 14 0.10
71 79 0.58
72 6 0.04
ACGTcount: A:0.12, C:0.23, G:0.22, T:0.43
Consensus pattern (69 bp):
CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTGTGTGCTCTCTGTTAGTACTTTG
TGTA
Found at i:17101880 original size:13 final size:13
Alignment explanation
Indices: 17101864--17101888 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17101854 TCAATCTTGA
17101864 AGATCAAAAAAGG
1 AGATCAAAAAAGG
17101877 AGATCAAAAAAG
1 AGATCAAAAAAG
17101889 AAAGCTATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.08, G:0.20, T:0.08
Consensus pattern (13 bp):
AGATCAAAAAAGG
Found at i:17102127 original size:31 final size:31
Alignment explanation
Indices: 17102058--17102131 Score: 89
Period size: 30 Copynumber: 2.4 Consensus size: 31
17102048 AAACTTTTCA
* ** *
17102058 AATAATTTAGTGATTACCTATATAACTTTTT
1 AATAATTTAATGATTACAAATATAAATTTTT
17102089 AA-AATTTAATGATTA-AAATATAAATTTATT
1 AATAATTTAATGATTACAAATATAAATTT-TT
17102119 AATAATTTAATGA
1 AATAATTTAATGA
17102132 CCATATAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 9 0.24
30 16 0.43
31 12 0.32
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (31 bp):
AATAATTTAATGATTACAAATATAAATTTTT
Found at i:17117782 original size:20 final size:20
Alignment explanation
Indices: 17117757--17117805 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
17117747 TTTTCTTTCT
17117757 ATTCTTTAACAGTAATATTA
1 ATTCTTTAACAGTAATATTA
17117777 ATTCTTTAACAGTAATATTA
1 ATTCTTTAACAGTAATATTA
*
17117797 ATCCTTTAA
1 ATTCTTTAA
17117806 TTTTTATCTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.39, C:0.12, G:0.04, T:0.45
Consensus pattern (20 bp):
ATTCTTTAACAGTAATATTA
Found at i:17120970 original size:18 final size:18
Alignment explanation
Indices: 17120947--17120986 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
17120937 TTTGTTCATG
17120947 GGTCGAGTTATTCGTTCA
1 GGTCGAGTTATTCGTTCA
17120965 GGTCGAGTTATTCGTTCA
1 GGTCGAGTTATTCGTTCA
17120983 GGTC
1 GGTC
17120987 TTAAAGTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.15, C:0.17, G:0.30, T:0.38
Consensus pattern (18 bp):
GGTCGAGTTATTCGTTCA
Found at i:17128697 original size:3 final size:3
Alignment explanation
Indices: 17128691--17128720 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
17128681 TCCACCCTCC
17128691 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
17128721 CCTATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:17129728 original size:44 final size:45
Alignment explanation
Indices: 17129669--17129760 Score: 132
Period size: 44 Copynumber: 2.1 Consensus size: 45
17129659 CATTTTGACC
*
17129669 TATTAAATATTTAACTAAATTACATAATATTTATTATTAATTATT
1 TATTAAATATTTAACTAAATTACATAATATTTATTATCAATTATT
* * * *
17129714 TATTTAAT-TTTAACTAAATTACATAGTGTTTATTGTCAATTATT
1 TATTAAATATTTAACTAAATTACATAATATTTATTATCAATTATT
17129758 TAT
1 TAT
17129761 ATGTAATACG
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 35 0.83
45 7 0.17
ACGTcount: A:0.39, C:0.05, G:0.03, T:0.52
Consensus pattern (45 bp):
TATTAAATATTTAACTAAATTACATAATATTTATTATCAATTATT
Found at i:17134436 original size:59 final size:58
Alignment explanation
Indices: 17134309--17134447 Score: 165
