Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015061.1 Kokia drynarioides strain JFW-HI SEQ_130105, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 399537
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 280 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:169 original size:7 final size:7
Alignment explanation
Indices: 157--194 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
147 CCTTCTTCTC
157 CTTCTTT
1 CTTCTTT
164 CTTCTTT
1 CTTCTTT
171 CTTTCTTT
1 C-TTCTTT
179 C-TCTTT
1 CTTCTTT
*
185 TTTCTTT
1 CTTCTTT
192 CTT
1 CTT
195 TTCTTCATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
6 5 0.19
7 15 0.56
8 7 0.26
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (7 bp):
CTTCTTT
Found at i:172 original size:4 final size:4
Alignment explanation
Indices: 158--195 Score: 51
Period size: 4 Copynumber: 9.5 Consensus size: 4
148 CTTCTTCTCC
*
158 TTCT TTC- TTCT TTCT TTCT TTCT CTTTT TTCT TTCT TT
1 TTCT TTCT TTCT TTCT TTCT TTCT -TTCT TTCT TTCT TT
196 TCTTCATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
3 3 0.10
4 24 0.80
5 3 0.10
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTCT
Found at i:183 original size:17 final size:16
Alignment explanation
Indices: 148--200 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 16
138 CCTTCTTCCC
*
148 CTTCTTCTCCTTC-TTT
1 CTTCTT-TCTTTCTTTT
164 CTTCTTTCTTTCTTTCT
1 CTTCTTTCTTTCTTT-T
*
181 CTTTTTTCTTTCTTTT
1 CTTCTTTCTTTCTTTT
197 CTTC
1 CTTC
201 ATTTTTCGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
15 5 0.16
16 12 0.38
17 15 0.47
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (16 bp):
CTTCTTTCTTTCTTTT
Found at i:1516 original size:12 final size:14
Alignment explanation
Indices: 1487--1530 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
1477 CATAAGTTAA
* *
1487 TTTAATATTTAATT
1 TTTAATATTAAAAT
*
1501 TTTTA-ATTAAAAT
1 TTTAATATTAAAAT
1514 TTTAATATTAAAAT
1 TTTAATATTAAAAT
1528 TTT
1 TTT
1531 CTTTTATCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTAATATTAAAAT
Found at i:9007 original size:21 final size:21
Alignment explanation
Indices: 8960--9018 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
8950 CCTTAAATAT
* *
8960 TAAATTTTGAATATTAAACTC
1 TAAACTTTGAATCTTAAACTC
8981 TAAACTTTGAATCTTAAAC-C
1 TAAACTTTGAATCTTAAACTC
* *
9001 TTGAACTTTCAATCTTAA
1 -TAAACTTTGAATCTTAA
9019 TTTCAAAGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 1 0.03
21 32 0.97
ACGTcount: A:0.39, C:0.15, G:0.05, T:0.41
Consensus pattern (21 bp):
TAAACTTTGAATCTTAAACTC
Found at i:16007 original size:20 final size:18
Alignment explanation
Indices: 15965--16007 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
15955 AGGAAAGCAC
15965 TATATTTAAATTTTATAT
1 TATATTTAAATTTTATAT
*
15983 AATATTTAAATTATTAATAT
1 TATATTTAAATT-TT-ATAT
16003 TATAT
1 TATAT
16008 AAAATCTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 11 0.52
19 2 0.10
20 8 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TATATTTAAATTTTATAT
Found at i:22244 original size:53 final size:53
Alignment explanation
Indices: 22167--22302 Score: 191
Period size: 53 Copynumber: 2.6 Consensus size: 53
22157 TCACATTTGT
* * ** *
22167 TAACTCACAATGACACAAATTCATCGGACCTTTAATCTGTAATAGGATTCATA
1 TAACTCACGATGACACAAAGTCATCAAACCTTTAATCCGTAATAGGATTCATA
* *
22220 TAACTCACGATGACACAGAGTCATCAAACCTTTAATCCGTAATAGGATTCGTA
1 TAACTCACGATGACACAAAGTCATCAAACCTTTAATCCGTAATAGGATTCATA
* *
22273 TAACTCATGATGACACATAGTCATCAAACC
1 TAACTCACGATGACACAAAGTCATCAAACC
22303 CTTTTGCATT
Statistics
Matches: 74, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
53 74 1.00
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (53 bp):
TAACTCACGATGACACAAAGTCATCAAACCTTTAATCCGTAATAGGATTCATA
Found at i:23216 original size:20 final size:22
Alignment explanation
Indices: 23169--23216 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
23159 TCATAATTAG
*
23169 TTTAGTTAATCACTTGTTTAAC
1 TTTAATTAATCACTTGTTTAAC
23191 TTTAATTAATC-CTT-TTT-AC
1 TTTAATTAATCACTTGTTTAAC
23210 TTCTAAT
1 TT-TAAT
23217 ATTTCTCATG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 4 0.17
20 7 0.29
21 3 0.12
22 10 0.42
ACGTcount: A:0.27, C:0.15, G:0.04, T:0.54
Consensus pattern (22 bp):
TTTAATTAATCACTTGTTTAAC
Found at i:25770 original size:2 final size:2
Alignment explanation
Indices: 25765--25796 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
25755 GATTTATATA
*
25765 TG TG TG TG TG TG TG TG TG TG TT TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
25797 GATATTATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.47, T:0.53
Consensus pattern (2 bp):
TG
Found at i:29821 original size:30 final size:30
Alignment explanation
Indices: 29785--29846 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
29775 GTTTGCCCTT
29785 TGATGATGGGAAAGTTCCTCATGTTGTATC
1 TGATGATGGGAAAGTTCCTCATGTTGTATC
29815 TGATGATGGGAAAGTTCCTCATGTTGTATC
1 TGATGATGGGAAAGTTCCTCATGTTGTATC
29845 TG
1 TG
29847 TTGTTTATGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.23, C:0.13, G:0.27, T:0.37
Consensus pattern (30 bp):
TGATGATGGGAAAGTTCCTCATGTTGTATC
Found at i:31940 original size:16 final size:15
Alignment explanation
Indices: 31882--31930 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
31872 TAAACAAACC
*
31882 TATTAATTATAAT-T
1 TATTAATTAAAATAT
*
31896 TATTAAATAAAAATAT
1 TATT-AATTAAAATAT
31912 TATTAATTAAAATAT
1 TATTAATTAAAATAT
31927 TATT
1 TATT
31931 TCAATAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
14 4 0.13
15 21 0.70
16 5 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TATTAATTAAAATAT
Found at i:32021 original size:43 final size:44
Alignment explanation
Indices: 31939--32024 Score: 156
Period size: 43 Copynumber: 2.0 Consensus size: 44
31929 TTTCAATAAA
31939 ATTTTTAAATTTCATATAAAAAAATCTATTAATCATATTTTATG
1 ATTTTTAAATTTCATATAAAAAAATCTATTAATCATATTTTATG
*
31983 ATTTTTAAATTTCATAT-AAAAAATCTATTAATCGTATTTTAT
1 ATTTTTAAATTTCATATAAAAAAATCTATTAATCATATTTTAT
32025 TAAACGAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
43 24 0.59
44 17 0.41
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.49
Consensus pattern (44 bp):
ATTTTTAAATTTCATATAAAAAAATCTATTAATCATATTTTATG
Found at i:35960 original size:24 final size:23
Alignment explanation
Indices: 35912--35960 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 23
35902 ATTAAATTAA
*
35912 TAAATTTTGTAAATGTTTAGGGT
1 TAAATTTTGTAAATGTTTAGAGT
*
35935 TAAATTTATTTAAAT-TTCTAGAGT
1 TAAATTT-TGTAAATGTT-TAGAGT
35959 TA
1 TA
35961 GATCTAATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.35, C:0.02, G:0.14, T:0.49
Consensus pattern (23 bp):
TAAATTTTGTAAATGTTTAGAGT
Found at i:41261 original size:20 final size:20
Alignment explanation
Indices: 41223--41262 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
41213 CAAATTTGAA
* *
41223 ATATTTTTGCATTTTCCTAT
1 ATATTTTTGCAATTCCCTAT
*
41243 ATATTTTTTCAATTCCCTAT
1 ATATTTTTGCAATTCCCTAT
41263 TGGAACCGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.17, G:0.03, T:0.57
Consensus pattern (20 bp):
ATATTTTTGCAATTCCCTAT
Found at i:45327 original size:29 final size:30
Alignment explanation
Indices: 45291--45354 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 30
45281 ACTTATTTCA
* *
45291 TTGTTAATTTTGTTATTAT-TTAGAGGCAT
1 TTGTTAATTTTATTACTATATTAGAGGCAT
45320 TTGTTAATTTTATTACTATATTAGAGGCAT
1 TTGTTAATTTTATTACTATATTAGAGGCAT
45350 TTGTT
1 TTGTT
45355 TGTTAAGTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 17 0.53
30 15 0.47
ACGTcount: A:0.25, C:0.05, G:0.16, T:0.55
Consensus pattern (30 bp):
TTGTTAATTTTATTACTATATTAGAGGCAT
Found at i:48755 original size:20 final size:20
Alignment explanation
Indices: 48732--48775 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
48722 CATAAAATTA
*
48732 TAAACA-ATTAGAAAAAATAG
1 TAAACATATT-GAAAAAATAC
*
48752 TAAACATATTTAAAAAATAC
1 TAAACATATTGAAAAAATAC
48772 TAAA
1 TAAA
48776 AATAATAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 18 0.86
21 3 0.14
ACGTcount: A:0.64, C:0.07, G:0.05, T:0.25
Consensus pattern (20 bp):
TAAACATATTGAAAAAATAC
Found at i:48902 original size:29 final size:29
Alignment explanation
Indices: 48818--48915 Score: 81
Period size: 29 Copynumber: 3.2 Consensus size: 29
48808 TACAAATTAT
48818 AAAATTAATAAAAACACATTTAAAATAT-TTAA
1 AAAATT-ATAAAAA-A-ATTTAAAA-ATCTTAA
** ** * *
48850 AATTTTATAAAAACGTATACAAATCTTAA
1 AAAATTATAAAAAAATTTAAAAATCTTAA
*
48879 AAAATTATAAAAAAATTTAAAAATCATAA
1 AAAATTATAAAAAAATTTAAAAATCTTAA
48908 AAATATTA
1 AAA-ATTA
48916 AATATTTTTT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
28 2 0.04
29 34 0.67
30 4 0.08
31 7 0.14
32 4 0.08
ACGTcount: A:0.61, C:0.06, G:0.01, T:0.32
Consensus pattern (29 bp):
AAAATTATAAAAAAATTTAAAAATCTTAA
Found at i:48917 original size:9 final size:9
Alignment explanation
Indices: 48889--49004 Score: 53
Period size: 9 Copynumber: 12.7 Consensus size: 9
48879 AAAATTATAA
48889 AAAAAT-TT
1 AAAAATATT
48897 AAAAATCA-T
1 AAAAAT-ATT
48906 AAAAATATT
1 AAAAATATT
*
48915 AAATAT-TT
1 AAAAATATT
***
48923 TTTAATATT
1 AAAAATATT
48932 AAAAATATT
1 AAAAATATT
*
48941 AAAATTGA-T
1 AAAAAT-ATT
* *
48950 ATAAATTTAT
1 AAAAATAT-T
48960 AAAAATTATT
1 AAAAA-TATT
*
48970 AAAAATCATG
1 AAAAAT-ATT
48980 AAAAAT-TAT
1 AAAAATAT-T
*
48989 AAATATTATT
1 AAA-AATATT
48999 AAAAAT
1 AAAAAT
49005 CTGATAAATT
Statistics
Matches: 78, Mismatches: 18, Indels: 23
0.66 0.15 0.19
Matches are distributed among these distances:
8 12 0.15
9 37 0.47
10 26 0.33
11 3 0.04
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (9 bp):
AAAAATATT
Found at i:48965 original size:10 final size:9
Alignment explanation
Indices: 48931--49096 Score: 74
