Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015339.1 Kokia drynarioides strain JFW-HI SEQ_130386, 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: 229081
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Warning! 127 characters in sequence are not A, C, G, or T
Found at i:250 original size:12 final size:12
Alignment explanation
Indices: 233--257 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
223 CAATATGTGT
233 AACTGGATTTTC
1 AACTGGATTTTC
245 AACTGGATTTTC
1 AACTGGATTTTC
257 A
1 A
258 TCGTCATTCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (12 bp):
AACTGGATTTTC
Found at i:978 original size:4 final size:4
Alignment explanation
Indices: 959--1023 Score: 69
Period size: 4 Copynumber: 16.0 Consensus size: 4
949 ACACATTACA
* * * *
959 TTTC TTTC CTTC -TTC TTTC TTTCC TCTC CTTC TTCC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTT-C TTTC TTTC TTTC TTTC TTTC TTTC
1007 TTTCC TTTC TTTC TTTC
1 TTT-C TTTC TTTC TTTC
1024 CCGTTTATTT
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
3 3 0.06
4 41 0.80
5 7 0.14
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (4 bp):
TTTC
Found at i:992 original size:17 final size:15
Alignment explanation
Indices: 959--1024 Score: 70
Period size: 13 Copynumber: 4.6 Consensus size: 15
949 ACACATTACA
959 TTTCTTTCCTTCTTC
1 TTTCTTTCCTTCTTC
974 TTTCTTTCC-TC-TC
1 TTTCTTTCCTTCTTC
*
987 CTTC-TTCCTTTCTTTC
1 TTTCTTTCC-TTC-TTC
1003 TTTCTTTCC-T-TTC
1 TTTCTTTCCTTCTTC
1016 TTTCTTTCC
1 TTTCTTTCC
1025 CGTTTATTTG
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
12 4 0.09
13 17 0.39
14 4 0.09
15 10 0.23
16 5 0.11
17 4 0.09
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTCTTTCCTTCTTC
Found at i:1009 original size:29 final size:27
Alignment explanation
Indices: 964--1021 Score: 80
Period size: 29 Copynumber: 2.1 Consensus size: 27
954 TTACATTTCT
964 TTCCTTCTTCTTTCTTTCCTCTCCTTC
1 TTCCTTCTTCTTTCTTTCCTCTCCTTC
* *
991 TTCCTTTCTTTCTTTCTTTCCTTTCTTTC
1 TTCC-TTC-TTCTTTCTTTCCTCTCCTTC
1020 TT
1 TT
1022 TCCCGTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 4 0.15
28 3 0.11
29 20 0.74
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (27 bp):
TTCCTTCTTCTTTCTTTCCTCTCCTTC
Found at i:14449 original size:69 final size:69
Alignment explanation
Indices: 14346--14483 Score: 267
Period size: 69 Copynumber: 2.0 Consensus size: 69
14336 AGTTACATAG
*
14346 CTTCAGATTAAATAATGAAATTAAATGAATGTATTTGATGGTATTCCAAAATATAGCAATATTAC
1 CTTCAGATTAAATAATGAAATTAAATGAATGTATTTGATGGTAATCCAAAATATAGCAATATTAC
14411 ACAA
66 ACAA
14415 CTTCAGATTAAATAATGAAATTAAATGAATGTATTTGATGGTAATCCAAAATATAGCAATATTAC
1 CTTCAGATTAAATAATGAAATTAAATGAATGTATTTGATGGTAATCCAAAATATAGCAATATTAC
14480 ACAA
66 ACAA
14484 AATGAAATCC
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.33
Consensus pattern (69 bp):
CTTCAGATTAAATAATGAAATTAAATGAATGTATTTGATGGTAATCCAAAATATAGCAATATTAC
ACAA
Found at i:16950 original size:28 final size:33
Alignment explanation
Indices: 16907--16970 Score: 84
Period size: 30 Copynumber: 2.1 Consensus size: 33
16897 TATCTTTAAA
16907 ATTTTTAGAGGATTAAA-T-TAAATTT-TCATT
1 ATTTTTAGAGGATTAAAGTGTAAATTTATCATT
*
16937 ATTTTT-GAGG-TTAAAGTGTAATTTTATCATT
1 ATTTTTAGAGGATTAAAGTGTAAATTTATCATT
16968 ATT
1 ATT
16971 AATTTAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
28 5 0.17
29 5 0.17
30 12 0.40
31 8 0.27
ACGTcount: A:0.33, C:0.03, G:0.12, T:0.52
Consensus pattern (33 bp):
ATTTTTAGAGGATTAAAGTGTAAATTTATCATT
Found at i:17682 original size:3 final size:3
Alignment explanation
Indices: 17674--17703 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
17664 TTCTGCAACT
*
17674 ATC ATC ATC ACC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
17704 GACTCCATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.37, G:0.00, T:0.30
Consensus pattern (3 bp):
ATC
Found at i:18672 original size:6 final size:6
Alignment explanation
Indices: 18663--18700 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
18653 TATGTATATA
18663 CATAGG CATAGG CATAGG CATAGG CATAGG CATAGG CA
1 CATAGG CATAGG CATAGG CATAGG CATAGG CATAGG CA
18701 AACAACTTGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.34, C:0.18, G:0.32, T:0.16
Consensus pattern (6 bp):
CATAGG
Found at i:24165 original size:3 final size:3
Alignment explanation
Indices: 24157--24196 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
24147 TTAATTAACC
*
24157 TAT TAT TAT TAC TAT TA- TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
24197 ACCTTTTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:24180 original size:20 final size:20
Alignment explanation
Indices: 24157--24194 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
24147 TTAATTAACC
24157 TATTATTATTACTATTATAT
1 TATTATTATTACTATTATAT
*
24177 TATTATTATTATTATTAT
1 TATTATTATTACTATTAT
24195 TAACCTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (20 bp):
TATTATTATTACTATTATAT
Found at i:24205 original size:20 final size:20
Alignment explanation
Indices: 24150--24206 Score: 51
Period size: 23 Copynumber: 2.7 Consensus size: 20
24140 TTTCGGCTTA
*
24150 ATTAACCTATTATTATTACT
1 ATTAACCTTTTATTATTACT
** *
24170 ATTATATTATTATTATTATTATT
1 ATTA-A-CCTT-TTATTATTACT
24193 ATTAACCTTTTATT
1 ATTAACCTTTTATT
24207 GGACACGTGT
Statistics
Matches: 28, Mismatches: 6, Indels: 6
0.70 0.15 0.15
Matches are distributed among these distances:
20 9 0.32
21 3 0.11
22 2 0.07
23 14 0.50
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.58
Consensus pattern (20 bp):
ATTAACCTTTTATTATTACT
Found at i:26257 original size:23 final size:25
Alignment explanation
Indices: 26220--26266 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 25
26210 ATATAAAAAT
26220 TTTAGAATAGTTATAGAGATTTTTA
1 TTTAGAATAGTTATAGAGATTTTTA
* *
26245 TTTA-AATA-TTATATATATTTTT
1 TTTAGAATAGTTATAGAGATTTTT
26267 TGCATTTCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 4 0.20
25 4 0.20
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (25 bp):
TTTAGAATAGTTATAGAGATTTTTA
Found at i:27579 original size:19 final size:19
Alignment explanation
Indices: 27535--27601 Score: 75
Period size: 18 Copynumber: 3.6 Consensus size: 19
27525 CAAAACGTAT
*
27535 ATTTTTAAAAAT-TATAAA
1 ATTTTAAAAAATATATAAA
*
27553 AATTTAAAAAATAT-TAAA
1 ATTTTAAAAAATATATAAA
* *
27571 CTTTCTAAAGAATATATAAA
1 ATTT-TAAAAAATATATAAA
27591 ATTTTAAAAAA
1 ATTTTAAAAAA
27602 GTCTAAAATA
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
18 16 0.41
19 16 0.41
20 7 0.18
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.37
Consensus pattern (19 bp):
ATTTTAAAAAATATATAAA
Found at i:28443 original size:130 final size:129
Alignment explanation
Indices: 28211--28474 Score: 465
Period size: 130 Copynumber: 2.0 Consensus size: 129
28201 CAAATTTAAT
*
28211 AAATATAATGCATCAAATATATTAAAAACATTAAAATAAATGTTTCCCAACAAATTGAAAAGACA
1 AAATATAATGCATCAAATATACTAAAAACATTAAAATAAATGTTTCCCAACAAATTGAAAAGACA
* * *