Period size: 58 Copynumber: 2.4 Consensus size: 58
17134299 TTAGATACCC
* * * * * *
17134309 GGAGGCAAAATGGTAATTTTAGTTGGAATTGGGTTAAAAATGGGATTTTTAGAAGTTT
1 GGAGGCAAAATGGTAATTTTTGGTGAAATTGGATTAAAAATGGGATTTTGAGAAGTTA
*
17134367 GGGGGCAAAATGGTAATTTTTGGTGAAATTGAGATTAAAAATGGGATTTTG-GAAAGTTA
1 GGAGGCAAAATGGTAATTTTTGGTGAAATTG-GATTAAAAATGGGATTTTGAG-AAGTTA
* *
17134426 GGAGGTAAAAT-CTAATTTTTGG
1 GGAGGCAAAATGGTAATTTTTGG
17134448 AAAGTTTGGG
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
58 38 0.55
59 31 0.45
ACGTcount: A:0.34, C:0.02, G:0.29, T:0.35
Consensus pattern (58 bp):
GGAGGCAAAATGGTAATTTTTGGTGAAATTGGATTAAAAATGGGATTTTGAGAAGTTA
Found at i:17134445 original size:29 final size:29
Alignment explanation
Indices: 17134413--17134596 Score: 171
Period size: 30 Copynumber: 6.1 Consensus size: 29
17134403 AAAAATGGGA
* *
17134413 TTTTGGAAAGTTAGGAGGT-AAAATCTAAT
1 TTTTGGAAAGTTTGG-GGTCAAAATGTAAT
17134442 TTTTGGAAAGTTTGGGGGTCAAAATGTAAT
1 TTTTGGAAAGTTT-GGGGTCAAAATGTAAT
*
17134472 TTTTTGAAAGTGTTGGGGTCAAAATGTAAT
1 TTTTGGAAAGT-TTGGGGTCAAAATGTAAT
* *
17134502 TTTTAGG-AAGTTTTGAGGTTAAAAATGT-AT
1 TTTT-GGAAAG-TTTG-GGGTCAAAATGTAAT
17134532 TTTTAGG-AAGTTTTGGGGTCAAAAATGTAAT
1 TTTT-GGAAAG-TTTGGGGTC-AAAATGTAAT
* *
17134563 TTTTAGG-AAGTTTCGGGGTCAAAATATGAT
1 TTTT-GGAAAGTTT-GGGGTCAAAATGTAAT
17134593 TTTT
1 TTTT
17134597 AAACAATTCA
Statistics
Matches: 136, Mismatches: 10, Indels: 17
0.83 0.06 0.10
Matches are distributed among these distances:
29 18 0.13
30 86 0.63
31 32 0.24
ACGTcount: A:0.32, C:0.03, G:0.26, T:0.40
Consensus pattern (29 bp):
TTTTGGAAAGTTTGGGGTCAAAATGTAAT
Found at i:17134488 original size:31 final size:30
Alignment explanation
Indices: 17134432--17134597 Score: 185
Period size: 30 Copynumber: 5.5 Consensus size: 30
17134422 GTTAGGAGGT
*
17134432 AAAATCTAATTTTT-GGAAAGTTTGGGGGTC
1 AAAATGTAATTTTTAGG-AAGTTTGGGGGTC
* *
17134462 AAAATGTAATTTTTTGAAAGTGTT-GGGGTC
1 AAAATGTAATTTTTAGGAAGT-TTGGGGGTC
* * *
17134492 AAAATGTAATTTTTAGGAAGTTTTGAGGTTA
1 AAAATGTAATTTTTAGGAAG-TTTGGGGGTC
*
17134523 AAAATGT-ATTTTTAGGAAGTTTTGGGGTC
1 AAAATGTAATTTTTAGGAAGTTTGGGGGTC
*
17134552 AAAAATGTAATTTTTAGGAAGTTTCGGGGTC
1 -AAAATGTAATTTTTAGGAAGTTTGGGGGTC
* *
17134583 AAAATATGATTTTTA
1 AAAATGTAATTTTTA
17134598 AACAATTCAG
Statistics
Matches: 116, Mismatches: 14, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
29 6 0.05
30 75 0.65
31 35 0.30
ACGTcount: A:0.33, C:0.04, G:0.24, T:0.40
Consensus pattern (30 bp):
AAAATGTAATTTTTAGGAAGTTTGGGGGTC
Found at i:17134564 original size:61 final size:60
Alignment explanation
Indices: 17134339--17134597 Score: 205
Period size: 61 Copynumber: 4.3 Consensus size: 60
17134329 AGTTGGAATT
* * * *
17134339 GGGTTAAAAATGGGATTTTTAG-AAGT-TTGGGGGCAAAATGGTAATTTTTGGTGAA--ATTG
1 GGGTTAAAAAT-GTATTTTTAGAAAGTGTTGGGGTCAAAAT-GTAATTTTTAG-GAAGTTTTG
* * * * * *
17134398 AGATTAAAAATGGGA-TTTTGGAAAGT-TAGGAGGT-AAAATCTAATTTTT-GGAAAG-TTTG
1 GGGTTAAAAAT-GTATTTTTAGAAAGTGTTGG-GGTCAAAATGTAATTTTTAGG-AAGTTTTG
* * *
17134456 GGGGTCAAAATGTAATTTTTTGAAAGTGTTGGGGTCAAAATGTAATTTTTAGGAAGTTTTG
1 GGGTTAAAAATGT-ATTTTTAGAAAGTGTTGGGGTCAAAATGTAATTTTTAGGAAGTTTTG
* * * *
17134517 AGGTTAAAAATGTATTTTTAGGAAGTTTTGGGGTCAAAAATGTAATTTTTAGGAAGTTTCG