Period size: 10 Copynumber: 17.6 Consensus size: 9
48921 TTTTTAATAT
48931 TAAAAA-TA
1 TAAAAATTA
*
48939 TTAAAATTGA
1 TAAAAATT-A
*
48949 TATAAATTTA
1 TA-AAAATTA
48959 TAAAAATTA
1 TAAAAATTA
*
48968 TTAAAAATCA
1 -TAAAAATTA
48978 TGAAAAATTA
1 T-AAAAATTA
*
48988 TAAATATTA
1 TAAAAATTA
48997 TTAAAAATCTGA
1 -TAAAAAT-T-A
*
49009 T--AAATTC
1 TAAAAATTA
*
49016 TAGTAAATTA
1 TA-AAAATTA
49026 TTAAAAAATTA
1 -T-AAAAATTA
*
49037 T-GAAATTA
1 TAAAAATTA
*
49045 TTAAAATATATT
1 -TAAAA-AT-TA
*
49057 TAAAATTTTA
1 TAAAA-ATTA
49067 TAAAAATTA
1 TAAAAATTA
49076 TAAAAA-TA
1 TAAAAATTA
*
49084 -ATAAATTA
1 TAAAAATTA
49092 TAAAA
1 TAAAA
49097 TGTAACACCT
Statistics
Matches: 120, Mismatches: 19, Indels: 37
0.68 0.11 0.21
Matches are distributed among these distances:
7 5 0.04
8 16 0.13
9 32 0.27
10 41 0.34
11 23 0.19
12 3 0.03
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (9 bp):
TAAAAATTA
Found at i:48969 original size:29 final size:29
Alignment explanation
Indices: 48931--49082 Score: 109
Period size: 29 Copynumber: 5.2 Consensus size: 29
48921 TTTTTAATAT
* * *
48931 TAAAAA-TATTAAAATTGAT-ATAAATTTA
1 TAAAAATTATTAAAAATCATGA-AAAATTA
48959 TAAAAATTATTAAAAATCATGAAAAATTA
1 TAAAAATTATTAAAAATCATGAAAAATTA
* * *
48988 TAAATATTATTAAAAATC-TGATAAATTC
1 TAAAAATTATTAAAAATCATGAAAAATTA
* *
49016 TAGTAAATTATTAAAAAATTATG--AAATTA
1 TA-AAAATTATT-AAAAATCATGAAAAATTA
* * *
49045 TTAAAATATATTTAAAATTTTAT-AAAAATTA
1 TAAAAAT-TA-TTAAAA-ATCATGAAAAATTA
49076 TAAAAAT
1 TAAAAAT
49083 AATAAATTAT
Statistics
Matches: 100, Mismatches: 14, Indels: 17
0.76 0.11 0.13
Matches are distributed among these distances:
28 20 0.20
29 53 0.53
30 13 0.13
31 14 0.14
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (29 bp):
TAAAAATTATTAAAAATCATGAAAAATTA
Found at i:49042 original size:19 final size:19
Alignment explanation
Indices: 49020--49097 Score: 76
Period size: 19 Copynumber: 4.2 Consensus size: 19
49010 AAATTCTAGT
*
49020 AAATTATTAAAAAATTATG
1 AAATTATTAAAAAATTATA
49039 AAATTATTAAAATATATT-TA
1 AAATTATTAAAA-A-ATTATA
49059 AAATT-TTATAAAAATTATA
1 AAATTATTA-AAAAATTATA
*
49078 AAA--A-TAATAAATTATA
1 AAATTATTAAAAAATTATA
49094 AAAT
1 AAAT
49098 GTAACACCTC
Statistics
Matches: 51, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
16 12 0.24
17 2 0.04
18 3 0.06
19 21 0.41
20 10 0.20
21 3 0.06
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (19 bp):
AAATTATTAAAAAATTATA
Found at i:49091 original size:16 final size:15
Alignment explanation
Indices: 49066--49096 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
49056 TTAAAATTTT
49066 ATAAAAATTATAAAA
1 ATAAAAATTATAAAA
49081 ATAATAAATTATAAAA
1 ATAA-AAATTATAAAA
49097 TGTAACACCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
ATAAAAATTATAAAA
Found at i:49208 original size:18 final size:18
Alignment explanation
Indices: 49185--49222 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
49175 ATTTAAAATC
49185 TAAAAAAATTGAATTACT
1 TAAAAAAATTGAATTACT
49203 TAAAAAAATTGAATTACT
1 TAAAAAAATTGAATTACT
49221 TA
1 TA
49223 GAAATTAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.34
Consensus pattern (18 bp):
TAAAAAAATTGAATTACT
Found at i:53316 original size:20 final size:19
Alignment explanation
Indices: 53293--53453 Score: 60
Period size: 18 Copynumber: 8.1 Consensus size: 19
53283 TTTTTATAAG
53293 TTTATATGAATTTTAATATT
1 TTTATAT-AATTTTAATATT
* **
53313 TTTA-ATAATTCTTTATAAA
1 TTTATATAATT-TTAATATT
*
53332 TTT-TATGATTTTAATACGTT
1 TTTATATAATTTTAATA--TT
* *
53352 TTTATAAAATTTAAAATATGT
1 TTTATATAATTT-TAATAT-T
* * * *
53373 TTATAATGTTATTTATTATAATA
1 TT-T-ATATAATTT-TAAT-ATT
*
53396 TTTATATATTTTTAAT-TCT
1 TTTATATAATTTTAATAT-T
* **
53415 TTT-TATAATTTTTATAAG
1 TTTATATAATTTTAATATT
53433 TTTATATCAATTTTAATATT
1 TTTATAT-AATTTTAATATT
53453 T
1 T
53454 ATTAATATTT
Statistics
Matches: 99, Mismatches: 28, Indels: 28
0.64 0.18 0.18
Matches are distributed among these distances:
18 23 0.23
19 21 0.21
20 21 0.21
21 15 0.15
22 6 0.06
23 11 0.11
24 2 0.02
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.58
Consensus pattern (19 bp):
TTTATATAATTTTAATATT
Found at i:53333 original size:29 final size:28
Alignment explanation
Indices: 53275--53428 Score: 82
Period size: 28 Copynumber: 5.2 Consensus size: 28
53265 TTCTATGATT
* * *
53275 TTTTTATATTTTT-ATAAGTTTATATGAA
1 TTTTAATATTTTTAATAA-TTTTTATAAA
53303 TTTTAATATTTTTAATAATTCTTTATAAA
1 TTTTAATATTTTTAATAATT-TTTATAAA
*
53332 TTTT-ATGA-TTTTAATACGTTTTTATAAAA
1 TTTTAAT-ATTTTTAATA-ATTTTTAT-AAA
* *
53361 TTTAAAATATGTTTATAAT-GTTATTTATTATAA
1 TTT-TAATAT-TTT-TAATAATT-TTTA-TA-AA
** *
53394 TATTTATATATTTTTAATTCTTTTTATAAT
1 T-TTTA-ATATTTTTAATAATTTTTATAAA
53424 TTTTA
1 TTTTA
53429 TAAGTTTATA
Statistics
Matches: 102, Mismatches: 8, Indels: 31
0.72 0.06 0.22
Matches are distributed among these distances:
28 29 0.28
29 27 0.26
30 3 0.03
31 7 0.07
32 16 0.16
33 14 0.14
34 6 0.06
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (28 bp):
TTTTAATATTTTTAATAATTTTTATAAA
Found at i:53427 original size:10 final size:9
Alignment explanation
Indices: 53275--53490 Score: 81
Period size: 10 Copynumber: 23.6 Consensus size: 9
53265 TTCTATGATT
53275 TTTTTAT-A
1 TTTTTATAA
53283 TTTTTATAA
1 TTTTTATAA
*
53292 GTTTATATGAA
1 -TTTTTAT-AA
*
53303 TTTTAAT-A
1 TTTTTATAA
53311 TTTTTAATAA
1 TTTTT-ATAA
53321 TTCTTTATAA
1 TT-TTTATAA
* *
53331 ATTTTATGA
1 TTTTTATAA
* *
53340 TTTTAATACG
1 TTTTTATA-A
53350 TTTTTATAA
1 TTTTTATAA
** *
53359 AATTTAAAA
1 TTTTTATAA
53368 TATGTTTATAA
1 T-T-TTTATAA
*
53379 -TGTTAT--
1 TTTTTATAA
*
53385 TTATTATAA
1 TTTTTATAA
*
53394 TATTTATATA
1 TTTTTATA-A
**
53404 TTTTTAATTC
1 TTTTT-ATAA
53414 TTTTTATAA
1 TTTTTATAA
53423 TTTTTATAA
1 TTTTTATAA
*
53432 GTTTATATCAA
1 -TTTTTAT-AA
*
53443 TTTTAAT-A
1 TTTTTATAA
*
53451 TTTAT-TAA
1 TTTTTATAA
*
53459 TATTTAT--
1 TTTTTATAA
*
53466 TTATTTATGA
1 TT-TTTATAA
53476 TTTTTAATAA
1 TTTTT-ATAA
53486 TTTTT
1 TTTTT
53491 TATGGAAAAA
Statistics
Matches: 150, Mismatches: 36, Indels: 42
0.66 0.16 0.18
Matches are distributed among these distances:
7 7 0.05
8 29 0.19
9 42 0.28
10 57 0.38
11 15 0.10
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (9 bp):
TTTTTATAA
Found at i:57167 original size:40 final size:40
Alignment explanation
Indices: 57092--57167 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 40
57082 GAAATAAATA
*
57092 AAAAGAAATTATGAAAATTATAACAAATTATAATAATGCT
1 AAAAGAAATTATGAAAATTATAACAAAATATAATAATGCT
57132 AAAAGAATATTTAT-AAAAGTTATAA-AAAATA-AATAA
1 AAAAGAA-A-TTATGAAAA-TTATAACAAAATATAATAA
57168 AAATATTATA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
40 12 0.38
41 10 0.31
42 10 0.31
ACGTcount: A:0.62, C:0.03, G:0.07, T:0.29
Consensus pattern (40 bp):
AAAAGAAATTATGAAAATTATAACAAAATATAATAATGCT
Found at i:57784 original size:15 final size:15
Alignment explanation
Indices: 57739--57786 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
57729 ATTGATATAT
*
57739 TTATAAAAAAAATTCA
1 TTATAAAAAAGATT-A
* * *
57755 TGATATAATAGATTA
1 TTATAAAAAAGATTA
57770 TTATAAAAAAGATTA
1 TTATAAAAAAGATTA
57785 TT
1 TT
57787 CTCATTCAAG
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
15 15 0.60
16 10 0.40
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (15 bp):
TTATAAAAAAGATTA
Found at i:76311 original size:22 final size:21
Alignment explanation
Indices: 76286--76338 Score: 70
Period size: 22 Copynumber: 2.5 Consensus size: 21
76276 AATTTAAAAT
76286 AAACATAATGAGGAGAGTTAC
1 AAACATAATGAGGAGAGTTAC
* * *
76307 AAAACCTTACGAGGAGAGTTAC
1 -AAACATAATGAGGAGAGTTAC
76329 AAACATAATG
1 AAACATAATG
76339 TTTTGTAGGT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
21 7 0.28
22 18 0.72
ACGTcount: A:0.47, C:0.13, G:0.21, T:0.19
Consensus pattern (21 bp):
AAACATAATGAGGAGAGTTAC
Found at i:80917 original size:21 final size:21
Alignment explanation
Indices: 80873--80926 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
80863 TCCATGTTTC
* *
80873 TTTAA-ATTGTTTTAAAATTGT
1 TTTAATATT-TTTTAAAAATCT
* *
80894 TTTTATTTTTTTTAAAAATCT
1 TTTAATATTTTTTAAAAATCT
80915 TTTAATATTTTT
1 TTTAATATTTTT
80927 AAATTTTGGT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.65
Consensus pattern (21 bp):
TTTAATATTTTTTAAAAATCT
Found at i:86873 original size:17 final size:17
Alignment explanation
Indices: 86848--86897 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
86838 TAAAACATGT
*
86848 TAAAAATAAACATA-TAC
1 TAAATATAAA-ATATTAC
86865 TAAATATAAAATATTAC
1 TAAATATAAAATATTAC
*
86882 TCTAATAT-AAATATTA
1 T-AAATATAAAATATTA
86898 AAAAATGTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 3 0.10
17 21 0.72
18 5 0.17
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (17 bp):
TAAATATAAAATATTAC
Found at i:89023 original size:24 final size:24
Alignment explanation
Indices: 88951--89016 Score: 132
Period size: 24 Copynumber: 2.8 Consensus size: 24
88941 TGTTATGGAA
88951 CCAGTAGAAAATGAAGATTCAACT
1 CCAGTAGAAAATGAAGATTCAACT
88975 CCAGTAGAAAATGAAGATTCAACT
1 CCAGTAGAAAATGAAGATTCAACT
88999 CCAGTAGAAAATGAAGAT
1 CCAGTAGAAAATGAAGAT
89017 CTAACTCTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.47, C:0.15, G:0.18, T:0.20
Consensus pattern (24 bp):
CCAGTAGAAAATGAAGATTCAACT
Found at i:99338 original size:6 final size:5
Alignment explanation
Indices: 99313--99362 Score: 50
Period size: 6 Copynumber: 9.6 Consensus size: 5
99303 AAAAATCACA
99313 AAAAG -AAAG AATAAG -AAAG AATAAG AATAAG AAAGAG AAAAG AAAAG
1 AAAAG AAAAG AA-AAG AAAAG AA-AAG AA-AAG AAA-AG AAAAG AAAAG
99360 AAA
1 AAA
99363 TATATTGCCA
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
4 7 0.17
5 14 0.35
6 19 0.47
ACGTcount: A:0.74, C:0.00, G:0.20, T:0.06