28276 TTAAAAAAGTTTTTATACTTAAATAACACTAACATAGTTACAACTTAGCAAGCAAATGTCTCTA
66 TTAAAAAAGTCTTTATACTTAAATAACACTAACATAGTTACAACTTAACAAACAAATGTCTCTA
28340 AAATATAATGCATCAAATATACTAAAAACATTAAAATAAATGTTTTCCCAACAAATTGAAAAGAC
1 AAATATAATGCATCAAATATACTAAAAACATTAAAATAAATG-TTTCCCAACAAATTGAAAAGAC
* *
28405 ATTAAAAAAGTCTTTATACTTAATTAACACTAACATAGTTGCAACTTAACAAACAAATGTCTCTA
65 ATTAAAAAAGTCTTTATACTTAAATAACACTAACATAGTTACAACTTAACAAACAAATGTCTCTA
28470 AAATA
1 AAATA
28475 GTAGCAAAAT
Statistics
Matches: 128, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
129 41 0.32
130 87 0.68
ACGTcount: A:0.50, C:0.14, G:0.06, T:0.29
Consensus pattern (129 bp):
AAATATAATGCATCAAATATACTAAAAACATTAAAATAAATGTTTCCCAACAAATTGAAAAGACA
TTAAAAAAGTCTTTATACTTAAATAACACTAACATAGTTACAACTTAACAAACAAATGTCTCTA
Found at i:35731 original size:36 final size:36
Alignment explanation
Indices: 35680--35751 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
35670 CTTTTGATTT
* *
35680 TGATAAAATTTGAAAATAAATCAAACCGAAAATTAA
1 TGATAAAATTCGAAAACAAATCAAACCGAAAATTAA
* *
35716 TGATAAAATTCGAAAACAAGTCAAATCGAAAATTAA
1 TGATAAAATTCGAAAACAAATCAAACCGAAAATTAA
35752 AAAGAAAAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.57, C:0.10, G:0.10, T:0.24
Consensus pattern (36 bp):
TGATAAAATTCGAAAACAAATCAAACCGAAAATTAA
Found at i:36952 original size:21 final size:23
Alignment explanation
Indices: 36903--36954 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
36893 AGAGAGTTAA
36903 ATTTAATAAAATAATATGGATGTGT
1 ATTTAATAAAATAATAT-G-TGTGT
36928 -TTTAATAAAAT-ATAT-TGTGT
1 ATTTAATAAAATAATATGTGTGT
36948 ATTTAAT
1 ATTTAAT
36955 TCAGTAACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
20 5 0.19
21 6 0.23
23 4 0.15
24 11 0.42
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (23 bp):
ATTTAATAAAATAATATGTGTGT
Found at i:38801 original size:29 final size:29
Alignment explanation
Indices: 38759--38825 Score: 125
Period size: 29 Copynumber: 2.3 Consensus size: 29
38749 TTAACTTTAA
38759 AAACTAATAAAATATAACATTTTGAATTC
1 AAACTAATAAAATATAACATTTTGAATTC
*
38788 AAACTAATGAAATATAACATTTTGAATTC
1 AAACTAATAAAATATAACATTTTGAATTC
38817 AAACTAATA
1 AAACTAATA
38826 TAATTTCTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.52, C:0.10, G:0.04, T:0.33
Consensus pattern (29 bp):
AAACTAATAAAATATAACATTTTGAATTC
Found at i:42774 original size:31 final size:31
Alignment explanation
Indices: 42739--42799 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
42729 TAGTTTACCG
* *
42739 ATTTAAATGGAAACATTC-GAATAGTTCAATA
1 ATTTAAATGAAAAC-TTCTGAATAATTCAATA
42770 ATTTAAATGAAAACTTCTGAATAATTCAAT
1 ATTTAAATGAAAACTTCTGAATAATTCAAT
42800 GACAATATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 3 0.11
31 24 0.89
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.34
Consensus pattern (31 bp):
ATTTAAATGAAAACTTCTGAATAATTCAATA
Found at i:45122 original size:25 final size:28
Alignment explanation
Indices: 45063--45123 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 28
45053 CTCTTTATTT
45063 TAAT-ATATATATATATATATATTATACGA
1 TAATAATATATATATATATATATTATA--A
*
45092 TGATAATA-ATATATAT-TATATTAT-A
1 TAATAATATATATATATATATATTATAA
45117 TAATAAT
1 TAATAAT
45124 CCGATTCAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
25 7 0.24
28 8 0.28
29 11 0.38
30 3 0.10
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (28 bp):
TAATAATATATATATATATATATTATAA
Found at i:45307 original size:2 final size:2
Alignment explanation
Indices: 45300--45326 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
45290 TCGATGTATC
45300 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
45327 GATCCTTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:48613 original size:16 final size:15
Alignment explanation
Indices: 48592--48621 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
48582 AATTATGTTT
48592 ATTTTTTTAAATTAAG
1 ATTTTTTT-AATTAAG
48608 ATTTTTTTAATTAA
1 ATTTTTTTAATTAA
48622 TGTATTGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (15 bp):
ATTTTTTTAATTAAG
Found at i:51317 original size:9 final size:9
Alignment explanation
Indices: 51305--51335 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
51295 GGATTAATTA
51305 AATTAACCG
1 AATTAACCG
51314 AATTAACCG
1 AATTAACCG
*
51323 AATTAACCA
1 AATTAACCG
51332 AATT
1 AATT
51336 TTATATATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.48, C:0.19, G:0.06, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:52812 original size:15 final size:17
Alignment explanation
Indices: 52784--52823 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
52774 TGCACCGCAG
52784 AATAAAATATATATTTT
1 AATAAAATATATATTTT
52801 AATAAAATATATATTTT
1 AATAAAATATATATTTT
52818 AATAAA
1 AATAAA
52824 TAATTACGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AATAAAATATATATTTT
Found at i:53087 original size:18 final size:18
Alignment explanation
Indices: 53052--53089 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
53042 TCGCTTTTTT
*
53052 TTTTTCAATTTTACTTTA
1 TTTTTCAATTTTAATTTA
53070 TTTTT-AATTTTATATTTA
1 TTTTTCAATTTTA-ATTTA
53088 TT
1 TT
53090 AAAAGTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTTCAATTTTAATTTA
Found at i:63116 original size:4 final size:4
Alignment explanation
Indices: 63094--63179 Score: 68
Period size: 4 Copynumber: 21.2 Consensus size: 4
63084 AACACGTTAC
* * * * *
63094 CTTT ATTT CCTT C-TT CTTT CTTT CCTCT CATT C-TT CTTT CTTT CCTCT
1 CTTT CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CTTT CTTT CTTT -CTTT
* *
63142 CCTT CTTC CTTT CTTT CTTT CTTT CCTTT CTTT CTTT C
1 CTTT CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CTTT C
63180 CCGTTTATTT
Statistics
Matches: 65, Mismatches: 12, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
3 6 0.09
4 49 0.75
5 10 0.15
ACGTcount: A:0.02, C:0.34, G:0.00, T:0.64
Consensus pattern (4 bp):
CTTT
Found at i:63129 original size:20 final size:20
Alignment explanation
Indices: 63104--63180 Score: 93
Period size: 20 Copynumber: 3.8 Consensus size: 20
63094 CTTTATTTCC
63104 TTCTTCTTTCTTTCCTCTCA
1 TTCTTCTTTCTTTCCTCTCA
*
63124 TTCTTCTTTCTTTCCTCTCC
1 TTCTTCTTTCTTTCCTCTCA
* *
63144 TTCTTCCTTTCTTT-CTTTCT
1 TTCTT-CTTTCTTTCCTCTCA
63164 TTCCTTTCTTTCTTTCC
1 TT-C-TTCTTTCTTTCC
63181 CGTTTATTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
20 30 0.60
21 17 0.34
22 3 0.06
ACGTcount: A:0.01, C:0.35, G:0.00, T:0.64
Consensus pattern (20 bp):
TTCTTCTTTCTTTCCTCTCA
Found at i:63167 original size:17 final size:17
Alignment explanation
Indices: 63094--63179 Score: 83
Period size: 17 Copynumber: 5.3 Consensus size: 17
63084 AACACGTTAC
*
63094 CTTTATTTCC-TTC-TT
1 CTTTCTTTCCTTTCTTT
* *
63109 CTTTCTTTCCTCTCATT
1 CTTTCTTTCCTTTCTTT
*
63126 C-TTCTTT-CTTTCCTCT
1 CTTTCTTTCCTTT-CTTT
*
63142 CCTTC-TTCCTTTCTTT
1 CTTTCTTTCCTTTCTTT
63158 CTTTCTTTCCTTTCTTT
1 CTTTCTTTCCTTTCTTT
63175 CTTTC
1 CTTTC
63180 CCGTTTATTT
Statistics
Matches: 58, Mismatches: 7, Indels: 10
0.77 0.09 0.13
Matches are distributed among these distances:
15 12 0.21
16 20 0.34
17 26 0.45
ACGTcount: A:0.02, C:0.34, G:0.00, T:0.64
Consensus pattern (17 bp):
CTTTCTTTCCTTTCTTT
Found at i:64905 original size:16 final size:17
Alignment explanation
Indices: 64884--64923 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
64874 ACTGCTATGT
*
64884 AATAAATATAT-TTATA
1 AATAAATATATGTTAAA
*
64900 AATAAATTTATGTTAAA
1 AATAAATATATGTTAAA
64917 AATAAAT
1 AATAAAT
64924 GAGTATTTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (17 bp):
AATAAATATATGTTAAA
Found at i:68838 original size:16 final size:15
Alignment explanation
Indices: 68809--68851 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
68799 GTCACTGTTC
*
68809 TAAATATTTAAAATTT
1 TAAA-ATTTAAAATAT
*
68825 TACAATTATAAAATAT
1 TAAAATT-TAAAATAT
68841 TAAAATTTAAA
1 TAAAATTTAAA
68852 TTAAAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 7 0.30
16 16 0.70
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (15 bp):
TAAAATTTAAAATAT
Found at i:73329 original size:13 final size:13
Alignment explanation
Indices: 73313--73356 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
73303 CACGTATTGA
73313 GCTCGCACGTTGG
1 GCTCGCACGTTGG
** *
73326 GCTCGCATATTGA
1 GCTCGCACGTTGG
*
73339 GCTCACACGTTGG
1 GCTCGCACGTTGG
73352 GCTCG
1 GCTCG
73357 TGTATTGAGC
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.14, C:0.30, G:0.32, T:0.25
Consensus pattern (13 bp):
GCTCGCACGTTGG
Found at i:73336 original size:26 final size:26
Alignment explanation
Indices: 73307--73371 Score: 103
Period size: 26 Copynumber: 2.5 Consensus size: 26
73297 TGAGTTCACG
*
73307 TATTGAGCTCGCACGTTGGGCTCGCA
1 TATTGAGCTCACACGTTGGGCTCGCA
**
73333 TATTGAGCTCACACGTTGGGCTCGTG
1 TATTGAGCTCACACGTTGGGCTCGCA
73359 TATTGAGCTCACA
1 TATTGAGCTCACA
73372 TGACATTAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.18, C:0.25, G:0.28, T:0.29
Consensus pattern (26 bp):
TATTGAGCTCACACGTTGGGCTCGCA
Found at i:73860 original size:11 final size:11
Alignment explanation
Indices: 73829--73870 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
73819 CCACATCAGC
*
73829 AAATGATTTTA
1 AAATTATTTTA
73840 AAATTA--TTA
1 AAATTATTTTA
73849 AAATTATTTTA
1 AAATTATTTTA
*
73860 AAATTAATTTA
1 AAATTATTTTA
73871 GAGTATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 9 0.33
11 18 0.67
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (11 bp):
AAATTATTTTA
Found at i:73944 original size:11 final size:11
Alignment explanation
Indices: 73925--73966 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
73915 TTTTATACTC
*
73925 TAAATTAATTT
1 TAAAATAATTT
73936 TAAAATAATTT
1 TAAAATAATTT
73947 T--AATAATTT
1 TAAAATAATTT
*
73956 TAAAATCATTT
1 TAAAATAATTT
73967 GCTGACGTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 9 0.33
11 18 0.67
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (11 bp):
TAAAATAATTT
Found at i:78438 original size:16 final size:16
Alignment explanation
Indices: 78393--78441 Score: 57
Period size: 16 Copynumber: 3.0 Consensus size: 16
78383 CAGCCATCAT
78393 TTTAAATATTCAAAA-A
1 TTTAAATATT-AAAATA
78409 TTTATAAT-TATAAAATA
1 TTTA-AATAT-TAAAATA
78426 TTTAAATATTAAAATA
1 TTTAAATATTAAAATA
78442 GAATATTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
16 19 0.66
17 10 0.34
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (16 bp):
TTTAAATATTAAAATA
Found at i:83386 original size:11 final size:10
Alignment explanation
Indices: 83361--83385 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
83351 TCAGAGAGGA
83361 TTTTTATTTT
1 TTTTTATTTT
83371 TTTTTATTTT
1 TTTTTATTTT
83381 TTTTT
1 TTTTT
83386 TTGGAGGGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTATTTT
Found at i:83770 original size:22 final size:23
Alignment explanation
Indices: 83745--83790 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
83735 CGTATTCTCC
*
83745 TTTTAGTTAAATTTT-ATCATTT
1 TTTTAATTAAATTTTGATCATTT
*
83767 TTTTAATTAAATTTTGATTATTT
1 TTTTAATTAAATTTTGATCATTT
83790 T
1 T
83791 AATGATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.65
Consensus pattern (23 bp):
TTTTAATTAAATTTTGATCATTT
Found at i:90172 original size:21 final size:21
Alignment explanation
Indices: 90145--90195 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
90135 AAAAATTTCA
90145 ATAAATA-AAAA-AATATAACT
1 ATAAATATAAAATAATATAA-T
90165 ATTAAATATTAAAATAATATAAT
1 A-TAAATA-TAAAATAATATAAT
90188 ATAAATAT
1 ATAAATAT
90196 TTTTTTTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
20 1 0.04
21 7 0.26
22 6 0.22
23 6 0.22
24 7 0.26
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
ATAAATATAAAATAATATAAT
Found at i:90183 original size:24 final size:22
Alignment explanation
Indices: 90150--90196 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 22
90140 TTTCAATAAA
90150 TAAAAAAATATAACTATTAAATAT
1 TAAAAAAATATAA-TA-TAAATAT
*
90174 TAAAATAATATAATATAAATAT
1 TAAAAAAATATAATATAAATAT
90196 T
1 T
90197 TTTTTTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 8 0.36
23 2 0.09
24 12 0.55
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (22 bp):
TAAAAAAATATAATATAAATAT
Found at i:92421 original size:16 final size:17
Alignment explanation
Indices: 92402--92443 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
92392 ATTAATTTTT
92402 AAATTTTTAAAA-ATAA
1 AAATTTTTAAAAGATAA
* * *
92418 AAATTATTAAAAGGTTA
1 AAATTTTTAAAAGATAA
92435 AAATTTTTA
1 AAATTTTTA
92444 TAACATTTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (17 bp):
AAATTTTTAAAAGATAA
Found at i:93876 original size:50 final size:50
Alignment explanation
Indices: 93818--93917 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
93808 ATCGATTTTT
93818 ACGAAATTGATTTAACATTGATTGGTTAAACCTGTTATTACCCAACACAA
1 ACGAAATTGATTTAACATTGATTGGTTAAACCTGTTATTACCCAACACAA
93868 ACGAAATTGATTTAACATTGATTGGTTAAACCTGTTATTACCCAACACAA
1 ACGAAATTGATTTAACATTGATTGGTTAAACCTGTTATTACCCAACACAA
93918 TTATTTTTCG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (50 bp):
ACGAAATTGATTTAACATTGATTGGTTAAACCTGTTATTACCCAACACAA
Found at i:94910 original size:2 final size:2
Alignment explanation
Indices: 94905--94936 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
94895 ACACACACAC
94905 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
94937 TTGTATTTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:95328 original size:44 final size:42
Alignment explanation
Indices: 95278--95399 Score: 118
Period size: 44 Copynumber: 2.8 Consensus size: 42
95268 ATAGGTCAAA
* * *
95278 TAATATTAACCAAACTTACATTAATAAGAGTTTAAGTGAGAAAC
1 TAATATTAA--AAACTTACATTAATCAGAGTTTAAATGAAAAAC
* * * *
95322 TAATATTAAAATAATATATACTAATCAGAGTTTAAATGAAAAAT
1 TAATATTAAAA-ACT-TACATTAATCAGAGTTTAAATGAAAAAC
*
95366 TAATATTAAAATAACCTACATTAATCAGAGTTTA
1 TAATATT-AAA-AACTTACATTAATCAGAGTTTA
95400 GATGGAGAAC
Statistics
Matches: 63, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
42 2 0.03
43 2 0.03
44 54 0.86
45 4 0.06
46 1 0.02
ACGTcount: A:0.50, C:0.09, G:0.08, T:0.33