1 GGGTTAAAAATGTATTTTTAGAAAGTGTTGGGGTC-AAAATGTAATTTTTAGGAAGTTTTG
*
17134578 GGGTCAAAATATG-ATTTTTA
1 GGGTTAAAA-ATGTATTTTTA
17134598 AACAATTCAG
Statistics
Matches: 164, Mismatches: 24, Indels: 22
0.78 0.11 0.10
Matches are distributed among these distances:
56 1 0.01
57 4 0.02
58 24 0.15
59 38 0.23
60 40 0.24
61 54 0.33
62 3 0.02
ACGTcount: A:0.33, C:0.03, G:0.27, T:0.37
Consensus pattern (60 bp):
GGGTTAAAAATGTATTTTTAGAAAGTGTTGGGGTCAAAATGTAATTTTTAGGAAGTTTTG
Found at i:17135732 original size:18 final size:18
Alignment explanation
Indices: 17135709--17135743 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
17135699 ATTCTTTTTT
*
17135709 TTATTTAATAATTATTAA
1 TTATTTAATAAATATTAA
17135727 TTATTTAATAAATATTA
1 TTATTTAATAAATATTA
17135744 TTAATAAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTATTTAATAAATATTAA
Found at i:17136483 original size:6 final size:6
Alignment explanation
Indices: 17136469--17136525 Score: 55
Period size: 6 Copynumber: 9.8 Consensus size: 6
17136459 GACTTCTTAA
* * * *
17136469 TTAATT TTAAAT TTAAAT TCAAA- TTAAAT TTAAAC TT-AAT TAAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
17136515 TTAAAC TTAAA
1 TTAAAT TTAAA
17136526 AGGAAAGTTT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
5 7 0.17
6 34 0.83
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (6 bp):
TTAAAT
Found at i:17136487 original size:17 final size:17
Alignment explanation
Indices: 17136469--17136524 Score: 69
Period size: 17 Copynumber: 3.2 Consensus size: 17
17136459 GACTTCTTAA
17136469 TTAATTTTAAATTTAAA-
1 TTAA-TTTAAATTTAAAC
*
17136486 TTCAAATTAAATTTAAAC
1 TT-AATTTAAATTTAAAC
*
17136504 TTAATTAAAATTTAAAC
1 TTAATTTAAATTTAAAC
17136521 TTAA
1 TTAA
17136525 AAGGAAAGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
17 30 0.88
18 4 0.12
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (17 bp):
TTAATTTAAATTTAAAC
Found at i:17136518 original size:23 final size:23
Alignment explanation
Indices: 17136467--17136525 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
17136457 TGGACTTCTT
* * *
17136467 AATTAATTTTAAATTTAAATTCA
1 AATTAAATTTAAACTTAAATTAA
17136490 AATTAAATTTAAACTT-AATTAA
1 AATTAAATTTAAACTTAAATTAA
*
17136512 AATTTAAACTTAAA
1 AA-TTAAATTTAAA
17136526 AGGAAAGTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 7 0.23
23 24 0.77
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (23 bp):
AATTAAATTTAAACTTAAATTAA
Found at i:17138829 original size:2 final size:2
Alignment explanation
Indices: 17138824--17138853 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
17138814 ATAATATTAA
17138824 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
17138854 TAATTTTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17140235 original size:25 final size:26
Alignment explanation
Indices: 17140207--17140255 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
17140197 TTTAAAAAAA
*
17140207 TTCAATTTTAAAA-TTTTAGGTCATC
1 TTCAATTTTAAAAGTTTCAGGTCATC
17140232 TTCAATTTTAAAAGTTTCAGGTCA
1 TTCAATTTTAAAAGTTTCAGGTCA
17140256 CATATTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (26 bp):
TTCAATTTTAAAAGTTTCAGGTCATC
Done.