Consensus pattern (5 bp):
AAAAG
Found at i:99340 original size:16 final size:17
Alignment explanation
Indices: 99318--99362 Score: 67
Period size: 16 Copynumber: 2.8 Consensus size: 17
99308 TCACAAAAAG
99318 AAAGAATAAGAAAGA-A
1 AAAGAATAAGAAAGAGA
*
99334 TAAGAATAAGAAAGAGA
1 AAAGAATAAGAAAGAGA
99351 AAAGAA-AAGAAA
1 AAAGAATAAGAAA
99363 TATATTGCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 20 0.77
17 6 0.23
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (17 bp):
AAAGAATAAGAAAGAGA
Found at i:99361 original size:10 final size:10
Alignment explanation
Indices: 99313--99362 Score: 50
Period size: 10 Copynumber: 4.8 Consensus size: 10
99303 AAAAATCACA
99313 AAAAG-AAAG
1 AAAAGAAAAG
99322 AATAAG-AAAG
1 AA-AAGAAAAG
99332 AATAAGAATAAG
1 AA-AAGAA-AAG
99344 AAAGAGAAAAG
1 AAA-AGAAAAG
99355 AAAAGAAA
1 AAAAGAAA
99363 TATATTGCCA
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
9 2 0.05
10 18 0.49
11 8 0.22
12 9 0.24
ACGTcount: A:0.74, C:0.00, G:0.20, T:0.06
Consensus pattern (10 bp):
AAAAGAAAAG
Found at i:102846 original size:28 final size:28
Alignment explanation
Indices: 102814--102895 Score: 94
Period size: 28 Copynumber: 3.0 Consensus size: 28
102804 GATCTGGTTT
* * *
102814 TAAACCTTAAATGTGAAATCCTAAACCC
1 TAAACCTTAAACGTAAAATACTAAACCC
*
102842 TAAACCTTAAACGTAAAATATTAAACCC
1 TAAACCTTAAACGTAAAATACTAAACCC
* * *
102870 TAAACCCTAAACAT-AAACACTAAACC
1 TAAACCTTAAACGTAAAATACTAAACC
102896 ATATGAGAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
27 10 0.22
28 36 0.78
ACGTcount: A:0.49, C:0.26, G:0.04, T:0.22
Consensus pattern (28 bp):
TAAACCTTAAACGTAAAATACTAAACCC
Found at i:102957 original size:17 final size:17
Alignment explanation
Indices: 102943--102978 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
102933 TAAATAAATG
102943 ATCAAATGAGTTAAAGT
1 ATCAAATGAGTTAAAGT
102960 ATCAAATGAGTTAAAGT
1 ATCAAATGAGTTAAAGT
102977 AT
1 AT
102979 ATGTAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.47, C:0.06, G:0.17, T:0.31
Consensus pattern (17 bp):
ATCAAATGAGTTAAAGT
Found at i:104486 original size:20 final size:21
Alignment explanation
Indices: 104461--104503 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
104451 ATATTATTTT
104461 ATTAC-TACTAACAAAATAAA
1 ATTACTTACTAACAAAATAAA
104481 ATTACTTACTAACAAAATAAA
1 ATTACTTACTAACAAAATAAA
104502 AT
1 AT
104504 AAAATTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.58, C:0.14, G:0.00, T:0.28
Consensus pattern (21 bp):
ATTACTTACTAACAAAATAAA
Found at i:104878 original size:4 final size:4
Alignment explanation
Indices: 104869--104926 Score: 66
Period size: 4 Copynumber: 14.2 Consensus size: 4
104859 AATAACATTC
104869 TTCT TTCT TTCT TTCT TT-T TTCT CCTTC- TTCT TTCT TTCT TTCTT TTCT
1 TTCT TTCT TTCT TTCT TTCT TTCT --TTCT TTCT TTCT TTCT TTC-T TTCT
*
104918 TTCC TTCT T
1 TTCT TTCT T
104927 CTTCTTCTCT
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
3 6 0.13
4 34 0.72
5 4 0.09
6 3 0.06
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (4 bp):
TTCT
Found at i:104905 original size:28 final size:28
Alignment explanation
Indices: 104866--104929 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
104856 TAAAATAACA
104866 TTCTTCTTTCTTTCTTTCTTTT-TTCTCC
1 TTCTTCTTTCTTTCTTTCTTTTCTT-TCC
104894 TTCTTCTTTCTTTCTTTCTTTTCTTTCC
1 TTCTTCTTTCTTTCTTTCTTTTCTTTCC
104922 TTCTTCTT
1 TTCTTCTT
104930 CTTCTCTCGT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
28 33 0.94
29 2 0.06
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (28 bp):
TTCTTCTTTCTTTCTTTCTTTTCTTTCC
Found at i:104907 original size:17 final size:17
Alignment explanation
Indices: 104869--104934 Score: 68
Period size: 17 Copynumber: 4.0 Consensus size: 17
104859 AATAACATTC
104869 TTCTTTC-T-TTCTTTCT
1 TTCTTTCTTCTTC-TTCT
*
104885 TT-TTTCTCCTTCTTCT
1 TTCTTTCTTCTTCTTCT
104901 TTCTTTCTTTCTT-TTCT
1 TTCTTTC-TTCTTCTTCT
*
104918 TTCCTTCTTCTTCTTCT
1 TTCTTTCTTCTTCTTCT
104935 CTCGTAGCTG
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
15 4 0.10
16 13 0.31
17 21 0.50
18 4 0.10
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (17 bp):
TTCTTTCTTCTTCTTCT
Found at i:105172 original size:27 final size:27
Alignment explanation
Indices: 105127--105179 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
105117 TAAAATACCC
105127 TTGGTGCCACCACTTAACATGGCACCT
1 TTGGTGCCACCACTTAACATGGCACCT
*
105154 TTGGTGCCGCCA-TTCAACATGGCACC
1 TTGGTGCCACCACTT-AACATGGCACC
105180 ACCCATGTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 2 0.08
27 22 0.92
ACGTcount: A:0.21, C:0.34, G:0.21, T:0.25
Consensus pattern (27 bp):
TTGGTGCCACCACTTAACATGGCACCT
Found at i:105813 original size:36 final size:36
Alignment explanation
Indices: 105740--105813 Score: 112
Period size: 36 Copynumber: 2.1 Consensus size: 36
105730 TCAAGGAGTT
* *
105740 AAAATTTTGAAAACAACTACAAAATCTTACCGGTAG
1 AAAATTTTGAAAACAACTACAAAATCCTACCGATAG
* *
105776 AAAATTTTGAAAACAACTACAGAATCCTATCGATAG
1 AAAATTTTGAAAACAACTACAAAATCCTACCGATAG
105812 AA
1 AA
105814 CTGGTAGTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.49, C:0.16, G:0.11, T:0.24
Consensus pattern (36 bp):
AAAATTTTGAAAACAACTACAAAATCCTACCGATAG
Found at i:107111 original size:18 final size:18
Alignment explanation
Indices: 107076--107152 Score: 84
Period size: 18 Copynumber: 4.3 Consensus size: 18
107066 GCAATCCAGA
* *
107076 ATGCTCTTACGAGCCAGT
1 ATGCTCTAACGAGCTAGT
*
107094 ATGCTCTAATGAG-TCAGT
1 ATGCTCTAACGAGCT-AGT
*
107112 ATGCTCAAACGAGCTAGT
1 ATGCTCTAACGAGCTAGT
* *
107130 ATGCTCCAATGAGCTAGT
1 ATGCTCTAACGAGCTAGT
107148 ATGCT
1 ATGCT
107153 TCCAATGAGC
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
18 49 0.98
19 1 0.02
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (18 bp):
ATGCTCTAACGAGCTAGT
Found at i:107124 original size:36 final size:36
Alignment explanation
Indices: 107084--107152 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
107074 GAATGCTCTT
*
107084 ACGAGCCAGTATGCTCTAATGAG-TCAGTATGCTCAA
1 ACGAGCCAGTATGCTCCAATGAGCT-AGTATGCTCAA
*
107120 ACGAGCTAGTATGCTCCAATGAGCTAGTATGCT
1 ACGAGCCAGTATGCTCCAATGAGCTAGTATGCT
107153 TCCAATGAGC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
36 29 0.97
37 1 0.03
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (36 bp):
ACGAGCCAGTATGCTCCAATGAGCTAGTATGCTCAA
Found at i:107169 original size:19 final size:18
Alignment explanation
Indices: 107086--107169 Score: 69
Period size: 18 Copynumber: 4.6 Consensus size: 18
107076 ATGCTCTTAC
* *
107086 GAGCCAGTATGCTCTAAT
1 GAGCCAATATGCTCCAAT
* * * *
107104 GAGTCAGTATGCTCAAAC
1 GAGCCAATATGCTCCAAT
* *
107122 GAGCTAGTATGCTCCAAT
1 GAGCCAATATGCTCCAAT
* *
107140 GAGCTAGTATGCTTCCAAT
1 GAGCCAATATGC-TCCAAT
107159 GAGCCAATATG
1 GAGCCAATATG
107170 TTAATCCTTC
Statistics
Matches: 56, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
18 41 0.73
19 15 0.27
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (18 bp):
GAGCCAATATGCTCCAAT
Found at i:109203 original size:26 final size:26
Alignment explanation
Indices: 109174--109242 Score: 111
Period size: 26 Copynumber: 2.7 Consensus size: 26
109164 TAACCTGTAA
109174 TGCTCACACGAGCTGTGAAATGGGTC
1 TGCTCACACGAGCTGTGAAATGGGTC
*
109200 TGCTCACACGAGCTATGAAATGGGTC
1 TGCTCACACGAGCTGTGAAATGGGTC
* *
109226 TGCTTACATGAGCTGTG
1 TGCTCACACGAGCTGTG
109243 GGTCTAAATG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.26
Consensus pattern (26 bp):
TGCTCACACGAGCTGTGAAATGGGTC
Found at i:109325 original size:184 final size:184
Alignment explanation
Indices: 109016--109357 Score: 479
Period size: 184 Copynumber: 1.9 Consensus size: 184
109006 TAACCATATA
* * * * *
109016 TGCTCACACGAGCTGTGAAATGGGTCTGCTCACACGAGTTGTGGGTCGAGATGTGGGGCTACACG
1 TGCTCACACGAGCTATGAAATGGGTCTGCTCACACGAGCTGTGGGTCGAAATGTGAGGCTACACA
* * * ** *
109081 ATGTTGCTTACACGAGCTGTGGAGAATCCGCAATAAATGCCGGACCTCAGCCATCGGTAGGACAT
66 ATGCTGCTTACACGAGCTATGGAGAATCCGCAACAAATGCAAGACCTCAACCATCGGTAGGACAT
*
109146 CTAAGACCAACACCCATATAACCTGTAATGCTCACACGAGCTGTGAAATGGGTC
131 CCAAGACCAACACCCATATAACCTGTAATGCTCACACGAGCTGTGAAATGGGTC
* * * * * **
109200 TGCTCACACGAGCTATGAAATGGGTCTGCTTACATGAGCTGTGGGTCTAAATGTTAGGTTATGCA
1 TGCTCACACGAGCTATGAAATGGGTCTGCTCACACGAGCTGTGGGTCGAAATGTGAGGCTACACA
*
109265 ATGCTG-TTCACACGAGCTATGGAGAATCCGCAACCAATGCAAGACCTCAACCATCGGTAGGACA
66 ATGCTGCTT-ACACGAGCTATGGAGAATCCGCAACAAATGCAAGACCTCAACCATCGGTAGGACA
*
109329 TCCAAGACCAGCACCCATATAACCTGTAA
130 TCCAAGACCAACACCCATATAACCTGTAA
109358 ATAACCTTTA
Statistics
Matches: 136, Mismatches: 21, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
183 2 0.01
184 134 0.99
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.22
Consensus pattern (184 bp):
TGCTCACACGAGCTATGAAATGGGTCTGCTCACACGAGCTGTGGGTCGAAATGTGAGGCTACACA
ATGCTGCTTACACGAGCTATGGAGAATCCGCAACAAATGCAAGACCTCAACCATCGGTAGGACAT
CCAAGACCAACACCCATATAACCTGTAATGCTCACACGAGCTGTGAAATGGGTC
Found at i:110193 original size:18 final size:18
Alignment explanation
Indices: 110167--110205 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
110157 TTGATCTAGA
* *
110167 TAATAATTCCCATCAATT
1 TAATAATTCCAATAAATT
*
110185 TAATCATTCCAATAAATT
1 TAATAATTCCAATAAATT
110203 TAA
1 TAA
110206 ATATTTAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.18, G:0.00, T:0.38
Consensus pattern (18 bp):
TAATAATTCCAATAAATT
Found at i:119150 original size:20 final size:20
Alignment explanation
Indices: 119125--119184 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
119115 CCGAAGGATG
119125 GATGGGTAAAGCTCAATTCT
1 GATGGGTAAAGCTCAATTCT
**
119145 GATGGG-GCAGTCTC--TT-T
1 GATGGGTAAAG-CTCAATTCT
119162 GGATGGGTAAAGCTCAATTCT
1 -GATGGGTAAAGCTCAATTCT
119183 GA
1 GA