Consensus pattern (42 bp):
TAATATTAAAAACTTACATTAATCAGAGTTTAAATGAAAAAC
Found at i:97097 original size:25 final size:26
Alignment explanation
Indices: 97046--97097 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 26
97036 TTAATCATCA
*
97046 ATTTAAACAAATATTAATTAAAATAT
1 ATTTAAACAAATATTAATCAAAATAT
* * *
97072 ATTTAAA-ACATATTGATCAAATTAT
1 ATTTAAACAAATATTAATCAAAATAT
97097 A
1 A
97098 AACACGTATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.38
Consensus pattern (26 bp):
ATTTAAACAAATATTAATCAAAATAT
Found at i:97750 original size:16 final size:17
Alignment explanation
Indices: 97722--97764 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
97712 AAAAAATTAG
97722 TTAAGATAT-ATGATAT-
1 TTAA-ATATAATGATATA
97738 TTAAATATAATGATATA
1 TTAAATATAATGATATA
*
97755 TAAAATATAA
1 TTAAATATAA
97765 AGTTTAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 4 0.17
16 11 0.46
17 9 0.38
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (17 bp):
TTAAATATAATGATATA
Found at i:97762 original size:17 final size:16
Alignment explanation
Indices: 97722--97764 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 16
97712 AAAAAATTAG
*
97722 TTAAGATAT-ATGATA
1 TTAAAATATAATGATA
*
97737 TTTAAATATAATGATA
1 TTAAAATATAATGATA
97753 TATAAAATATAA
1 T-TAAAATATAA
97765 AGTTTAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 7 0.30
16 7 0.30
17 9 0.39
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (16 bp):
TTAAAATATAATGATA
Found at i:97798 original size:25 final size:24
Alignment explanation
Indices: 97770--97845 Score: 66
Period size: 25 Copynumber: 3.0 Consensus size: 24
97760 TATAAAGTTT
97770 AAATACTTTTTAAATAATTAATATA
1 AAATA-TTTTTAAATAATTAATATA
* * *
97795 AAATATTTCTAAAATTGATGATATATA
1 AAATATTT-TTAAA-TAATTA-ATATA
97822 AAATA-TTTTAAA-AATTAAATATA
1 AAATATTTTTAAATAATT-AATATA
97845 A
1 A
97846 TAAATAAGAT
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
23 8 0.20
24 4 0.10
25 13 0.32
26 6 0.15
27 10 0.24
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (24 bp):
AAATATTTTTAAATAATTAATATA
Found at i:97850 original size:25 final size:24
Alignment explanation
Indices: 97777--97851 Score: 66
Period size: 27 Copynumber: 3.0 Consensus size: 24
97767 TTTAAATACT
97777 TTTTAAATAATTAATAT-A-AAATA
1 TTTTAAA-AATTAATATAATAAATA
*
97800 TTTCT-AAAATTGATGATATATAAAATA
1 TTT-TAAAAATTAAT-ATA-AT-AAATA
97827 TTTTAAAAATTAAATATAATAAATA
1 TTTTAAAAATT-AATATAATAAATA
97852 AGATTTAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 14
0.72 0.03 0.24
Matches are distributed among these distances:
22 6 0.14
23 7 0.17
24 1 0.02
25 6 0.14
26 3 0.07
27 17 0.40
28 2 0.05
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (24 bp):
TTTTAAAAATTAATATAATAAATA
Found at i:97872 original size:28 final size:31
Alignment explanation
Indices: 97828--97908 Score: 91
Period size: 31 Copynumber: 2.7 Consensus size: 31
97818 TATAAAATAT
*
97828 TTTAAA-AATTAAATATAATAAAT-AA-G-A
1 TTTAAATAATTTAATATAATAAATAAAGGAA
*
97855 TTTAAATAATTTATTATAAT-AATAAAGGATA
1 TTTAAATAATTTAATATAATAAATAAAGGA-A
*
97886 TTTAAATAATTTAACATAATAAA
1 TTTAAATAATTTAATATAATAAA
97909 AACACAAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
27 9 0.20
28 13 0.30
29 1 0.02
31 19 0.43
32 2 0.05
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.38
Consensus pattern (31 bp):
TTTAAATAATTTAATATAATAAATAAAGGAA
Found at i:98624 original size:18 final size:17
Alignment explanation
Indices: 98591--98631 Score: 64
Period size: 18 Copynumber: 2.4 Consensus size: 17
98581 TAATAAAAAT
98591 ATAATTTTATTATTTTA
1 ATAATTTTATTATTTTA
*
98608 ATAATTTATATTTTTTTA
1 ATAATTT-TATTATTTTA
98626 ATAATT
1 ATAATT
98632 AAAAAATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
ATAATTTTATTATTTTA
Found at i:102078 original size:146 final size:146
Alignment explanation
Indices: 101813--102104 Score: 494
Period size: 146 Copynumber: 2.0 Consensus size: 146
101803 AATTTTTTAT
* * * *
101813 TTAAATACATTTTGTTGTAAAGCAAATATCATATTAATATATATGTTAAATAATGATTATATATT
1 TTAAATACATTATGTTATAAAGAAAATATCATATTAATATATATGTTAAATAATAATTATATATT
*
101878 TATATTAACACACTAATTCAATAACAAATACTTAAAAACTTAAAAAAATGATCTAATTAAGTAAT
66 TATATTAACACACTAATCCAATAACAAATACTTAAAAACTTAAAAAAATGATCTAATTAAGTAAT
101943 TCAATTCAAAATATAA
131 TCAATTCAAAATATAA
* *
101959 TTAAATATATTATGTTATAAAGAAAATATTATATTAATATATATGTTAAATAATAATTATATATT
1 TTAAATACATTATGTTATAAAGAAAATATCATATTAATATATATGTTAAATAATAATTATATATT
* *
102024 TATATTAGCACACTAATCCAATAACAAATACTTAAAAACTTAAAAAAATTATCTAATTAAGTAAT
66 TATATTAACACACTAATCCAATAACAAATACTTAAAAACTTAAAAAAATGATCTAATTAAGTAAT
*
102089 TCAATTTAAAATATAA
131 TCAATTCAAAATATAA
102105 AATTTTAAGA
Statistics
Matches: 136, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
146 136 1.00
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (146 bp):
TTAAATACATTATGTTATAAAGAAAATATCATATTAATATATATGTTAAATAATAATTATATATT
TATATTAACACACTAATCCAATAACAAATACTTAAAAACTTAAAAAAATGATCTAATTAAGTAAT
TCAATTCAAAATATAA
Found at i:102217 original size:11 final size:12
Alignment explanation
Indices: 102194--102220 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
102184 TTTTACTGTG
102194 TTAAAATTTTTT
1 TTAAAATTTTTT
102206 TTAAAATTTTTT
1 TTAAAATTTTTT
102218 TTA
1 TTA
102221 GAGCATTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TTAAAATTTTTT
Found at i:103132 original size:25 final size:26
Alignment explanation
Indices: 103104--103152 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
103094 TAATATATCA
*
103104 AATACATTTAAAA-ACATTAAAAATG
1 AATAAATTTAAAATACATTAAAAATG
103129 AATAAATTTAAAATACATTAAAAA
1 AATAAATTTAAAATACATTAAAAA
103153 ATTTATATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.63, C:0.06, G:0.02, T:0.29
Consensus pattern (26 bp):
AATAAATTTAAAATACATTAAAAATG
Found at i:103297 original size:20 final size:19
Alignment explanation
Indices: 103275--103409 Score: 61
Period size: 21 Copynumber: 6.9 Consensus size: 19
103265 AAATAACATC
103275 CAAACAACAAAAATAATAA
1 CAAACAACAAAAATAATAA
103294 CCAAA-ATAGCAACAAA-AATAA
1 -CAAACA-A-CAA-AAATAATAA
* *
103315 C-AACAA-AACAATATTAA
1 CAAACAACAAAAATAATAA
103332 -AAACAACAAAAATAACAATAA
1 CAAACAACAAAAAT---AATAA
103353 -AAACAACAACAAA-AATAA
1 CAAACAACAA-AAATAATAA
* * *
103371 CAGCAAAAACAATAAAAAATAG
1 CA--AACAACAA-AAATAATAA
*
103393 CAACCAA-AAAAATAATA
1 CAAACAACAAAAATAATA
103410 TATTTTTTTT
Statistics
Matches: 90, Mismatches: 10, Indels: 32
0.68 0.08 0.24
Matches are distributed among these distances:
16 2 0.02
17 11 0.12
18 17 0.19
19 7 0.08
20 10 0.11
21 31 0.34
22 12 0.13
ACGTcount: A:0.71, C:0.16, G:0.02, T:0.10
Consensus pattern (19 bp):
CAAACAACAAAAATAATAA
Found at i:103311 original size:12 final size:12
Alignment explanation
Indices: 103277--103379 Score: 90
Period size: 12 Copynumber: 8.9 Consensus size: 12
103267 ATAACATCCA
103277 AACAACAAAAAT
1 AACAACAAAAAT
* *
103289 AATAACCAAAAT
1 AACAACAAAAAT
*
103301 AGCAACAAAAAT
1 AACAACAAAAAT
103313 AACAAC---AA-
1 AACAACAAAAAT
* *
103321 AACAATATTAAA-
1 AACAACA-AAAAT
103333 AACAACAAAAAT
1 AACAACAAAAAT
* *
103345 AACAATAAAAAC
1 AACAACAAAAAT
103357 AACAACAAAAAT
1 AACAACAAAAAT
*
103369 AACAGCAAAAA
1 AACAACAAAAA
103380 CAATAAAAAA
Statistics
Matches: 72, Mismatches: 14, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
8 5 0.07
9 2 0.03
11 3 0.04
12 62 0.86
ACGTcount: A:0.72, C:0.17, G:0.02, T:0.10
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:103324 original size:44 final size:44
Alignment explanation
Indices: 103263--103402 Score: 111
Period size: 44 Copynumber: 3.1 Consensus size: 44
103253 AAAAATGCAT
* * * * *
103263 AAAAATAACATCCAAACAACA-AAAATAATAACCAAAATAGCAAC
1 AAAAATAACAACAAAACAACATAAAA-AACAACAAAAATAACAAC
* * *
103307 AAAAATAACAACAAAACAATATTAAAAACAACAAAAATAACAAT
1 AAAAATAACAACAAAACAACATAAAAAACAACAAAAATAACAAC
* * ** * *
103351 AAAAACAACAACAAAAATAACAGCAAAAACAATAAAAAATAGCAACC
1 AAAAATAACAAC-AAAACAACATAAAAAACAA-CAAAAATAACAA-C
103398 AAAAA
1 AAAAA
103403 AATAATATAT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
44 43 0.57
45 18 0.24
46 10 0.13
47 5 0.07
ACGTcount: A:0.71, C:0.17, G:0.02, T:0.10
Consensus pattern (44 bp):
AAAAATAACAACAAAACAACATAAAAAACAACAAAAATAACAAC
Found at i:103342 original size:56 final size:57
Alignment explanation
Indices: 103276--103384 Score: 157
Period size: 56 Copynumber: 1.9 Consensus size: 57
103266 AATAACATCC
* * * *
103276 AAACAACAAAAATAATAACCAAAATAGCAACAAAAATAACAAC-AAAACAATATTAA
1 AAACAACAAAAATAACAACAAAAACAACAACAAAAATAACAACAAAAACAATATTAA
* *
103332 AAACAACAAAAATAACAATAAAAACAACAACAAAAATAACAGCAAAAACAATA
1 AAACAACAAAAATAACAACAAAAACAACAACAAAAATAACAACAAAAACAATA
103385 AAAAATAGCA
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
56 37 0.80
57 9 0.20
ACGTcount: A:0.72, C:0.17, G:0.02, T:0.10
Consensus pattern (57 bp):
AAACAACAAAAATAACAACAAAAACAACAACAAAAATAACAACAAAAACAATATTAA
Found at i:112632 original size:35 final size:35
Alignment explanation
Indices: 112586--112657 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
112576 TATAATAATT
112586 CAAAATAAATAGATTTGAATGTACTTAAATGTAAA
1 CAAAATAAATAGATTTGAATGTACTTAAATGTAAA
* *
112621 CAAAATAAATAGATTTGAGTGTACTTGAATGTAAA
1 CAAAATAAATAGATTTGAATGTACTTAAATGTAAA
112656 CA
1 CA
112658 TACTCTAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.49, C:0.07, G:0.14, T:0.31
Consensus pattern (35 bp):
CAAAATAAATAGATTTGAATGTACTTAAATGTAAA
Found at i:116945 original size:6 final size:6
Alignment explanation
Indices: 116926--116958 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
116916 GCAAGCTCGA
*
116926 CTCAGG CTCTGG CTCAGG CTCAGG CTCAGG CTC
1 CTCAGG CTCAGG CTCAGG CTCAGG CTCAGG CTC
116959 GACTCACAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.12, C:0.36, G:0.30, T:0.21
Consensus pattern (6 bp):
CTCAGG
Found at i:119129 original size:16 final size:15
Alignment explanation
Indices: 119089--119129 Score: 52
Period size: 13 Copynumber: 2.9 Consensus size: 15
119079 TTTCAATTTT
119089 ATTTT-AATAATAAA
1 ATTTTAAATAATAAA
119103 A-TTTAAA-AATAATA
1 ATTTTAAATAATAA-A
119117 ATTTTAAATAATA
1 ATTTTAAATAATA
119130 TTATTCACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 8 0.35
14 5 0.22
15 6 0.26
16 4 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATTTTAAATAATAAA
Found at i:119696 original size:14 final size:15
Alignment explanation
Indices: 119674--119714 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
119664 TCAAAAAAAT
*
119674 AAATTATTTTT-TAA
1 AAATCATTTTTATAA
119688 AAATCATTTTTCATAA
1 AAATCATTTTT-ATAA
119704 AAA-CATTTTTA
1 AAATCATTTTTA
119715 ATGAAACAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 11 0.46
15 7 0.29
16 6 0.25
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (15 bp):
AAATCATTTTTATAA
Found at i:121179 original size:1 final size:1
Alignment explanation
Indices: 121168--121206 Score: 51
Period size: 1 Copynumber: 39.0 Consensus size: 1
121158 GAAAGATCAC
* * *
121168 AAAAAAGAAAAAAAAGAAAAAAAAGAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
121207 GGTAAAGACA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (1 bp):
A
Found at i:121182 original size:9 final size:9
Alignment explanation
Indices: 121168--121206 Score: 71
Period size: 9 Copynumber: 4.4 Consensus size: 9
121158 GAAAGATCAC
121168 AAAAAAGAA
1 AAAAAAGAA
121177 AAAAAAGAA
1 AAAAAAGAA
121186 AAAAAAGAA
1 AAAAAAGAA
121195 AAAAAA-AA
1 AAAAAAGAA
121203 AAAA
1 AAAA
121207 GGTAAAGACA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
8 6 0.20
9 24 0.80
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:125789 original size:31 final size:31
Alignment explanation
Indices: 125751--125819 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
125741 AGTTAGTCCC
* * * *
125751 TGAACTTGGTAATTG-TTCTCATATTGGGGCT
1 TGAACTTGGCAAATGTTTC-CACATTGAGGCT
125782 TGAACTTGGCAAATGTTTCCACATTGAGGCT
1 TGAACTTGGCAAATGTTTCCACATTGAGGCT
125813 TGAACTT
1 TGAACTT
125820 TAGAGTTGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 30 0.91
32 3 0.09
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.38
Consensus pattern (31 bp):
TGAACTTGGCAAATGTTTCCACATTGAGGCT
Found at i:125956 original size:58 final size:59
Alignment explanation
Indices: 125837--125947 Score: 172
Period size: 59 Copynumber: 1.9 Consensus size: 59
125827 GAAGGAAATA
125837 TCAGGGACTAACTTGGACAAAAAAAGGTACAGGCCCTAATGTGAGAACAATTGTCAAGT
1 TCAGGGACTAACTTGGACAAAAAAAGGTACAGGCCCTAATGTGAGAACAATTGTCAAGT
* * *
125896 TCAGGGACTAACTTGGTCAAAAAAA-GTTCAGGCTCC-AATGTGGGAACAATTG
1 TCAGGGACTAACTTGGACAAAAAAAGGTACAGGC-CCTAATGTGAGAACAATTG
125948 CTGAGTTCAA
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
58 22 0.46
59 26 0.54
ACGTcount: A:0.37, C:0.17, G:0.24, T:0.22
Consensus pattern (59 bp):
TCAGGGACTAACTTGGACAAAAAAAGGTACAGGCCCTAATGTGAGAACAATTGTCAAGT
Found at i:137378 original size:98 final size:97
Alignment explanation
Indices: 137191--137378 Score: 236
Period size: 98 Copynumber: 1.9 Consensus size: 97
137181 GAAAAGGATG
* * * *
137191 TTCGATTATCTCGATTTGAAGAAAATTCGCACCTAGTGAGTTAAGGCACAAATTTTCAGAATCAG
1 TTCGATTATCTCGATTTAAAGAAAAATCGCACCTAGTAAGTTAAGGCACAAATTTTCAAAATCAG
* *
137256 AGATAAAGAAGCATTGCCTCGATTTAAGGGTA
66 AAATAAAGAAGCATCGCCTCGATTTAAGGGTA
* * *
137288 TTCGATTATTTCGATTTAAAGAAAAAATCGCGCCTAGTAAGTTAAGGCACGAATTTTCAAAACTC
1 TTCGATTATCTCGATTTAAAG-AAAAATCGCACCTAGTAAGTTAAGGCACAAATTTTCAAAA-TC
* *
137353 -GAAATAAAAGAA-TATCGCCTTGATTT
64 AGAAAT-AAAGAAGCATCGCCTCGATTT
137379 TAAAGTTTTT
Statistics
Matches: 77, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
97 19 0.25
98 50 0.65
99 8 0.10
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (97 bp):
TTCGATTATCTCGATTTAAAGAAAAATCGCACCTAGTAAGTTAAGGCACAAATTTTCAAAATCAG
AAATAAAGAAGCATCGCCTCGATTTAAGGGTA
Found at i:137704 original size:59 final size:60
Alignment explanation
Indices: 137639--138007 Score: 357
Period size: 59 Copynumber: 6.2 Consensus size: 60
137629 CACTCGGGGG
* * * *