119185 AGGTAGATGG
Statistics
Matches: 30, Mismatches: 4, Indels: 12
0.65 0.09 0.26
Matches are distributed among these distances:
17 1 0.03
18 11 0.37
19 4 0.13
20 13 0.43
21 1 0.03
ACGTcount: A:0.25, C:0.15, G:0.30, T:0.30
Consensus pattern (20 bp):
GATGGGTAAAGCTCAATTCT
Found at i:126581 original size:12 final size:12
Alignment explanation
Indices: 126535--126581 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
126525 GTCACCACTG
126535 TCATCGTCATCA
1 TCATCGTCATCA
*
126547 TCATCATCATCA
1 TCATCGTCATCA
* *
126559 TCA-CTGCCATCG
1 TCATC-GTCATCA
126571 TCATCGTCATC
1 TCATCGTCATC
126582 TCCAAGACAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
11 1 0.04
12 26 0.93
13 1 0.04
ACGTcount: A:0.23, C:0.36, G:0.09, T:0.32
Consensus pattern (12 bp):
TCATCGTCATCA
Found at i:131364 original size:27 final size:28
Alignment explanation
Indices: 131312--131364 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
131302 AATTATGGTT
*
131312 CAATAAACTTTTTGAGATTTCTTTTTGA
1 CAATAAACTTTTTGAGATTACTTTTTGA
131340 CAATAAA-TTTTTGAGA-TACTATTTT
1 CAATAAACTTTTTGAGATTACT-TTTT
131365 CTAATTGATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 3 0.13
27 13 0.57
28 7 0.30
ACGTcount: A:0.32, C:0.09, G:0.09, T:0.49
Consensus pattern (28 bp):
CAATAAACTTTTTGAGATTACTTTTTGA
Found at i:143528 original size:17 final size:18
Alignment explanation
Indices: 143506--143544 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
143496 AAATTTATTA
* *
143506 ATTAAAGTATA-TATATC
1 ATTAAAATATATTAAATC
143523 ATTAAAATATATTAAATC
1 ATTAAAATATATTAAATC
143541 ATTA
1 ATTA
143545 TAAAAATTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (18 bp):
ATTAAAATATATTAAATC
Found at i:143768 original size:90 final size:90
Alignment explanation
Indices: 143639--143802 Score: 256
Period size: 90 Copynumber: 1.8 Consensus size: 90
143629 CCCATCCTTT
* * *
143639 TTTTTTTTTGCACTCATTTGGCTACTTGAACTTTCAAAATGCATCAAAAAGACCCTCAAACCTTT
1 TTTTTTTTTGCACTCAATTGGCAACTTGAACTTTCAAAATGCATAAAAAAGACCCTCAAACCTTT
143704 TCAAAAAAAGAAATTAAGCCCCTAC
66 TCAAAAAAAGAAATTAAGCCCCTAC
* * * **
143729 TTTTTTTTTGCACTCAATTGGGAACTTGAATTTTTAAAATGCATAAAAAAGACCCTCAAATTTTT
1 TTTTTTTTTGCACTCAATTGGCAACTTGAACTTTCAAAATGCATAAAAAAGACCCTCAAACCTTT
143794 TCAAAAAAA
66 TCAAAAAAA
143803 AAAAGTAATT
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
90 66 1.00
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.35
Consensus pattern (90 bp):
TTTTTTTTTGCACTCAATTGGCAACTTGAACTTTCAAAATGCATAAAAAAGACCCTCAAACCTTT
TCAAAAAAAGAAATTAAGCCCCTAC
Found at i:143942 original size:20 final size:20
Alignment explanation
Indices: 143905--143961 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 20
143895 AAAATTAGAA
143905 AAAAAAATCGTAAAAAAAATATT
1 AAAAAAATCGT---AAAAATATT
* *
143928 AAAAAAATTGTAAAAATTTT
1 AAAAAAATCGTAAAAATATT
*
143948 ATAAAAATCGTAAA
1 AAAAAAATCGTAAA
143962 GAAATTATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 20 0.67
23 10 0.33
ACGTcount: A:0.65, C:0.04, G:0.05, T:0.26
Consensus pattern (20 bp):
AAAAAAATCGTAAAAATATT
Found at i:143952 original size:22 final size:22
Alignment explanation
Indices: 143884--143954 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 22
143874 AAATTTTAAT
* * * *
143884 AAAAAATTATTAAAATTAGAAA
1 AAAAAATTGTAAAAATTATATA
* **
143906 AAAAAATCGTAAAAAAAATATTA
1 AAAAAATTGTAAAAATTATA-TA
*
143929 AAAAAATTGTAAAAATTTTATA
1 AAAAAATTGTAAAAATTATATA
143951 AAAA
1 AAAA
143955 TCGTAAAGAA
Statistics
Matches: 37, Mismatches: 11, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
22 20 0.54
23 17 0.46
ACGTcount: A:0.68, C:0.01, G:0.04, T:0.27
Consensus pattern (22 bp):
AAAAAATTGTAAAAATTATATA
Found at i:143997 original size:10 final size:10
Alignment explanation
Indices: 143919--144047 Score: 51
Period size: 10 Copynumber: 13.4 Consensus size: 10
143909 AAATCGTAAA
143919 AAAAATATTA-
1 AAAAA-ATTAT
*
143929 AAAAAATTGT
1 AAAAAATTAT
*
143939 -AAAAATTTT
1 AAAAAATTAT
**
143948 ATAAAAATCGT
1 A-AAAAATTAT
143959 AAAGAAATTAT
1 AAA-AAATTAT
*
143970 AAAATA-TAT
1 AAAAAATTAT
*
143979 -AGAAA-TAT
1 AAAAAATTAT
143987 AAAAAATTAT
1 AAAAAATTAT
**
143997 AAAATTTTAT
1 AAAAAATTAT
** *
144007 AAAGTAGTA-
1 AAAAAATTAT
*
144016 AGAAAATTAT
1 AAAAAATTAT
144026 AAAAAA--AT
1 AAAAAATTAT
144034 AAAGAAA-TAT
1 AAA-AAATTAT
144044 AAAA
1 AAAA
144048 TTCGTAAAAA
Statistics
Matches: 90, Mismatches: 20, Indels: 19
0.70 0.16 0.15
Matches are distributed among these distances:
8 11 0.12
9 27 0.30
10 36 0.40
11 16 0.18
ACGTcount: A:0.64, C:0.01, G:0.06, T:0.29
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:144007 original size:57 final size:58
Alignment explanation
Indices: 143929--144047 Score: 154
Period size: 57 Copynumber: 2.1 Consensus size: 58
143919 AAAAATATTA
* * * *
143929 AAAAAATTGTAAAAATTTTATAAAAATCGTAA-AGAAATTAT-AAAATATATAGAAATAT
1 AAAAAATTATAAAAATTTTAT-AAAATAGTAAGA-AAATTATAAAAAAATAAAGAAATAT
*
143987 AAAAAATTAT-AAAATTTTATAAAGTAGTAAGAAAATTATAAAAAAATAAAGAAATAT
1 AAAAAATTATAAAAATTTTATAAAATAGTAAGAAAATTATAAAAAAATAAAGAAATAT
144044 AAAA
1 AAAA
144048 TTCGTAAAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
56 15 0.28
57 30 0.56
58 9 0.17
ACGTcount: A:0.64, C:0.01, G:0.07, T:0.29
Consensus pattern (58 bp):
AAAAAATTATAAAAATTTTATAAAATAGTAAGAAAATTATAAAAAAATAAAGAAATAT
Found at i:144321 original size:16 final size:17
Alignment explanation
Indices: 144302--144339 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
144292 TTTATGATTT
144302 TTTTTAA-AAATATGAA
1 TTTTTAATAAATATGAA
* *
144318 TTTTTAATAAATTTTAA
1 TTTTTAATAAATATGAA
144335 TTTTT
1 TTTTT
144340 TTATATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
TTTTTAATAAATATGAA
Found at i:144348 original size:46 final size:45
Alignment explanation
Indices: 144279--144396 Score: 136
Period size: 46 Copynumber: 2.6 Consensus size: 45
144269 ATTTCTACAA
144279 AAAATTTTATTTTTTTATGATTTTTTTTAAAA-AT-ATGAATTTT-T
1 AAAATTTTATTTTTTTAT-ATTTTTTTTAAAATATAAT-AATTTTCT
* *
144323 AATAAATTTTAATTTTTTTATATTTTTATTAAAATTTAATAATTTTCT
1 -A-AAATTTT-ATTTTTTTATATTTTTTTTAAAATATAATAATTTTCT
*
144371 AAAA-TTTATTTTTTTATAATTTTTTT
1 AAAATTTTATTTTTTTATATTTTTTTT
144397 CTAATTTTTA
Statistics
Matches: 64, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
44 17 0.27
45 4 0.06
46 22 0.34
47 18 0.28
48 3 0.05
ACGTcount: A:0.35, C:0.01, G:0.02, T:0.63
Consensus pattern (45 bp):
AAAATTTTATTTTTTTATATTTTTTTTAAAATATAATAATTTTCT
Found at i:144368 original size:27 final size:27
Alignment explanation
Indices: 144317--144368 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
144307 AAAAATATGA
* **
144317 ATTTTTAATAAATTTTAATTTTTTTAT
1 ATTTTTAATAAAATTTAATAATTTTAT
*
144344 ATTTTTATTAAAATTTAATAATTTT
1 ATTTTTAATAAAATTTAATAATTTT
144369 CTAAAATTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (27 bp):
ATTTTTAATAAAATTTAATAATTTTAT
Found at i:152869 original size:43 final size:43
Alignment explanation
Indices: 152810--152924 Score: 167
Period size: 43 Copynumber: 2.7 Consensus size: 43
152800 AATTTAGATT
* *
152810 TTTTGATTTTTTTTATTTTGTTACTATTTCGGTTTAAAATCAA
1 TTTTAATTTATTTTATTTTGTTACTATTTCGGTTTAAAATCAA
* *
152853 TTTTAATTTGTTTTATTTTGTTACTATTTCGGTTTAAAATTAA
1 TTTTAATTTATTTTATTTTGTTACTATTTCGGTTTAAAATCAA
* * *
152896 TTTTAATTAAATTTATTGTGTTACTATTT
1 TTTTAATTTATTTTATTTTGTTACTATTT
152925 GGAGTTCTTA
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 65 1.00
ACGTcount: A:0.25, C:0.05, G:0.09, T:0.61
Consensus pattern (43 bp):
TTTTAATTTATTTTATTTTGTTACTATTTCGGTTTAAAATCAA
Found at i:153246 original size:19 final size:20
Alignment explanation
Indices: 153222--153259 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
153212 CAAATCAATA
153222 TTAGGGG-CTTATTTATTAG
1 TTAGGGGTCTTATTTATTAG
*
153241 TTAGGGGTTTTATTTATTA
1 TTAGGGGTCTTATTTATTA
153260 AAAAAACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.21, C:0.03, G:0.24, T:0.53
Consensus pattern (20 bp):
TTAGGGGTCTTATTTATTAG
Found at i:153540 original size:63 final size:59
Alignment explanation
Indices: 153425--153653 Score: 167
Period size: 63 Copynumber: 3.9 Consensus size: 59
153415 TCTATAAGTT
* * *
153425 AAAACCAAAAAAATTATTTTTTTAAT-TGTGATGGGACTTAGTG-CTGATCATTAGACGGCC
1 AAAACCAAAAAAATTATTTTTTT-ATCTGTGAT-GGACTTGGTGTC-GACCATTAAACGGCC
* ** *
153485 AAAACTCAAAAAATTTAATATTTTTTATCTGTGATGGAACTTGGTGTCGACCATTAAATTGTC
1 AAAAC-CAAAAAAATT-AT-TTTTTTATCTGTGATGG-ACTTGGTGTCGACCATTAAACGGCC
* *
153548 AGAACCTAAAAAAATTATTTTTTTTATCTGTGATAGGACTTGGTGTCG----------GCCC
1 AAAACC-AAAAAAATTA-TTTTTTTATCTGTGAT-GGACTTGGTGTCGACCATTAAACGGCC
* *
153600 AAAACCCAAAAAATTATTATTTTTATCTGTGATGAGACTTGGTGCCGACCATTA
1 AAAACCAAAAAAATTATT-TTTTTATCTGTGATG-GACTTGGTGTCGACCATTA
153654 GGTGACTAAG
Statistics
Matches: 136, Mismatches: 15, Indels: 38
0.72 0.08 0.20
Matches are distributed among these distances:
50 3 0.02
51 34 0.25
52 6 0.04
60 5 0.04
61 9 0.07
62 34 0.25
63 44 0.32
64 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (59 bp):
AAAACCAAAAAAATTATTTTTTTATCTGTGATGGACTTGGTGTCGACCATTAAACGGCC
Found at i:153589 original size:62 final size:60
Alignment explanation
Indices: 153426--153595 Score: 166
Period size: 62 Copynumber: 2.8 Consensus size: 60
153416 CTATAAGTTA
* * * *
153426 AAACC-AAAAAAATTATTTTTTTAAT-TGTGATGGGACTTAGTG-CTGATCATTAGACGGCC
1 AAACCTAAAAAAATTATTTTTTTTATCTGTGAT-GGACTTGGTGTC-GACCATTAAACGGCC
* * * ** *
153485 AAAACTCAAAAAATTTAATATTTTTTATCTGTGATGGAACTTGGTGTCGACCATTAAATTGTC
1 AAACCT-AAAAAAATT-ATTTTTTTTATCTGTGATGG-ACTTGGTGTCGACCATTAAACGGCC
153548 AGAACCTAAAAAAATTATTTTTTTTATCTGTGATAGGACTTGGTGTCG
1 A-AACCTAAAAAAATTATTTTTTTTATCTGTGAT-GGACTTGGTGTCG
153596 GCCCAAAACC
Statistics