137639 AAAAATGGTAA-TTTTGGGAAAGTTAGGGGTCAAAAATAGAATTTTTAGATA-TTTGAGGGT
1 AAAAATGGTAATTTTTGGAAAAATTA-GGGTCAAAAATGGAA-TTTTAGAAAGTTTGAGGGT
* * * * *
137699 -AAAATGGCACTTTTTGGAAAAATCAGGGTCAAAAATGGAATTTTGGAAAGTTTGGGGGT
1 AAAAATGGTAATTTTTGGAAAAATTAGGGTCAAAAATGGAATTTTAGAAAGTTTGAGGGT
* * * * *
137758 AAAAAAT-GTAATTTTTGGAAAAAATAAGGTTAAAAATGAAATTTTAGAAAATTT-AGGGGT
1 -AAAAATGGTAATTTTTGGAAAAATTAGGGTCAAAAATGGAATTTTAGAAAGTTTGA-GGGT
* *
137818 -AAAATGGTAATTTTTGGAAAAATTAGGGTAAAAAATGGAATTTTAGAAAGTTCG-GGGT
1 AAAAATGGTAATTTTTGGAAAAATTAGGGTCAAAAATGGAATTTTAGAAAGTTTGAGGGT
* * * * * *
137876 AAAAAT-GTAATTTTTGGGAAAATCAAGGTCAAAAATGGAATTTTGGAAAGTTTAATGGT
1 AAAAATGGTAATTTTTGGAAAAATTAGGGTCAAAAATGGAATTTTAGAAAGTTTGAGGGT
* * * * *
137935 AAAAAT-GTAATTTTTGGGAAAA-TCGAGGTCGAAAATGAAATTTTGGAAAGTTT-AGGGGT
1 AAAAATGGTAATTTTTGGAAAAATTAG-GGTCAAAAATGGAATTTTAGAAAGTTTGA-GGGT
137994 -AAAATGGTAATTTT
1 AAAAATGGTAATTTT
138008 AGATAGTTTA
Statistics
Matches: 258, Mismatches: 39, Indels: 25
0.80 0.12 0.08
Matches are distributed among these distances:
58 63 0.24
59 137 0.53
60 53 0.21
61 5 0.02
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.32
Consensus pattern (60 bp):
AAAAATGGTAATTTTTGGAAAAATTAGGGTCAAAAATGGAATTTTAGAAAGTTTGAGGGT
Found at i:137765 original size:30 final size:29
Alignment explanation
Indices: 137634--138020 Score: 179
Period size: 29 Copynumber: 13.1 Consensus size: 29
137624 TTGGTCACTC
*
137634 GGGGGAAAAATGGTAATTTTGGGAAAG-TTA
1 GGGGTAAAAATGG-AATTTT-GGAAAGTTTA
* * *
137664 GGGGTCAAAAATAGAATTTTTAGATA-TTT-
1 GGGGT-AAAAATGGAA-TTTTGGAAAGTTTA
* ** *
137693 GAGGGT-AAAATGGCACTTTTTGGAAAAATCA
1 G-GGGTAAAAATGG-A-ATTTTGGAAAGTTTA
*
137724 -GGGTCAAAAATGGAATTTTGGAAAGTTTG
1 GGGGT-AAAAATGGAATTTTGGAAAGTTTA
* ***
137753 GGGGTAAAAAATGTAATTTTTGGAAAAAATA
1 GGGGT-AAAAATGGAA-TTTTGGAAAGTTTA
* * * * *
137784 AGGTTAAAAATGAAATTTTAGAAAATTTA
1 GGGGTAAAAATGGAATTTTGGAAAGTTTA
**
137813 GGGGT-AAAATGGTAATTTTTGGAAAAATTA
1 GGGGTAAAAATGG-AA-TTTTGGAAAGTTTA
* *
137843 -GGGTAAAAAATGGAATTTTAGAAAG-TTC
1 GGGGT-AAAAATGGAATTTTGGAAAGTTTA
* * *
137871 GGGGTAAAAATGTAATTTTTGGGAAA-ATCA
1 GGGGTAAAAATGGAA-TTTT-GGAAAGTTTA
*
137901 -AGGTCAAAAATGGAATTTTGGAAAGTTTA
1 GGGGT-AAAAATGGAATTTTGGAAAGTTTA
** * * *
137930 ATGGTAAAAATGTAATTTTTGGGAAA--ATC
1 GGGGTAAAAATGGAA-TTTT-GGAAAGTTTA
* * *
137959 GAGGTCGAAAATGAAATTTTGGAAAGTTTA
1 GGGGT-AAAAATGGAATTTTGGAAAGTTTA
* *
137989 GGGGT-AAAATGGTAATTTTAGATAGTTTA
1 GGGGTAAAAATGG-AATTTTGGAAAGTTTA
138018 GGG
1 GGG
138021 ACCTTCAAGG
Statistics
Matches: 271, Mismatches: 57, Indels: 59
0.70 0.15 0.15
Matches are distributed among these distances:
28 39 0.14
29 102 0.38
30 87 0.32
31 43 0.16
ACGTcount: A:0.40, C:0.03, G:0.26, T:0.31
Consensus pattern (29 bp):
GGGGTAAAAATGGAATTTTGGAAAGTTTA
Found at i:137945 original size:117 final size:118
Alignment explanation
Indices: 137666--138007 Score: 399
Period size: 117 Copynumber: 2.9 Consensus size: 118
137656 GAAAGTTAGG
* * * * * *
137666 GGTCAAAAATAGAATTTTTAG-ATATTTGAGGGTAAAATGGCACTTTTTGGAAAAATCAGGGTCA
1 GGTCAAAAAT-GAAATTTTAGAAAATTTAAGGGTAAAATGGTAATTTTTGGAAAAATTAGGGTCA
*
137730 AAAATGGAATTTTGGAAAGTTTGGGGGTAAAAAATGTAATTTTTGGAAAAAATAA
65 AAAATGGAATTTTGGAAAGTTTAGGGGT-AAAAATGTAATTTTTGGAAAAAATAA
* * *
137785 GGTTAAAAATGAAATTTTAGAAAATTTAGGGGTAAAATGGTAATTTTTGGAAAAATTAGGGTAAA
1 GGTCAAAAATGAAATTTTAGAAAATTTAAGGGTAAAATGGTAATTTTTGGAAAAATTAGGGTCAA
* * *
137850 AAATGGAATTTTAGAAAG-TTCGGGGTAAAAATGTAATTTTTGG-GAAAATCAA
66 AAATGGAATTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTTGGAAAAAAT-AA
* * * * * *
137902 GGTCAAAAATGGAATTTTGGAAAGTTTAATGGTAAAAAT-GTAATTTTTGGGAAAA-TCGAGGTC
1 GGTCAAAAATGAAATTTTAGAAAATTTAAGGGT-AAAATGGTAATTTTTGGAAAAATTAG-GGTC
* *
137965 GAAAATGAAATTTTGGAAAGTTTAGGGGT-AAAATGGTAATTTT
64 AAAAATGGAATTTTGGAAAGTTTAGGGGTAAAAAT-GTAATTTT
138008 AGATAGTTTA
Statistics
Matches: 192, Mismatches: 25, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
116 7 0.04
117 86 0.45
118 36 0.19
119 63 0.33
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.32
Consensus pattern (118 bp):
GGTCAAAAATGAAATTTTAGAAAATTTAAGGGTAAAATGGTAATTTTTGGAAAAATTAGGGTCAA
AAATGGAATTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTTGGAAAAAATAA
Found at i:138005 original size:29 final size:30
Alignment explanation
Indices: 137634--138007 Score: 178
Period size: 30 Copynumber: 12.7 Consensus size: 30
137624 TTGGTCACTC
* * *
137634 GGGGGAAAAATGGTAATTTTGGGAAAGTTA
1 GGGGTAAAAATGGTAATTTTGGAAAATTTA
* * *
137664 GGGGTCAAAAATAG-AATTTT-TAGATATTT-
1 GGGGT-AAAAATGGTAATTTTGGA-AAATTTA
* * * *
137693 GAGGGT-AAAATGGCACTTTTTGGAAAAATCA
1 G-GGGTAAAAATGGTA-ATTTTGGAAAATTTA
* *
137724 -GGGTCAAAAATGG-AATTTTGGAAAGTTTG
1 GGGGT-AAAAATGGTAATTTTGGAAAATTTA
**
137753 GGGGTAAAAAAT-GTAATTTTTGGAAAAAATA
1 GGGGT-AAAAATGGTAA-TTTTGGAAAATTTA
* * * *
137784 AGGTTAAAAAT-GAAATTTTAGAAAATTTA
1 GGGGTAAAAATGGTAATTTTGGAAAATTTA
*
137813 GGGGT-AAAATGGTAATTTTTGGAAAAATTA
1 GGGGTAAAAATGGTAA-TTTTGGAAAATTTA
* * *
137843 -GGGTAAAAAATGG-AATTTTAG-AAAGTTC
1 GGGGT-AAAAATGGTAATTTTGGAAAATTTA
*
137871 GGGGTAAAAAT-GTAATTTTTGGGAAAA-TCA
1 GGGGTAAAAATGGTAA-TTTT-GGAAAATTTA
* *
137901 -AGGTCAAAAATGG-AATTTTGGAAAGTTTA
1 GGGGT-AAAAATGGTAATTTTGGAAAATTTA
** *
137930 ATGGTAAAAAT-GTAATTTTTGGGAAAA--TC
1 GGGGTAAAAATGGTAA-TTTT-GGAAAATTTA
* * * *
137959 GAGGTCGAAAAT-GAAATTTTGGAAAGTTTA
1 GGGGT-AAAAATGGTAATTTTGGAAAATTTA
137989 GGGGT-AAAATGGTAATTTT
1 GGGGTAAAAATGGTAATTTT
138008 AGATAGTTTA
Statistics
Matches: 259, Mismatches: 53, Indels: 65
0.69 0.14 0.17
Matches are distributed among these distances:
27 1 0.00
28 40 0.15
29 83 0.32
30 91 0.35
31 44 0.17
ACGTcount: A:0.41, C:0.03, G:0.25, T:0.31
Consensus pattern (30 bp):
GGGGTAAAAATGGTAATTTTGGAAAATTTA
Found at i:139829 original size:17 final size:17
Alignment explanation
Indices: 139809--139872 Score: 55
Period size: 17 Copynumber: 3.9 Consensus size: 17
139799 AATTTTAAAT
139809 TTAAAATAAATTTAATC
1 TTAAAATAAATTTAATC
139826 TT--AATAAATTTAAAT-
1 TTAAAATAAATTT-AATC
*
139841 TTAAAAT-AATTCTAAAC
1 TTAAAATAAATT-TAATC
**
139858 TTGTAATAAATTTAA
1 TTAAAATAAATTTAA
139873 AATAATGATT
Statistics
Matches: 38, Mismatches: 3, Indels: 12
0.72 0.06 0.23
Matches are distributed among these distances:
15 11 0.29
16 9 0.24
17 14 0.37
18 4 0.11
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.42
Consensus pattern (17 bp):
TTAAAATAAATTTAATC
Found at i:139839 original size:32 final size:34
Alignment explanation
Indices: 139802--139873 Score: 105
Period size: 32 Copynumber: 2.2 Consensus size: 34
139792 TATTTCAAAT
*
139802 TTTAAATTTAAAATAAATT-TAATC-T-TAATAAA
1 TTTAAATTTAAAAT-AATTCTAAACTTGTAATAAA
139834 TTTAAATTTAAAATAATTCTAAACTTGTAATAAA
1 TTTAAATTTAAAATAATTCTAAACTTGTAATAAA
139868 TTTAAA
1 TTTAAA
139874 ATAATGATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
31 4 0.11
32 18 0.50
33 1 0.03
34 13 0.36
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.43
Consensus pattern (34 bp):
TTTAAATTTAAAATAATTCTAAACTTGTAATAAA