Matches: 90, Mismatches: 13, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
59 4 0.04
61 8 0.09
62 39 0.43
63 34 0.38
64 5 0.06
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (60 bp):
AAACCTAAAAAAATTATTTTTTTTATCTGTGATGGACTTGGTGTCGACCATTAAACGGCC
Found at i:157241 original size:17 final size:18
Alignment explanation
Indices: 157219--157253 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
157209 AAATATTTTC
*
157219 CTAAATT-TTATTTTTAT
1 CTAAATTGTAATTTTTAT
157236 CTAAATTGTAATTTTTAT
1 CTAAATTGTAATTTTTAT
157254 TATTTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.60
Consensus pattern (18 bp):
CTAAATTGTAATTTTTAT
Found at i:157823 original size:17 final size:17
Alignment explanation
Indices: 157803--157836 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
157793 TGAATTTTTC
* *
157803 CTAAATTTTATTTTTAT
1 CTAAATTATAATTTTAT
157820 CTAAATTATAATTTTAT
1 CTAAATTATAATTTTAT
157837 TATTTTTTAT
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:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (17 bp):
CTAAATTATAATTTTAT
Found at i:160760 original size:57 final size:57
Alignment explanation
Indices: 160660--160773 Score: 156
Period size: 57 Copynumber: 2.0 Consensus size: 57
160650 GTTAATTCCA
* * **
160660 ATGTTGATCTTAACATTGTTGTGGTATTTGGTGTGACAACTTCAAATAAAACTTTGT
1 ATGTTGATCTCAACACTGTTGTGGTATTTGGCATGACAACTTCAAATAAAACTTTGT
* * * *
160717 ATGTTGATCTCAACACTGTTGTGGTATTTTGCATGGCATCTTCAAATAAGACTTTGT
1 ATGTTGATCTCAACACTGTTGTGGTATTTGGCATGACAACTTCAAATAAAACTTTGT
160774 TCTTATGGGT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
57 49 1.00
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.41
Consensus pattern (57 bp):
ATGTTGATCTCAACACTGTTGTGGTATTTGGCATGACAACTTCAAATAAAACTTTGT
Found at i:165609 original size:60 final size:60
Alignment explanation
Indices: 165521--165636 Score: 171
Period size: 60 Copynumber: 1.9 Consensus size: 60
165511 TAGTTGGATG
* *
165521 ACCAAATTGAAAAAAATTGATAGTTGAGTGACCAAAGAAGGAAAGAAACAATAATTGAGTA
1 ACCAAATTGAAAAAAATTAATAGTTGAGTGACCAAA-AAGAAAAGAAACAATAATTGAGTA
* **
165582 ACCAAATT-AAAAAAATTAATAGTTGAGTGACTAAAAAGAAAAGGGACAATAATTG
1 ACCAAATTGAAAAAAATTAATAGTTGAGTGACCAAAAAGAAAAGAAACAATAATTG
165637 GGTGACCTGT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
59 17 0.34
60 25 0.50
61 8 0.16
ACGTcount: A:0.53, C:0.08, G:0.18, T:0.21
Consensus pattern (60 bp):
ACCAAATTGAAAAAAATTAATAGTTGAGTGACCAAAAAGAAAAGAAACAATAATTGAGTA
Found at i:165623 original size:29 final size:30
Alignment explanation
Indices: 165531--165623 Score: 84
Period size: 29 Copynumber: 3.1 Consensus size: 30
165521 ACCAAATTGA
*
165531 AAAAAATTGATAGTTGAGTGACCAAAGAAGG
1 AAAAAATTAATAGTTGAGTGACCAAAGAA-G
* * * **
165562 AAAGAAA-CAATAATTGAGTAACCAAATTA-
1 AAA-AAATTAATAGTTGAGTGACCAAAGAAG
*
165591 AAAAAATTAATAGTTGAGTGACTAAA-AAG
1 AAAAAATTAATAGTTGAGTGACCAAAGAAG
165620 AAAA
1 AAAA
165624 GGGACAATAA
Statistics
Matches: 48, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
28 4 0.08
29 22 0.46
31 19 0.40
32 3 0.06
ACGTcount: A:0.56, C:0.06, G:0.17, T:0.20
Consensus pattern (30 bp):
AAAAAATTAATAGTTGAGTGACCAAAGAAG
Found at i:165919 original size:29 final size:29
Alignment explanation
Indices: 165887--165942 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
165877 TCACCCAACT
* * *
165887 ATAAAAAATTTTCATTTTAGGCACTCAAA
1 ATAAAAAATTTACAATTTAAGCACTCAAA
165916 ATAAAAAATTTACAATTTAAGCACTCA
1 ATAAAAAATTTACAATTTAAGCACTCA
165943 CGTTACATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.48, C:0.14, G:0.05, T:0.32
Consensus pattern (29 bp):
ATAAAAAATTTACAATTTAAGCACTCAAA
Found at i:166441 original size:51 final size:50
Alignment explanation
Indices: 166386--166498 Score: 133
Period size: 49 Copynumber: 2.3 Consensus size: 50
166376 GTATATATAT
* * **
166386 TTAATTTCTTTTAAAATTAGGA-TCAAATTGATA-ATATTTATAAATTTTGAG
1 TTAATTT-TTTTAAAATTAGGACT-AAATCGATATA-ATATATAAAAATTGAG
*
166437 TTAA-TTTTTTAAAATTATGACTAAATCGATATAATATATAAAAATTGAG
1 TTAATTTTTTTAAAATTAGGACTAAATCGATATAATATATAAAAATTGAG
166486 TTAATTTTTTTAA
1 TTAATTTTTTTAA
166499 CTATCACGTC
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
49 38 0.70
50 12 0.22
51 4 0.07
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.47
Consensus pattern (50 bp):
TTAATTTTTTTAAAATTAGGACTAAATCGATATAATATATAAAAATTGAG
Found at i:166841 original size:2 final size:2
Alignment explanation
Indices: 166789--166823 Score: 54
Period size: 2 Copynumber: 17.5 Consensus size: 2
166779 AAGTTAACCT
166789 TC TC TC TC TC TC TC TC TC TC TC TC TC ATC -C TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC -TC TC TC TC T
166824 TTCGTTCAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 28 0.90
3 2 0.06
ACGTcount: A:0.03, C:0.49, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:168284 original size:22 final size:22
Alignment explanation
Indices: 168254--168304 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
168244 AAGTATCAGG
*
168254 TTTATCTCCTACGGTTACAAGC
1 TTTACCTCCTACGGTTACAAGC
168276 TTTACCTCCTACGGTTACAAGC
1 TTTACCTCCTACGGTTACAAGC
168298 TTTACCT
1 TTTACCT
168305 TTTAGAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.22, C:0.29, G:0.12, T:0.37
Consensus pattern (22 bp):
TTTACCTCCTACGGTTACAAGC
Found at i:170653 original size:16 final size:18
Alignment explanation
Indices: 170629--170665 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
170619 CAGATTAAGA
*
170629 TAATGTTAAA-GTT-TGT
1 TAATCTTAAAGGTTCTGT
170645 TAATCTTAAAGGTTCTGT
1 TAATCTTAAAGGTTCTGT
170663 TAA
1 TAA
170666 AATAATTTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 9 0.50
17 3 0.17
18 6 0.33
ACGTcount: A:0.32, C:0.05, G:0.16, T:0.46
Consensus pattern (18 bp):
TAATCTTAAAGGTTCTGT
Found at i:171855 original size:4 final size:4
Alignment explanation
Indices: 171846--171875 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
171836 GCATTGCATC
171846 AGAA AGAA AGAA AGAA AG-A AGAA AGAA AGA
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGA
171876 CCCCCTAAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:187883 original size:2 final size:2
Alignment explanation
Indices: 187876--187912 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
187866 TTATCTCTTT
187876 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
187913 NNNNNNNNNN
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:200638 original size:159 final size:158
Alignment explanation
Indices: 200351--200638 Score: 357
Period size: 157 Copynumber: 1.8 Consensus size: 158
200341 GCTTGTGCTA
* **
200351 CAATAAATTTATTTATTTTTCGAATTAATTATAATAATTGATATTAATTTATTTCATTCTCCGGA
1 CAATAAATTTATTTATTTCTCGAATTAATTATAATAATTGATATTAATTTACCTCATTCTCCGGA
* * * **
200416 AACTTGGTCTGGAGTCTACTACTACAATAATATTTTTTAATTTTCTGAAATAATTATAATAATTT
66 AACTTGGCCTGGAGTCTACTACTACAATAACATTTTTTAATTATCCAAAATAATTATAATAATTT
200481 CTATTATTTCGTTTTGAATATGGTGTTG
131 CTATTATTTCGTTTTGAATATGGTGTTG
* * *
200509 CAATAAATTT-TTTATATTCTGGAA-TAATTATAATAATTGCTATTTAATTTACCTCATT-TTCG
1 CAATAAATTTATTTAT-TTCTCGAATTAATTATAATAATTGATA-TTAATTTACCTCATTCTCCG
** * * * * *
200571 GGTACTTGGCCTTGAGTTTAGCCTACTACAATTACATTTTTTTATTATCCAAAATAGTTATAATA
64 GAAACTTGGCCTGGAGTCTA--CTACTACAATAACATTTTTTAATTATCCAAAATAATTATAATA
200636 ATT
127 ATT
200639 GCAACTTATT
Statistics
Matches: 108, Mismatches: 18, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
157 40 0.37
158 29 0.27
159 39 0.36
ACGTcount: A:0.32, C:0.11, G:0.10, T:0.47
Consensus pattern (158 bp):
CAATAAATTTATTTATTTCTCGAATTAATTATAATAATTGATATTAATTTACCTCATTCTCCGGA
AACTTGGCCTGGAGTCTACTACTACAATAACATTTTTTAATTATCCAAAATAATTATAATAATTT
CTATTATTTCGTTTTGAATATGGTGTTG
Found at i:200738 original size:90 final size:89
Alignment explanation
Indices: 200507--201238 Score: 515
Period size: 90 Copynumber: 8.2 Consensus size: 89
200497 AATATGGTGT
* * * **
200507 TGCAATAA-ATTTTTTATATTCTGGAATAATTATAATAATTGCTATTTAATTT-ACCTCATTTTC
1 TGCAATAATATTTTTTATTTTCCGAAATAATTATAATAATTGCTATTT-ATTTCATTTCATTTTC
* * *
200570 -GGGTACTTGGCCTTGAGTTTAGCCTAC
65 AGGGCACTTGG-CTTGAGTCTAG--TGC
* * * * * * *
200597 TACAATTACAT-TTTTTTATTATCCAAAATAGTTATAATAATTGCAACTTATTTCATTTTATTTT
1 TGCAA-TA-ATATTTTTTATTTTCCGAAATAATTATAATAATTGCTATTTATTTCATTTCATTTT
* * * *
200661 CGGGGCACTTAGGCTCGAGTCTAATGT
64 CAGGGCACTT-GGCTTGAGTCTAGTGC
* *
200688 TGCAATAATATTTTTTATTTTCCGGAATAATTATAATAATTGCTATTTATTTCATTTAATTTAT-
1 TGCAATAATATTTTTTATTTTCCGAAATAATTATAATAATTGCTATTTATTTCATTTCATTT-TC
* * * *
200752 GGGGCACTTGGGCTTGATTTTGGTGC
65 AGGGCACTT-GGCTTGAGTCTAGTGC
** * * ** * **
200778 TATAATAATATTTTTTATTTTCTGAAATAATTATAATAATTGTTATCCATTTCATTTTATTCCCA
1 TGCAATAATATTTTTTATTTTCCGAAATAATTATAATAATTGCTATTTATTTCATTTCATTTTCA
** *
200843 GAACACTTGGACTTGAGTCTGGTGC
66 GGGCACTTGG-CTTGAGTCTAGTGC
* * * *
200868 TGCGATAA-ATTTTTTATTTTTCGAAATAATTATAATAGTTG-TAAATTTATTTCATTTCATTCT
1 TGCAATAATATTTTTTATTTTCCGAAATAATTATAATAATTGCT--ATTTATTTCATTTCATTTT
* *
200931 CAAGGCACTTAGACTTGAGTCTAGTGC
64 CAGGGCACTT-GGCTTGAGTCTAGTGC
* * * * * * * *
200958 TGCGACAATATTTTTTTATTTT-CAAAATAATTATAATAGTTACGATTTATTTTATTTTATTTTC
1 TGCAATAATA-TTTTTTATTTTCCGAAATAATTATAATAATTGCTATTTATTTCATTTCATTTTC
* * *
201022 AGGGTATTTGGGCTTGAGTCT-GATGT
65 AGGGCACTT-GGCTTGAGTCTAG-TGC
* * * * * * *
201048 TGTAATAATATTTTGT-TTTT--GGAATAATTGTAATAATTTCTA-TTATTTCATTCCATTTT-T
1 TGCAATAATATTTTTTATTTTCCGAAATAATTATAATAATTGCTATTTATTTCATTTCATTTTCA
* * * *
201108 GGGCTCTTTGGCTTAAGTCTCGTTC
66 GGGCAC-TTGGCTTGAGTCTAGTGC
* * **
201133 TGCAATAATATTTTTTTATTTT-CTAGAATAATTATAAGAATTGCTATTTATTTCATTTCATTCC
1 TGCAATAATA-TTTTTTATTTTCCGA-AATAATTATAATAATTGCTATTTATTTCATTTCATTTT
** * *
201197 CAAAGAACTTGGGTTTGAGTCTAGTGC
64 CAGGGCACTT-GGCTTGAGTCTAGTGC
201224 TGCAATAAT-TTTTTT
1 TGCAATAATATTTTTT
201239 GGAATATTTA
Statistics
Matches: 501, Mismatches: 115, Indels: 53
0.75 0.17 0.08
Matches are distributed among these distances:
85 23 0.05
86 22 0.04
87 20 0.04
88 5 0.01
89 63 0.13
90 246 0.49
91 55 0.11
92 50 0.10
93 15 0.03
94 2 0.00
ACGTcount: A:0.28, C:0.12, G:0.14, T:0.47
Consensus pattern (89 bp):
TGCAATAATATTTTTTATTTTCCGAAATAATTATAATAATTGCTATTTATTTCATTTCATTTTCA
GGGCACTTGGCTTGAGTCTAGTGC
Found at i:201535 original size:92 final size:91
Alignment explanation
Indices: 201315--201632 Score: 309
Period size: 92 Copynumber: 3.4 Consensus size: 91
201305 TATTTTCGAA
* * * *
201315 AATAATTATAATAATTGTTATTTATTTTATATCATTTTCAAGGCATTTGGGCTTGAGTCTCGTGC
1 AATAATTATAATAATTGATATTTATTTTATTTCATTTTCAA-GCACTTGGACTTGAGTCT-G-G-
* *
201380 TGCAATAATAATAATTTT-TTTTATTTTTCAG
62 TGCAATAATAAT-TTTTTATTTTATTTTT-GG
* * * * * *
201411 AATAACTATAATAATTGCTATTTATTTCATTTCATTTTCGGAA-CACTTGAATTTAAGTCTGGTG
1 AATAATTATAATAATTGATATTTATTTTATTTCATTTTC--AAGCACTTGGACTTGAGTCTGGTG
*
201475 CACTAATAATTTTTTATTTTATTTTTGG
64 CAATAATAATTTTTTATTTTATTTTTGG
* * * **
201503 AATAATTATAATAATTGATATTTATTTTATTTCATTCTCAAGGCACTTGGCCTTGAGTATAATGC
1 AATAATTATAATAATTGATATTTATTTTATTTCATTTTCAA-GCACTTGGACTTGAGTCTGGTGC
**
201568 TGTAAT-ATTTTTTATTTTATTTTTTGG
65 AATAATAATTTTTTATTTTA-TTTTTGG
* * * *
201595 AATAGTTATAATTATCGATATTTATTTTATTTTATTTT
1 AATAATTATAATAATTGATATTTATTTTATTTCATTTT
201633 ATTTTTAGGA
Statistics
Matches: 186, Mismatches: 30, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
90 2 0.01
91 13 0.07
92 99 0.53
93 21 0.11
94 1 0.01
95 1 0.01
96 47 0.25
98 2 0.01
ACGTcount: A:0.29, C:0.09, G:0.11, T:0.51
Consensus pattern (91 bp):
AATAATTATAATAATTGATATTTATTTTATTTCATTTTCAAGCACTTGGACTTGAGTCTGGTGCA
ATAATAATTTTTTATTTTATTTTTGG
Found at i:202012 original size:91 final size:90
Alignment explanation
Indices: 201243--202294 Score: 548
Period size: 90 Copynumber: 11.5 Consensus size: 90
201233 TTTTTTGGAA
* * * * * * *
201243 TATTTATTTTAGTTCATTTTTAAGGCACTTGGG-TTTCAGTATGGTGTTGTAATAATATTTTTTA
1 TATTTATTTTATTTCATTTTCAGGGCACTTGGGCTTTGAGTATGGTGCTGCAATAATTTTTTTTA
201307 TTTTCGAAAATAATTATAATAATTGT
66 TTTTC-AAAATAATTATAATAATTGT
* * * * *
201333 TATTTATTTTATATCATTTTCAAGGCATTTGGGC-TTGAGTCTCGTGCTGCAATAATAATAATTT
1 TATTTATTTTATTTCATTTTCAGGGCACTTGGGCTTTGAGTATGGTGCTGC------AATAATTT
* * *
201397 TTTTTATTTTTCAGAATAACTATAATAATTGC
60 TTTTTA-TTTTCAAAATAATTATAATAATTGT
* * ** * * *
201429 TATTTATTTCATTTCATTTTC-GGAACACTT-GAATTTAAGTCTGGTGC-ACTAATAATTTTTTA
1 TATTTATTTTATTTCATTTTCAGG-GCACTTGGGCTTTGAGTATGGTGCTGC-AATAA--TTTT-
*** *
201491 TTTTATTTTTGGAATAATTATAATAATTGA
61 TTTTATTTTCAAAATAATTATAATAATTGT
* * * ** * *
201521 TATTTATTTTATTTCATTCTCAAGGCACTT-GGCCTTGAGTATAATGCTGTAATATTTTTTATTT
1 TATTTATTTTATTTCATTTTCAGGGCACTTGGGCTTTGAGTATGGTGCTGCAATA-ATTTT-TTT
*** *
201585 TATTTTTTGGAATAGTTATAATTATCGATAT-T
64 TA-TTTTCAAAATAATTATAA-TA---AT-TGT
* * * *** * *
201617 TATTTTATTTTATTTTATTTTTAGGACACTTCAACTTT-AGTA-GAGTGCTGTAATAA-TATTTT
1 TA-TTTATTTTATTTCATTTTCAGGGCACTTGGGCTTTGAGTATG-GTGCTGCAATAATTTTTTT
201679 TATTTTCAAAATAATTATAATAATTGT
64 TATTTTCAAAATAATTATAATAATTGT
* * * * * * * * **
201706 TATTTATTTTATTTCATTTTCAGGGTAATTGAGC-TTGAGTTTAGCGCTACAATAGTAAATTTTT
1 TATTTATTTTATTTCATTTTCAGGGCACTTGGGCTTTGAGTATGGTGCTGCAATAAT-TTTTTTT
* *
201770 ATTTTTAAGAATAATTATAATAATTAT
65 ATTTTCAA-AATAATTATAATAATTGT
* * * * * *
201797 TATTTATTTTATTTCATTTTTAAGGCATTTGGAC-TTGAGTTTGGTGCTGCAATAAATTTTTTTA
1 TATTTATTTTATTTCATTTTCAGGGCACTTGGGCTTTGAGTATGGTGCTGCAATAATTTTTTTTA
* * *
201861 TTTTCTCATAGAATTATAATAATT-T
66 TTTTC-AAAATAATTATAATAATTGT
* * *
201886 CTATTTATTTCATTTCA--TTCATTGGACACTGGGGCTTTGAGTATGGTGCTGCAATAATTTTTT
1 -TATTTATTTTATTTCATTTTCA--GGGCACTTGGGCTTTGAGTATGGTGCTGCAATAATTTTTT
* *
201949 TTATTTTCCAAAATAATTTTAATAATTTT
63 TTATTTT-CAAAATAATTATAATAATTGT
* * * * ** * * ** * *
201978 TATTTAATTTATTTTATTTTCAGGGTACTTGGGCTTGGTTCTAATGCTCCTAAAATATATATATA
1 TATTTATTTTATTTCATTTTCAGGGCACTTGGGCTTTG-AGT-ATGGTGCTGCAATA-AT-TTTT
* * * * **
202043 TATATATT--AAATTATTATGATAATTAC
62 TTTATTTTCAAAATAATTATAATAATTGT
* * * * *
202070 TATTTATTTCATTTCATTTCATTCCCTGGGGACTTGGGC-TTGAGTTTGGTGTTGCAATAATATT
1 TATTTATTTTATTTCA-TT--TT--CAGGGCACTTGGGCTTTGAGTATGGTGCTGCAATAAT-TT
* *
202134 TTATTATTTTTCGAAATAATTATAATAATTGT
60 TTTTTA-TTTTCAAAATAATTATAATAATTGT
* * * * * * * **
202166 TATTAATCTTATTTCATTATC-GAGCACTTGGAC-TTGAGTCTGATGCCACAATAATTTCTTTTT
1 TATTTATTTTATTTCATTTTCAGGGCACTTGGGCTTTGAGTATGGTGCTGCAATAATTT-TTTTT
** * *
202229 ATTTTTTGAAATAATTAAAATAATAGT
65 A-TTTTCAAAATAATTATAATAATTGT
* *
202256 TATTTATTTCATTTCA--TTCCGAGGCACTTGGGC-TTGAGT
1 TATTTATTTTATTTCATTTTCAG-GGCACTTGGGCTTTGAGT
202295 CTAGTACTAC
Statistics
Matches: 735, Mismatches: 172, Indels: 110
0.72 0.17 0.11
Matches are distributed among these distances:
87 2 0.00
88 42 0.06
89 9 0.01
90 187 0.25
91 145 0.20
92 112 0.15
93 46 0.06
94 18 0.02
95 18 0.02
96 98 0.13
97 55 0.07
98 3 0.00
ACGTcount: A:0.29, C:0.09, G:0.13, T:0.49
Consensus pattern (90 bp):
TATTTATTTTATTTCATTTTCAGGGCACTTGGGCTTTGAGTATGGTGCTGCAATAATTTTTTTTA
TTTTCAAAATAATTATAATAATTGT
Found at i:202313 original size:2 final size:2
Alignment explanation
Indices: 202306--202333 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
202296 TAGTACTACA
202306 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
202334 TGGAATAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:202327 original size:278 final size:278
Alignment explanation
Indices: 201825--202325 Score: 601
Period size: 278 Copynumber: 1.8 Consensus size: 278
201815 TTTAAGGCAT
* *
201825 TTGGACTTGAGTTTGGTGCTGCAATAAATTTTTTTATTTTCTCATAGAATTATAATAATTTCTAT
1 TTGGACTTGAGTTTGGTGCTGCAATAAATTTTATTATTTTCTCAAAGAATTATAATAATTTCTAT
* * * * **
201890 TTATTTCATTTCATTCATTGGACACTGGGGCTTTGAGTATGGTGCTGCAATAATTTTTTTTATTT
66 TAATTTCATTTCATTCATCGGACACTGGGACTTTGAGTATGATGCCACAATAATTTTTTTTATTT
** ** * * *
201955 TCCAAAATAATTTTAATAATTTTTATTTAATTTATTTTATTTTCAGGGTACTTGGGCTTGGTTCT
131 TCCAAAATAATTAAAATAATAGTTATTTAATTTATTTCATTTCCAGGGCACTTGGGCTTGGTTCT
* *
202020 AATGCTCCTAAAATATATATATATATATATTAAATTATTATGATAATTACTATTTATTTCATTTC
196 AATACTACTAAAATATATATATATATATATTAAATTATTATGATAATTACTATTTATTTCATTTC
202085 ATTTCATTCCCTGGGGAC
261 ATTTCATTCCCTGGGGAC
* * *
202103 TTGGGCTTGAGTTTGGTGTTGCAATAATATTTTATTATTTT-TCGAAATAATTATAATAATTGT-
1 TTGGACTTGAGTTTGGTGCTGCAATAA-ATTTTATTATTTTCTC-AAAGAATTATAATAATT-TC
* *
202166 TATTAATCTT-ATTTCATT-ATC-GAGCACTTGGAC-TTGAGTCTGATGCCACAATAATTTCTTT
63 TATTAAT-TTCATTTCATTCATCGGA-CACTGGGACTTTGAGTATGATGCCACAATAATTT-TTT
***
202227 TTATTTTTTGAAATAATTAAAATAATAGTTATTT-ATTTCATTTCA-TTCC-GAGGCACTTGGGC
125 TTATTTTCCAAAATAATTAAAATAATAGTTATTTAATTT-ATTTCATTTCCAG-GGCACTTGGGC
* *
202289 TTGAG-TCTAGTACTAC-AATATATATATATATATATAT
188 TTG-GTTCTAATACTACTAAAATATATATATATATATAT
202326 ATATATATTG
Statistics
Matches: 187, Mismatches: 27, Indels: 20
0.80 0.12 0.09
Matches are distributed among these distances:
276 21 0.11
277 50 0.27
278 72 0.39
279 41 0.22
280 3 0.02
ACGTcount: A:0.29, C:0.11, G:0.13, T:0.47
Consensus pattern (278 bp):
TTGGACTTGAGTTTGGTGCTGCAATAAATTTTATTATTTTCTCAAAGAATTATAATAATTTCTAT
TAATTTCATTTCATTCATCGGACACTGGGACTTTGAGTATGATGCCACAATAATTTTTTTTATTT
TCCAAAATAATTAAAATAATAGTTATTTAATTTATTTCATTTCCAGGGCACTTGGGCTTGGTTCT
AATACTACTAAAATATATATATATATATATTAAATTATTATGATAATTACTATTTATTTCATTTC
ATTTCATTCCCTGGGGAC
Found at i:202611 original size:92 final size:90
Alignment explanation
Indices: 202484--202710 Score: 285
Period size: 92 Copynumber: 2.5 Consensus size: 90
202474 TGCAACATAC
* * *
202484 TTTTATTTTTCGGAATAATTATAATAATTTCTATTTATTTCATTTCATTTCTAGACCATTTGGGT
1 TTTTATTTTTTGGAATAATTATAATAATTTTTATTTATTTCATTTCATTTCTAGACCATTTGGGC
* **
202549 TTGAGTTTGATGCTGTTATAATAATT
66 TTGAGTTTGATACTGCAATAAT-ATT
* * * * *
202575 TTTATATTTTTTGGAACAATTATAATAATTTTTATTTATTTCATTTTATTTTTGGAGCATTTGGG
1 TTT-TATTTTTTGGAATAATTATAATAATTTTTATTTATTTCATTTCATTTCTAGACCATTTGGG
*
202640 CTTGAGTTTGGTACTGCAATAATATT
65 CTTGAGTTTGATACTGCAATAATATT
* *
202666 TTTTATTTTCTGAAATAATTATAATAATTTTT-TTTCCATTTCATT
1 TTTTATTTTTTGGAATAATTATAATAATTTTTATTT--ATTTCATT
202711 CTCAAGGCCG
Statistics
Matches: 118, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
89 3 0.03
90 26 0.22
91 17 0.14
92 72 0.61
ACGTcount: A:0.27, C:0.08, G:0.11, T:0.54
Consensus pattern (90 bp):
TTTTATTTTTTGGAATAATTATAATAATTTTTATTTATTTCATTTCATTTCTAGACCATTTGGGC
TTGAGTTTGATACTGCAATAATATT
Found at i:206486 original size:21 final size:20
Alignment explanation
Indices: 206460--206541 Score: 87
Period size: 21 Copynumber: 4.0 Consensus size: 20
206450 AAAACATAGA
206460 AAAAGAATAAAGAAAAAAATT
1 AAAAGAATAAAGAAAAAAA-T
*
206481 AAAAGAATGAAGAAAAAAAT
1 AAAAGAATAAAGAAAAAAAT
*
206501 AAAGGAA-AAAGCAAAAGAGAAT
1 AAAAGAATAAAG-AAAA-A-AAT
206523 AAAA-AATAAAGAAATAAAA
1 AAAAGAATAAAGAAA-AAAA
206542 AGAAAATTAC
Statistics
Matches: 52, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
19 3 0.06
20 13 0.25
21 25 0.48
22 11 0.21
ACGTcount: A:0.76, C:0.01, G:0.13, T:0.10
Consensus pattern (20 bp):
AAAAGAATAAAGAAAAAAAT
Found at i:206522 original size:34 final size:34
Alignment explanation
Indices: 206457--206540 Score: 80
Period size: 34 Copynumber: 2.4 Consensus size: 34
206447 AGGAAAACAT
**
206457 AGAAAAAGAATAAAGAAAAAAATTAAAAGAATGA
1 AGAAAAAGAATAAAGAAAAAAACAAAAAGAATGA
* * *
206491 AGAAAAA-AATAAAGGAAAAAGCAAAAGAGAATAA
1 AGAAAAAGAATAAAGAAAAAAACAAAA-AGAATGA
*
206525 AAAATAAAGAAATAAA
1 AGAA-AAAG-AATAAA
206541 AAGAAAATTA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
33 15 0.38
34 16 0.40
35 3 0.08
37 6 0.15
ACGTcount: A:0.75, C:0.01, G:0.14, T:0.10
Consensus pattern (34 bp):