Found at i:139873 original size:17 final size:16
Alignment explanation
Indices: 139813--139873 Score: 63
Period size: 15 Copynumber: 3.8 Consensus size: 16
139803 TTAAATTTAA
*
139813 AATAAATTTAATC-TT
1 AATAAATTTAAACTTT
139828 AATAAATTTAAA-TTT
1 AATAAATTTAAACTTT
*
139843 AAAATAATTCTAAACTTGT
1 AATA-AATT-TAAACTT-T
139862 AATAAATTTAAA
1 AATAAATTTAAA
139874 ATAATGATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
15 16 0.42
16 4 0.11
17 8 0.21
18 6 0.16
19 4 0.11
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (16 bp):
AATAAATTTAAACTTT
Found at i:140654 original size:98 final size:98
Alignment explanation
Indices: 140484--140674 Score: 265
Period size: 98 Copynumber: 1.9 Consensus size: 98
140474 TGTTTGTAAC
* * * * *
140484 GTACAAGGTTCGCCGTTGGGGCTAAAACCCTTCCCTTTGTGTCTTTGCGGTATTGGATCCGCCAT
1 GTACAAGGGTCGCCGTTGCGACTAAAACCCTTCCCTTTGTGTCTTTGCAGTACTGGATCCGCCAT
* *
140549 TGTGGCTTAGATCTTTCCCTTCATGTCTCTGAG
66 TGCGGCTTAAATCTTTCCCTTCATGTCTCTGAG
* * * * * *
140582 GTACAAGGGTCGCCGTTGCGACTTAAACCCTTCTCTTTGTGTCTTTGTAGTACTGGATTCGGCGT
1 GTACAAGGGTCGCCGTTGCGACTAAAACCCTTCCCTTTGTGTCTTTGCAGTACTGGATCCGCCAT
140647 TGCGGCTTAAATCTTTCCCTTCATGTCT
66 TGCGGCTTAAATCTTTCCCTTCATGTCT
140675 TTGCGGTAGA
Statistics
Matches: 80, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
98 80 1.00
ACGTcount: A:0.15, C:0.25, G:0.24, T:0.37
Consensus pattern (98 bp):
GTACAAGGGTCGCCGTTGCGACTAAAACCCTTCCCTTTGTGTCTTTGCAGTACTGGATCCGCCAT
TGCGGCTTAAATCTTTCCCTTCATGTCTCTGAG
Found at i:140674 original size:49 final size:49
Alignment explanation
Indices: 140484--140682 Score: 125
Period size: 49 Copynumber: 4.1 Consensus size: 49
140474 TGTTTGTAAC
* * * * * ** *
140484 GTACAAGGTTCGCCGTTGGGGCTAAAACCCTTCCCTTTGTGTCTTTGCG
1 GTACAAGGGTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTTTGAG
** * * * * *
140533 GTA-TTGGATCCGCCATTGTGGCTTAGATCTTTCCCTTCATGTCTCTGAG
1 GTACAAGGGT-CGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTTTGAG
* * * * **
140582 GTACAAGGGTCGCCGTTGCGACTTAAACCCTTCTCTTTGTGTCTTTGTA-
1 GTACAAGGGTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTTTG-AG
* * * *
140631 GTAC-TGGATTCGGCGTTGCGGCTTAAATCTTTCCCTTCATGTCTTTGCG
1 GTACAAGG-GTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTTTGAG
140680 GTA
1 GTA
140683 GATCCTTCCC
Statistics
Matches: 109, Mismatches: 36, Indels: 10
0.70 0.23 0.06
Matches are distributed among these distances:
48 5 0.05
49 100 0.92
50 4 0.04
ACGTcount: A:0.15, C:0.25, G:0.24, T:0.37
Consensus pattern (49 bp):
GTACAAGGGTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTTTGAG
Found at i:140821 original size:49 final size:49
Alignment explanation
Indices: 140759--140942 Score: 182
Period size: 49 Copynumber: 3.8 Consensus size: 49
140749 TCTTCGTGGA
* *
140759 ACTGGATCCGCCGTTGCGGCTTAGATCTTT-CCTTTCATGTCTCTGAGGT
1 ACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTTCAT-TCTCTGAGGT
* *
140808 ACAAGG-TTCGCCGTTGTGGCTTAAATCTTTCCCTTT-ATATCTCT-ATGGT
1 AC-TGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTTCAT-TCTCTGA-GGT
* * * *
140857 ACTGGATTTGCCGTTGTGGCTTAAATCTTTCCCTTTTCA-TCTTTGTGGT
1 ACTGGATTCGCCGTTGCGGCTTAAATCTTTCCC-TTTCATTCTCTGAGGT
* *
140906 ACTGGATCCGCCGTTGCGGTCTTAGATCTTT-CCTTTC
1 ACTGGATTCGCCGTTGCGG-CTTAAATCTTTCCCTTTC
140943 GTGTTTCATG
Statistics
Matches: 114, Mismatches: 13, Indels: 17
0.79 0.09 0.12
Matches are distributed among these distances:
48 7 0.06
49 86 0.75
50 20 0.18
51 1 0.01
ACGTcount: A:0.14, C:0.24, G:0.21, T:0.41
Consensus pattern (49 bp):
ACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTTCATTCTCTGAGGT
Found at i:140892 original size:99 final size:100
Alignment explanation
Indices: 140688--140892 Score: 249
Period size: 99 Copynumber: 2.1 Consensus size: 100
140678 CGGTAGATCC
* *
140688 TTCCC-TTCATGCTTCTGAGGTACAAGGTTCGTCATTGCGACTTAAACCTTTCCCTTTTGTATCT
1 TTCCCTTTCATGCTTCTGAGGTACAAGGTTCGCCATTGCGACTTAAACCTTTCCCTTTTATATCT
* *
140752 TCGTGGAACTGGATCCGCCGTTGCGGCTTAGATCT
66 TCATGGAACTGGATCCGCCGTTGCGGCTTAAATCT
* * * *
140787 TT-CCTTTCATG-TCTCTGAGGTACAAGGTTCGCCGTTGTGGCTTAAATCTTTCCC-TTTATATC
1 TTCCCTTTCATGCT-TCTGAGGTACAAGGTTCGCCATTGCGACTTAAACCTTTCCCTTTTATATC
* ** *
140849 -TCTATGGTACTGGATTTGCCGTTGTGGCTTAAATCT
65 TTC-ATGGAACTGGATCCGCCGTTGCGGCTTAAATCT
140885 TTCCCTTT
1 TTCCCTTT
140893 TCATCTTTGT
Statistics
Matches: 90, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
97 2 0.02
98 39 0.43
99 49 0.54
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (100 bp):
TTCCCTTTCATGCTTCTGAGGTACAAGGTTCGCCATTGCGACTTAAACCTTTCCCTTTTATATCT
TCATGGAACTGGATCCGCCGTTGCGGCTTAAATCT
Found at i:145186 original size:19 final size:18
Alignment explanation
Indices: 145159--145197 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
145149 AAAGTAAATT
*
145159 TAAGAATGATTGTATGGTA
1 TAAGAATGAGTGTAT-GTA
*
145178 TAAGTATGAGTGTATGTA
1 TAAGAATGAGTGTATGTA
145196 TA
1 TA
145198 CAAAATTCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.36, C:0.00, G:0.26, T:0.38
Consensus pattern (18 bp):
TAAGAATGAGTGTATGTA
Found at i:148115 original size:29 final size:29
Alignment explanation
Indices: 148082--148165 Score: 82
Period size: 29 Copynumber: 2.8 Consensus size: 29
148072 GGCCCTATTT
148082 AAAATTACATTTTTACCCTCGAACTTTCC-
1 AAAATTACATTTTTACCCT-GAACTTTCCA
* * *
148111 AAAATTCCATTTTTTA-CCTTAATTTTTCCA
1 AAAATTACA-TTTTTACCCTGAA-CTTTCCA
*
148141 AAAATTACAATTTTACCCTTGAACT
1 AAAATTACATTTTTACCC-TGAACT
148166 CATACATTCA
Statistics
Matches: 43, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
28 2 0.05
29 21 0.49
30 17 0.40
31 3 0.07
ACGTcount: A:0.33, C:0.23, G:0.02, T:0.42
Consensus pattern (29 bp):
AAAATTACATTTTTACCCTGAACTTTCCA
Found at i:150447 original size:15 final size:16
Alignment explanation
Indices: 150421--150457 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
150411 ATAATTAAAC
150421 AAGAAT-TTGAGA-GG
1 AAGAATGTTGAGATGG
150435 AAGAATGTTGAGATGG
1 AAGAATGTTGAGATGG
*
150451 AAAAATG
1 AAGAATG
150458 ATAGAAAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 6 0.30
15 6 0.30
16 8 0.40
ACGTcount: A:0.46, C:0.00, G:0.32, T:0.22
Consensus pattern (16 bp):
AAGAATGTTGAGATGG
Found at i:151276 original size:11 final size:11
Alignment explanation
Indices: 151254--151285 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
151244 TTTGCATTCA
151254 CGCATT-CATT
1 CGCATTGCATT
151264 CGCATTGCATT
1 CGCATTGCATT
151275 CGCATTGCATT
1 CGCATTGCATT
151286 TAAACGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.29
11 15 0.71
ACGTcount: A:0.19, C:0.28, G:0.16, T:0.38
Consensus pattern (11 bp):
CGCATTGCATT
Found at i:154318 original size:18 final size:18
Alignment explanation
Indices: 154292--154344 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
154282 GACGATGATC
* **
154292 AATTCAAATGATTATCTT
1 AATTAAAATGATTAAATT
154310 AATTAAAATGATTAAATT
1 AATTAAAATGATTAAATT
*
154328 AATTCAAAATAATTAAA
1 AATT-AAAATGATTAAA