AGAAAAAGAATAAAGAAAAAAACAAAAAGAATGA
Found at i:209692 original size:2 final size:2
Alignment explanation
Indices: 209685--209729 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
209675 ACTACCATTA
*
209685 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC 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
209727 AT A
1 AT A
209730 AAGAAAAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:222346 original size:17 final size:17
Alignment explanation
Indices: 222326--222359 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
222316 TAAGACTCGG
222326 GAAAGAA-AAAGAAATAA
1 GAAAGAACAAA-AAATAA
222343 GAAAGAACAAAAAATAA
1 GAAAGAACAAAAAATAA
222360 ATCTTACATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.76, C:0.03, G:0.15, T:0.06
Consensus pattern (17 bp):
GAAAGAACAAAAAATAA
Found at i:226485 original size:17 final size:18
Alignment explanation
Indices: 226458--226491 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
226448 GCTTCGGAGA
226458 ATATGCCAAAATCTTCAC
1 ATATGCCAAAATCTTCAC
226476 ATAT-CCAAAATCTTCA
1 ATATGCCAAAATCTTCA
226492 TAATTTTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.41, C:0.26, G:0.03, T:0.29
Consensus pattern (18 bp):
ATATGCCAAAATCTTCAC
Found at i:234822 original size:15 final size:16
Alignment explanation
Indices: 234785--234827 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 16
234775 TTACAATTTG
*
234785 AATTTAATTTTTATCT
1 AATTTAATTTTTATAT
*
234801 AAATTAATTTTTA-AT
1 AATTTAATTTTTATAT
234816 AATTTAATTTTT
1 AATTTAATTTTT
234828 GAATTTCAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (16 bp):
AATTTAATTTTTATAT
Found at i:242192 original size:30 final size:30
Alignment explanation
Indices: 242156--242218 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
242146 TGATGTGAGA
*
242156 AAATTGTATGGATCTAACATGACTCACTTT
1 AAATTGTATGGATCGAACATGACTCACTTT
242186 AAATTGTATGGATCGAACATGACTCACTTT
1 AAATTGTATGGATCGAACATGACTCACTTT
242216 AAA
1 AAA
242219 ATTCAACTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (30 bp):
AAATTGTATGGATCGAACATGACTCACTTT
Found at i:242224 original size:107 final size:107
Alignment explanation
Indices: 242091--242296 Score: 394
Period size: 107 Copynumber: 1.9 Consensus size: 107
242081 TGAAAAAGCC
242091 TCGAACATGACTCACTTTAAAATTCAACTATTAGTGTTGTCTTTTTAAATGCACTTGATGTGAGA
1 TCGAACATGACTCACTTTAAAATTCAACTATTAGTGTTGTCTTTTTAAATGCACTTGATGTGAGA
*
242156 AAATTGTATGGATCTAACATGACTCACTTTAAATTGTATGGA
66 AAATTGTATGGATCTAACATAACTCACTTTAAATTGTATGGA
*
242198 TCGAACATGACTCACTTTAAAATTCAACTATTAGTGTTGTCTTTTTAAATGCATTTGATGTGAGA
1 TCGAACATGACTCACTTTAAAATTCAACTATTAGTGTTGTCTTTTTAAATGCACTTGATGTGAGA
242263 AAATTGTATGGATCTAACATAACTCACTTTAAAT
66 AAATTGTATGGATCTAACATAACTCACTTTAAAT
242297 GTGATGTTAT
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
107 97 1.00
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (107 bp):
TCGAACATGACTCACTTTAAAATTCAACTATTAGTGTTGTCTTTTTAAATGCACTTGATGTGAGA
AAATTGTATGGATCTAACATAACTCACTTTAAATTGTATGGA
Found at i:255211 original size:29 final size:30
Alignment explanation
Indices: 255147--255212 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 30
255137 GAGGGAGTGG
*
255147 TAAATTT-TTATTTTTACTACTAATAATAA
1 TAAATTTATTATTTTTAATACTAATAATAA
* * * *
255176 TATATTTATT-TTTTTAATATTAATATTAT
1 TAAATTTATTATTTTTAATACTAATAATAA
255205 TAAATTTA
1 TAAATTTA
255213 AAATATGATA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
29 28 0.93
30 2 0.07
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (30 bp):
TAAATTTATTATTTTTAATACTAATAATAA
Found at i:271399 original size:16 final size:15
Alignment explanation
Indices: 271368--271405 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
271358 TTGACTCAAG
271368 ATAAAAATATCAAAA
1 ATAAAAATATCAAAA
271383 ATAAAAATAT-ATGAAA
1 ATAAAAATATCA--AAA
271399 ATAAAAA
1 ATAAAAA
271406 AAATAATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 1 0.05
15 10 0.48
16 10 0.48
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (15 bp):
ATAAAAATATCAAAA
Found at i:274049 original size:6 final size:6
Alignment explanation
Indices: 274038--274077 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
274028 TAATCGTGGG
274038 GGAGAT GGAGAT GGAGAT GGAGAT GGAGAT GGAGAT GGAG
1 GGAGAT GGAGAT GGAGAT GGAGAT GGAGAT GGAGAT GGAG
274078 GAGGGAGGGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.33, C:0.00, G:0.53, T:0.15
Consensus pattern (6 bp):
GGAGAT
Found at i:277664 original size:30 final size:30
Alignment explanation
Indices: 277599--277666 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
277589 TAAAAATTAG
*
277599 TATATG-ATAATTTCCAGCCATATAAGTAA
1 TATATGAATAATTTCAAGCCATATAAGTAA
** *
277628 -ATATGAATAATTTCAAGTTATGTAAGTAA
1 TATATGAATAATTTCAAGCCATATAAGTAA
277657 TATATGAATA
1 TATATGAATA
277667 TACTCGAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 5 0.15
29 19 0.58
30 9 0.27
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.37
Consensus pattern (30 bp):
TATATGAATAATTTCAAGCCATATAAGTAA
Found at i:280558 original size:2 final size:2
Alignment explanation
Indices: 280551--280585 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
280541 GTAATTCATT
280551 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
280586 TAGTCACTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:280790 original size:54 final size:54
Alignment explanation
Indices: 280726--280831 Score: 135
Period size: 55 Copynumber: 2.0 Consensus size: 54
280716 AAAATATTTG
* *
280726 GTGACAAAAAAATT-TAAATAATTGAATGAAC-ATTTTATAATTTTTCATAATTAA
1 GTGACAAAAAAATTATAAATAATTAAAT-AACTATTTTATAACTTTT-ATAATTAA
* * *
280780 GTGATAAAAAAATTATTATTAATTAAATAACTATTTTATAACTTTTATAATT
1 GTGACAAAAAAATTATAAATAATTAAATAACTATTTTATAACTTTTATAATT
280832 GGATGAAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
54 22 0.49
55 23 0.51
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.42
Consensus pattern (54 bp):
GTGACAAAAAAATTATAAATAATTAAATAACTATTTTATAACTTTTATAATTAA
Found at i:280843 original size:54 final size:54
Alignment explanation
Indices: 280723--280846 Score: 130
Period size: 54 Copynumber: 2.3 Consensus size: 54
280713 TCCAAAATAT
* * *
280723 TTGG-TGACAAAAAAATTTAAATAATTGAATGAACATTTTATAATTTTTCATAA
1 TTGGATGAAAAAAAAATTTAAATAATTAAATGAACATTTTATAACTTTTCATAA
* * * *
280776 TT-AAGTGATAAAAAAATTATTATTAATTAAAT-AACTATTTTATAACTTTT-ATAA
1 TTGGA-TGAAAAAAAAATT-TAAATAATTAAATGAAC-ATTTTATAACTTTTCATAA
280830 TTGGATGAAAAAAAAAT
1 TTGGATGAAAAAAAAAT
280847 ATAAGAAAGT
Statistics
Matches: 58, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
53 2 0.03
54 32 0.55
55 24 0.41
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.40
Consensus pattern (54 bp):
TTGGATGAAAAAAAAATTTAAATAATTAAATGAACATTTTATAACTTTTCATAA
Found at i:283505 original size:12 final size:12
Alignment explanation
Indices: 283490--283519 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
283480 CATTAAGAAC
283490 AAAAAAATATAA
1 AAAAAAATATAA
*
283502 AAAATAATATAA
1 AAAAAAATATAA
283514 AAAAAA
1 AAAAAA
283520 CCTAACAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (12 bp):
AAAAAAATATAA
Found at i:290460 original size:18 final size:17
Alignment explanation
Indices: 290437--290479 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 17
290427 GAGCTTGTTT
290437 TTAATTAAATAAATT-TAA
1 TTAATTAAA-AAATTAT-A
290455 TTAATTGAAAAAATTATA
1 TTAATT-AAAAAATTATA
290473 TTAATTA
1 TTAATTA
290480 CACCTTGAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 1 0.04
18 18 0.78
19 4 0.17
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (17 bp):
TTAATTAAAAAATTATA
Found at i:299168 original size:13 final size:13
Alignment explanation
Indices: 299150--299192 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
299140 AAATAAAATG
299150 TTTATATTTTTTA
1 TTTATATTTTTTA
* * *
299163 TTTATAATTATAA
1 TTTATATTTTTTA
299176 TTTATATTTTATTA
1 TTTATATTTT-TTA
299190 TTT
1 TTT
299193 GATTTAAATA
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
13 18 0.78
14 5 0.22
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTATATTTTTTA
Found at i:300157 original size:6 final size:7
Alignment explanation
Indices: 300138--300162 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
300128 GTGATCTCTC
300138 TCTTTTT
1 TCTTTTT
300145 TCTTTTT
1 TCTTTTT
300152 TCTTTTT
1 TCTTTTT
300159 TCTT
1 TCTT
300163 ACTGCTCTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (7 bp):
TCTTTTT
Found at i:303628 original size:2 final size:2
Alignment explanation
Indices: 303621--303658 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
303611 AACTTGATGT
*
303621 GA GA GA GA CA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
303659 ACATAGGCAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.03, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:311157 original size:24 final size:24
Alignment explanation
Indices: 311130--311180 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
311120 GGGGTCGAGA
311130 GTTGATTTAATCAAGGAATCTCGT
1 GTTGATTTAATCAAGGAATCTCGT
311154 GTTGATTTAATCAAGGAATCTCGT
1 GTTGATTTAATCAAGGAATCTCGT
311178 GTT
1 GTT
311181 TTGCTAATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.39
Consensus pattern (24 bp):
GTTGATTTAATCAAGGAATCTCGT
Found at i:339192 original size:20 final size:20
Alignment explanation
Indices: 339164--339211 Score: 80
Period size: 19 Copynumber: 2.5 Consensus size: 20
339154 AGTTCAATAT
*
339164 AAAATATTAATATTAATTTA
1 AAAAAATTAATATTAATTTA
339184 AAAAAATT-ATATTAATTTA
1 AAAAAATTAATATTAATTTA
339203 AAAAAATTA
1 AAAAAATTA
339212 CGTGAAATAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 19 0.73
20 7 0.27
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
AAAAAATTAATATTAATTTA
Found at i:344091 original size:28 final size:28
Alignment explanation
Indices: 344036--344097 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
344026 TTCGTGAACA
* * *
344036 TTAAACAAATGAACATGAACACATAATT
1 TTAAATAAATGAACATGAACAAAAAATT
344064 TTAAATAAATGAACATGAACAAAAAATT
1 TTAAATAAATGAACATGAACAAAAAATT
*
344092 TAAAAT
1 TTAAAT
344098 TTTTAACGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.58, C:0.10, G:0.06, T:0.26
Consensus pattern (28 bp):
TTAAATAAATGAACATGAACAAAAAATT
Found at i:348669 original size:15 final size:15
Alignment explanation
Indices: 348649--348688 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
348639 TGGGGAAGCG
348649 GCGGCGGAGGCGGCA
1 GCGGCGGAGGCGGCA
348664 GCGGCGGAGGCGGCA
1 GCGGCGGAGGCGGCA
348679 GCGGCGGAGG
1 GCGGCGGAGG
348689 AGGATGGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.12, C:0.25, G:0.62, T:0.00
Consensus pattern (15 bp):
GCGGCGGAGGCGGCA
Found at i:352273 original size:29 final size:29
Alignment explanation
Indices: 352217--352281 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
352207 TATTAAAAGG
* *
352217 CCTTCAAGATCTATTTTCATGCATTTGAAC
1 CCTTCAAGATCTATTTTCATCCAATTG-AC
*
352247 CCTTCAA-ATCTATTTTCATCCAATTGAG
1 CCTTCAAGATCTATTTTCATCCAATTGAC
352275 CCTTCAA
1 CCTTCAA
352282 TCTGACAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
28 8 0.25
29 17 0.53
30 7 0.22
ACGTcount: A:0.28, C:0.26, G:0.08, T:0.38
Consensus pattern (29 bp):
CCTTCAAGATCTATTTTCATCCAATTGAC
Found at i:362929 original size:15 final size:15
Alignment explanation
Indices: 362881--362929 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
362871 AACCTTCTGA
*
362881 TGATTCTCTACCAAT
1 TGATTCTCTACCAGT
* *
362896 TGAATCTCTAACAGT
1 TGATTCTCTACCAGT
362911 TGATTCTCTACCAGT
1 TGATTCTCTACCAGT
362926 TGAT
1 TGAT
362930 GCCATGTAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.27, C:0.22, G:0.12, T:0.39
Consensus pattern (15 bp):
TGATTCTCTACCAGT
Found at i:372601 original size:194 final size:194
Alignment explanation
Indices: 372272--372659 Score: 749
Period size: 194 Copynumber: 2.0 Consensus size: 194
372262 ACGATCTCGG
*
372272 TCAAGGATAACAAATGATGATAAAGAGCATATGTTAAATATTAAAAAGATAATAGCTCAACAAAT
1 TCAAGGATAACAAATGATGATAAAGAGCATATGTTAAATATTAAAAAGATAATAACTCAACAAAT
*
372337 ATGTAATAAAACAATTAGATAAAATTGCATATAAAATTTATTTTTCATATTATTTTTATTAGTAA
66 ATGCAATAAAACAATTAGATAAAATTGCATATAAAATTTATTTTTCATATTATTTTTATTAGTAA
*
372402 TTGTGTTATCAATCACTTTTTAAACTAACATAATACATATGATGGTTTGATTTGATTTTTGTTA
131 TTGTGTTATCAATCACTTTTTAAACTAACATAATACATATGATGGTTTGAATTGATTTTTGTTA
372466 TCAAGGATAACAAATGATGATAAAGAGCATATGTTAAATATTAAAAAGATAATAACTCAACAAAT
1 TCAAGGATAACAAATGATGATAAAGAGCATATGTTAAATATTAAAAAGATAATAACTCAACAAAT
372531 ATGCAATAAAACAATTAGATAAAATTGCATATAAAATTTATTTTTCATATTATTTTTATTAGTAA
66 ATGCAATAAAACAATTAGATAAAATTGCATATAAAATTTATTTTTCATATTATTTTTATTAGTAA
372596 TTGTGTTATCAATCACTTTTTAAACTAACATAATACATATGATGGTTTGAATTGATTTTTGTTA
131 TTGTGTTATCAATCACTTTTTAAACTAACATAATACATATGATGGTTTGAATTGATTTTTGTTA
372660 CGTGTAGAAA
Statistics
Matches: 191, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
194 191 1.00
ACGTcount: A:0.43, C:0.08, G:0.11, T:0.39
Consensus pattern (194 bp):
TCAAGGATAACAAATGATGATAAAGAGCATATGTTAAATATTAAAAAGATAATAACTCAACAAAT
ATGCAATAAAACAATTAGATAAAATTGCATATAAAATTTATTTTTCATATTATTTTTATTAGTAA
TTGTGTTATCAATCACTTTTTAAACTAACATAATACATATGATGGTTTGAATTGATTTTTGTTA
Found at i:378646 original size:21 final size:21
Alignment explanation
Indices: 378609--378649 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
378599 ATAATTATCG
378609 TTTTAAATTATACTATTTATGT
1 TTTTAAATTATA-TATTTATGT
378631 TTTTAAATGTAT-TATTTAT
1 TTTTAAAT-TATATATTTAT
378650 ATTTATATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.39
22 8 0.44
23 3 0.17
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (21 bp):
TTTTAAATTATATATTTATGT
Found at i:379007 original size:9 final size:9
Alignment explanation
Indices: 378995--379132 Score: 95
Period size: 9 Copynumber: 14.9 Consensus size: 9
378985 TTAGTTTTAC
378995 ATTTTTATA
1 ATTTTTATA
379004 ATTTATTAT-
1 ATTT-TTATA
379013 ATTTTTATA
1 ATTTTTATA
*
379022 ATTTTTTTA
1 ATTTTTATA
*
379031 ATTTTAATGA
1 ATTTTTAT-A
* *
379041 GTTTATATTA
1 ATTTTTA-TA
*
379051 ATTTTAAT-
1 ATTTTTATA
379059 ATTTTTACT-
1 ATTTTTA-TA
*
379068 ATTTTT-TT
1 ATTTTTATA
379076 ATTTTTATA
1 ATTTTTATA
*
379085 ATTATTTTAAA
1 A-T-TTTTATA
379096 ATTTTTATA
1 ATTTTTATA
*
379105 ATTTTTTATG
1 A-TTTTTATA
379115 ATTTTTAATA
1 ATTTTT-ATA
*
379125 AGTTTTAT
1 ATTTTTAT
379133 GGGAAAATTA
Statistics
Matches: 102, Mismatches: 16, Indels: 22
0.73 0.11 0.16
Matches are distributed among these distances:
7 1 0.01
8 16 0.16
9 46 0.45
10 31 0.30
11 8 0.08
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.65
Consensus pattern (9 bp):
ATTTTTATA
Found at i:379012 original size:27 final size:27
Alignment explanation
Indices: 378986--379132 Score: 72
Period size: 29 Copynumber: 5.3 Consensus size: 27
378976 TAAGTTTTAT
*
378986 TAGTTTTA-CATTTTTATAATTTATTA
1 TAGTTTTATAATTTTTATAATTTATTA
* * *
379012 TATTTTTATAATTTTTTTAATTT-TAA
1 TAGTTTTATAATTTTTATAATTTATTA
*
379038 TGAGTTTATATTAATTTTAAT-ATTT-TTA
1 T-AGTTT-TA-TAATTTTTATAATTTATTA
* * *
379066 CTA-TTTTTTTATTTTTATAATTATTTTAA
1 -TAGTTTTATAATTTTTATAATT-TATT-A
* * *
379095 AATTTTTATAATTTTTTATGATTT-TTAA
1 TAGTTTTATAA-TTTTTATAATTTATT-A
379123 TAAGTTTTAT
1 T-AGTTTTAT
379133 GGGAAAATTA
Statistics
Matches: 92, Mismatches: 17, Indels: 21
0.71 0.13 0.16
Matches are distributed among these distances:
25 8 0.09
26 14 0.15
27 20 0.22
28 16 0.17
29 24 0.26
30 10 0.11
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.65
Consensus pattern (27 bp):
TAGTTTTATAATTTTTATAATTTATTA
Found at i:379025 original size:63 final size:62
Alignment explanation
Indices: 378952--379105 Score: 145
Period size: 63 Copynumber: 2.4 Consensus size: 62
378942 CATTTCGATG
*
378952 TTTTT-TAATTTTAAACATTTTAAATAAGTTT-TATTAGTTTT-ACATTTTTA-TAATTTATTAT
1 TTTTTATAATTTTAAA-ATTTT-AATAAGTTTATATTAATTTTAACATTTTTACT-ATTT-TTAT
379013 A
62 A
** * * *
379014 TTTTTATAATTTTTTTAATTTTAATGAGTTTATATTAATTTTAATATTTTTACTATTTTTTTA
1 TTTTTATAA-TTTTAAAATTTTAATAAGTTTATATTAATTTTAACATTTTTACTATTTTTATA
*
379077 TTTTTATAATTATTTTAAAATTTTTATAA
1 TTTTTAT-A--ATTTTAAAATTTTAATAA
379106 TTTTTTATGA
Statistics
Matches: 74, Mismatches: 10, Indels: 13
0.76 0.10 0.13
Matches are distributed among these distances:
62 13 0.18
63 28 0.38
64 18 0.24
65 14 0.19
66 1 0.01
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (62 bp):
TTTTTATAATTTTAAAATTTTAATAAGTTTATATTAATTTTAACATTTTTACTATTTTTATA
Found at i:379065 original size:20 final size:20
Alignment explanation
Indices: 379007--379104 Score: 68
Period size: 20 Copynumber: 5.1 Consensus size: 20
378997 TTTTATAATT
* *
379007 TATTATATTTTTATAATTTT-
1 TATTA-ATTTTAATATTTTTA
*
379027 T-TTAATTTTAATGA-GTTTA
1 TATTAATTTTAAT-ATTTTTA
379046 TATTAATTTTAATATTTTTA
1 TATTAATTTTAATATTTTTA
379066 CTATT--TTTT--TATTTTTA
1 -TATTAATTTTAATATTTTTA
*
379083 TAATT-ATTTTAAAATTTTTA
1 T-ATTAATTTTAATATTTTTA
379103 TA
1 TA
379105 ATTTTTTATG
Statistics
Matches: 65, Mismatches: 4, Indels: 19
0.74 0.05 0.22
Matches are distributed among these distances:
16 1 0.02
17 11 0.17
18 14 0.22
19 11 0.17
20 24 0.37
21 4 0.06
ACGTcount: A:0.32, C:0.01, G:0.02, T:0.65
Consensus pattern (20 bp):
TATTAATTTTAATATTTTTA
Found at i:379083 original size:37 final size:36
Alignment explanation
Indices: 379042--379113 Score: 101
Period size: 37 Copynumber: 2.0 Consensus size: 36
379032 TTTTAATGAG
* *
379042 TTTAT-ATTAATTTTAATATTTTTACTATTTTTTTATT
1 TTTATAATT-ATTTTAAAATTTTTA-TAATTTTTTATT
379079 TTTATAATTATTTTAAAATTTTTATAATTTTTTAT
1 TTTATAATTATTTTAAAATTTTTATAATTTTTTAT
379114 GATTTTTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
36 10 0.31
37 19 0.59
38 3 0.09
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (36 bp):
TTTATAATTATTTTAAAATTTTTATAATTTTTTATT
Found at i:379092 original size:11 final size:10
Alignment explanation
Indices: 379077--379130 Score: 56
Period size: 10 Copynumber: 5.3 Consensus size: 10
379067 TATTTTTTTA
379077 TTTTTATAAT
1 TTTTTATAAT
*
379087 TATTTTA-AAA
1 T-TTTTATAAT
379097 TTTTTATAAT
1 TTTTTATAAT
*
379107 TTTTTATGAT
1 TTTTTATAAT
*
379117 TTTTAATAAGT
1 TTTTTATAA-T
379128 TTT
1 TTT
379131 ATGGGAAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
9 5 0.14
10 22 0.61
11 9 0.25
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:391359 original size:2 final size:2
Alignment explanation
Indices: 391352--391378 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
391342 TGAAAGCCAA
391352 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
391379 GAGGAAGAAC
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:392720 original size:86 final size:86
Alignment explanation
Indices: 392622--392793 Score: 344
Period size: 86 Copynumber: 2.0 Consensus size: 86
392612 TAATTTTTTA
392622 AGAATTAAATCAAATTTTTATCATTTTTAAGAGGGATCAAAGTGTAATATTACCTTTGCTAATTT
1 AGAATTAAATCAAATTTTTATCATTTTTAAGAGGGATCAAAGTGTAATATTACCTTTGCTAATTT
392687 AAATTTTTATATATTTTAAAG
66 AAATTTTTATATATTTTAAAG
392708 AGAATTAAATCAAATTTTTATCATTTTTAAGAGGGATCAAAGTGTAATATTACCTTTGCTAATTT
1 AGAATTAAATCAAATTTTTATCATTTTTAAGAGGGATCAAAGTGTAATATTACCTTTGCTAATTT
392773 AAATTTTTATATATTTTAAAG
66 AAATTTTTATATATTTTAAAG
392794 GGTTTTAATG
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 86 1.00
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.44
Consensus pattern (86 bp):
AGAATTAAATCAAATTTTTATCATTTTTAAGAGGGATCAAAGTGTAATATTACCTTTGCTAATTT
AAATTTTTATATATTTTAAAG
Done.