154345 GTCACCAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
18 19 0.63
19 11 0.37
ACGTcount: A:0.53, C:0.06, G:0.04, T:0.38
Consensus pattern (18 bp):
AATTAAAATGATTAAATT
Found at i:154342 original size:19 final size:18
Alignment explanation
Indices: 154308--154344 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
154298 AATGATTATC
*
154308 TTAATTAAAATGATTAAA
1 TTAATTAAAATAATTAAA
154326 TTAATTCAAAATAATTAAA
1 TTAATT-AAAATAATTAAA
154345 GTCACCAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (18 bp):
TTAATTAAAATAATTAAA
Found at i:154918 original size:14 final size:15
Alignment explanation
Indices: 154894--154924 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
154884 AATGTTGTTG
154894 TTAATATAAGAGAAT
1 TTAATATAAGAGAAT
154909 TTAA-ATAAGAGAAT
1 TTAATATAAGAGAAT
154923 TT
1 TT
154925 GAGTTTGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.52, C:0.00, G:0.13, T:0.35
Consensus pattern (15 bp):
TTAATATAAGAGAAT
Found at i:156958 original size:3 final size:3
Alignment explanation
Indices: 156945--156982 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
156935 TTAATTAATC
*
156945 TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
156983 TATAACATTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:168372 original size:194 final size:193
Alignment explanation
Indices: 167985--168425 Score: 509
Period size: 194 Copynumber: 2.3 Consensus size: 193
167975 GAAACCGACG
* *
167985 CGATGGTTGAGGTACCGTATATGTTGCGAGTCCTCGACAGCTCGTGCGAGCAGCATGTCGAGAAA
1 CGATGGTTGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAG-ATGTCGAGAAA
* *
168050 TGAGAAAAGAAATATGGATCCTAAATGGATTATAGGCCTTACGATGGCTGACTTATGCATAAGTG
65 TGAGAAAAGAAACATGGATCCTAAATGGATTATAGGCCCTACGATGGCTGACTTATGCATAAGTG
* * * *
168115 CATATTCTCGACAGCTCGTGTGAGCAGCATCGTTAGGGAACAGTTATATGGACAGATACCGTAT
130 CATACTCTCGACAGCTCGTGTGAGCAGAATCGTTAGGGAACAGTTATATAGACAGACACCGTAT
* * *** *
168179 TGATGGTTGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAG-TTTTTTG-ACT
1 CGATGGTTGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGATGTCGAGAAAT
* * *
168242 CGAG-AAAGAGACATGGATCCTAAATGGATTATAGGCCCTACGATGG-TGGGA-TTATGCTTTA-
66 -GAGAAAAGAAACATGGATCCTAAATGGATTATAGGCCCTACGATGGCT--GACTTATGCATAAG
* * *
168303 TGCATGCTCTCGATAGCTCGTGTGAGCAGAATCGTTAGGGAACAATT-TATAGTACAGACAAGCA
128 TGCATACTCTCGACAGCTCGTGTGAGCAGAATCGTTAGGGAACAGTTATATAG-ACAG---A-CA
168367 CCGTAT
188 CCGTAT
* * * ** * *
168373 CAATGGCTGGGGTACCGCATACATTGCGAGTCATCGACATCTCGTGTGAGCAG
1 CGATGGTTGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAG
168426 CATCGAGTAT
Statistics
Matches: 211, Mismatches: 28, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
189 4 0.02
190 47 0.22
191 49 0.23
192 8 0.04
193 1 0.00
194 102 0.48
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.27
Consensus pattern (193 bp):
CGATGGTTGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGATGTCGAGAAAT
GAGAAAAGAAACATGGATCCTAAATGGATTATAGGCCCTACGATGGCTGACTTATGCATAAGTGC
ATACTCTCGACAGCTCGTGTGAGCAGAATCGTTAGGGAACAGTTATATAGACAGACACCGTAT
Found at i:177662 original size:30 final size:31
Alignment explanation
Indices: 177609--177691 Score: 84
Period size: 31 Copynumber: 2.7 Consensus size: 31
177599 TTTGGGTTGT
*
177609 GACTAAAATT--TCAAATTTTAAAAAGTACAAA
1 GACTAAAATTGATCAAA--TTAAAAAATACAAA
* *
177640 GACT-AAATTGA-CCAATTAAAAAATACAAT
1 GACTAAAATTGATCAAATTAAAAAATACAAA
*
177669 GATTAAAATTGATCAAATTAAAA
1 GACTAAAATTGATCAAATTAAAA
177692 TATGATGACT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
29 15 0.35
30 12 0.28
31 16 0.37
ACGTcount: A:0.55, C:0.10, G:0.07, T:0.28
Consensus pattern (31 bp):
GACTAAAATTGATCAAATTAAAAAATACAAA
Found at i:178173 original size:30 final size:31
Alignment explanation
Indices: 178137--178208 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 31
178127 GTTACGTGTA
*
178137 ACAAAACAATCACTTAACTT-T-GAAAATGTG
1 ACAAAACAATCACTAAACTTATCGAAAA-GTG
* *
178167 ACAAAACAGTCACTAAAGTTATCGAAAAGTG
1 ACAAAACAATCACTAAACTTATCGAAAAGTG
*
178198 ACAAAATAATC
1 ACAAAACAATC
178209 CTCTTGTTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
30 17 0.49
31 13 0.37
32 5 0.14
ACGTcount: A:0.50, C:0.17, G:0.11, T:0.22
Consensus pattern (31 bp):
ACAAAACAATCACTAAACTTATCGAAAAGTG
Found at i:179699 original size:30 final size:30
Alignment explanation
Indices: 179659--179724 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
179649 TGACGAAAAA
*
179659 GGACTATTTTGTCACATTTTAAAAGTTGAG
1 GGACTGTTTTGTCACATTTTAAAAGTTGAG
* *
179689 GGACTGTTTTGTCATATTTTCAAAGTTGAG
1 GGACTGTTTTGTCACATTTTAAAAGTTGAG
179719 GGACTG
1 GGACTG
179725 AAATGTAAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.26, C:0.11, G:0.24, T:0.39
Consensus pattern (30 bp):
GGACTGTTTTGTCACATTTTAAAAGTTGAG
Found at i:181019 original size:20 final size:20
Alignment explanation
Indices: 180982--181020 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
180972 AACAATATGA
* *
180982 ACCAATAGACACCGATATAG
1 ACCAATACACACCAATATAG
*
181002 ACCAATACATACCAATATA
1 ACCAATACACACCAATATA
181021 AGCTGATATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.49, C:0.26, G:0.08, T:0.18
Consensus pattern (20 bp):
ACCAATACACACCAATATAG
Found at i:182569 original size:21 final size:22
Alignment explanation
Indices: 182534--182576 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
182524 ATCGATTCGA
* *
182534 TTAAATAAATCGTAAAATATTT
1 TTAAATAAATAGTAAAAAATTT
182556 TTAAA-AAATAGTAAAAAATTT
1 TTAAATAAATAGTAAAAAATTT
182577 ATTCAACCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (22 bp):
TTAAATAAATAGTAAAAAATTT
Found at i:192974 original size:12 final size:11
Alignment explanation
Indices: 192952--192981 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
192942 CATTAGCTAT
192952 ATAAAAAATAA
1 ATAAAAAATAA
192963 ATAAATAAATAA
1 ATAAA-AAATAA
192975 ATAAAAA
1 ATAAAAA
192982 GAATCCAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (11 bp):
ATAAAAAATAA
Found at i:225776 original size:17 final size:17
Alignment explanation
Indices: 225725--225792 Score: 68
Period size: 17 Copynumber: 4.1 Consensus size: 17
225715 ATATGAAAAA
225725 TTAAGGAAGATGGAAGG
1 TTAAGGAAGATGGAAGG
* ** * *
225742 TTAAAGATTAAGGGAGG
1 TTAAGGAAGATGGAAGG
225759 TTAAGGAAGATGGAAGG
1 TTAAGGAAGATGGAAGG
*
225776 TTAA--AAGATGAAAGG
1 TTAAGGAAGATGGAAGG
225791 TT
1 TT
225793 GAACATCCAT
Statistics
Matches: 40, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
15 12 0.30
17 28 0.70
ACGTcount: A:0.43, C:0.00, G:0.35, T:0.22
Consensus pattern (17 bp):
TTAAGGAAGATGGAAGG
Found at i:228125 original size:16 final size:17
Alignment explanation
Indices: 228097--228130 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
228087 TGATAATTCA
*
228097 TTCCAATCTGTTTCTTT
1 TTCCAATCTGTTTATTT
228114 TTCCAA-CTGTTTATTT
1 TTCCAATCTGTTTATTT
228130 T
1 T
228131 CTCCCCCTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.15, C:0.21, G:0.06, T:0.59
Consensus pattern (17 bp):
TTCCAATCTGTTTATTT
Done.