Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010480.1 Kokia drynarioides strain JFW-HI SEQ_125382, 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: 287878
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 46 characters in sequence are not A, C, G, or T
Found at i:213 original size:16 final size:16
Alignment explanation
Indices: 167--215 Score: 62
Period size: 17 Copynumber: 3.0 Consensus size: 16
157 CTTCTATTCC
*
167 TTCTTTTGTTTCTTTT
1 TTCTTTTATTTCTTTT
*
183 TTCTTTTCTTTTCTTTT
1 TTCTTTT-ATTTCTTTT
*
200 TTCTTTTATATCTTTT
1 TTCTTTTATTTCTTTT
216 ATATATATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 14 0.48
17 15 0.52
ACGTcount: A:0.04, C:0.14, G:0.02, T:0.80
Consensus pattern (16 bp):
TTCTTTTATTTCTTTT
Found at i:220 original size:2 final size:2
Alignment explanation
Indices: 215--257 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
205 TTATATCTTT
215 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
257 T
1 T
258 TAATTGGTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:9009 original size:6 final size:6
Alignment explanation
Indices: 8998--9039 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
8988 TAATACCTCG
8998 CACCAA CACCAA CACCAA CACCAA CACCAA CACCAA CACCAA
1 CACCAA CACCAA CACCAA CACCAA CACCAA CACCAA CACCAA
9040 TATATATATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (6 bp):
CACCAA
Found at i:15016 original size:16 final size:17
Alignment explanation
Indices: 14995--15045 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 17
14985 GTAATTTTAG
*
14995 TTTTATTAATT-TAAAA
1 TTTTATAAATTATAAAA
15011 TTTTATAAATTATAAAA
1 TTTTATAAATTATAAAA
**
15028 AGTT-TAAATTA-AAAA
1 TTTTATAAATTATAAAA
15043 TTT
1 TTT
15046 ACTATTTTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
15 5 0.17
16 17 0.59
17 7 0.24
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (17 bp):
TTTTATAAATTATAAAA
Found at i:15548 original size:9 final size:9
Alignment explanation
Indices: 15536--15579 Score: 56
Period size: 8 Copynumber: 5.0 Consensus size: 9
15526 TAATTGTAAT
15536 ATTTTTTAA
1 ATTTTTTAA
15545 ATTTTTTAA
1 ATTTTTTAA
15554 A-TTTTTAA
1 ATTTTTTAA
15562 AGTTTTTT-A
1 A-TTTTTTAA
*
15571 TTTTTTTAA
1 ATTTTTTAA
15580 TGATGATGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
8 14 0.45
9 12 0.39
10 5 0.16
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (9 bp):
ATTTTTTAA
Found at i:15559 original size:18 final size:18
Alignment explanation
Indices: 15536--15579 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
15526 TAATTGTAAT
15536 ATTTTTTAAA-TTTTTTA
1 ATTTTTTAAAGTTTTTTA
*
15553 AATTTTTAAAGTTTTTTA
1 ATTTTTTAAAGTTTTTTA
*
15571 TTTTTTTAA
1 ATTTTTTAA
15580 TGATGATGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (18 bp):
ATTTTTTAAAGTTTTTTA
Found at i:18363 original size:20 final size:21
Alignment explanation
Indices: 18326--18364 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
18316 TGATTTTTGG
**
18326 AAAATTTAAATTTGATTAAGT
1 AAAATTTAAATTAAATTAAGT
18347 AAAA-TTAAATTAAATTAA
1 AAAATTTAAATTAAATTAA
18365 AAAAATATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (21 bp):
AAAATTTAAATTAAATTAAGT
Found at i:20049 original size:74 final size:73
Alignment explanation
Indices: 19966--20117 Score: 196
Period size: 74 Copynumber: 2.1 Consensus size: 73
19956 TGCGCTCTGC
* * *
19966 AGATCCGGTTAATTCCTTCCCCTTCAATTAGATTTTTGAATTTAAGATTTGCGTATTTTCATAGC
1 AGATCCGGTTAATTCCTTCCCCTCCAATTAGAGTTTCGAATTTAAGATTTGCGTA-TTTCATAGC
20031 TCTTGTTTT
65 TCTTGTTTT
* * ** * * *
20040 AGATCCGGTTGATTCTTTTTCCTCCAATTAGGGTTTCGAATTTATGATTTGCGTATTTCATGGCT
1 AGATCCGGTTAATTCCTTCCCCTCCAATTAGAGTTTCGAATTTAAGATTTGCGTATTTCATAGCT
*
20105 TTTGTTTT
66 CTTGTTTT
20113 AGATC
1 AGATC
20118 TGCTGTTAGT
Statistics
Matches: 67, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
73 21 0.31
74 46 0.69
ACGTcount: A:0.20, C:0.16, G:0.16, T:0.47
Consensus pattern (73 bp):
AGATCCGGTTAATTCCTTCCCCTCCAATTAGAGTTTCGAATTTAAGATTTGCGTATTTCATAGCT
CTTGTTTT
Found at i:39764 original size:25 final size:25
Alignment explanation
Indices: 39732--39779 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
39722 ATTTTTTTAT
*
39732 AAATATATTTATATGAATATAATTG
1 AAATATATTTACATGAATATAATTG
*
39757 AAATATATTTACATGTATATAAT
1 AAATATATTTACATGAATATAAT
39780 ATATAATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (25 bp):
AAATATATTTACATGAATATAATTG
Found at i:45346 original size:21 final size:21
Alignment explanation
Indices: 45322--45376 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
45312 TTAGTTAAAA
*
45322 TGTATCAGTAGAAAGGAGACT
1 TGTATCGGTAGAAAGGAGACT
45343 TGTATCGGTAGAAAGGAGACT
1 TGTATCGGTAGAAAGGAGACT
45364 TGTATCGGTAGAA
1 TGTATCGGTAGAA
45377 TGATAATATC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.35, C:0.09, G:0.31, T:0.25
Consensus pattern (21 bp):
TGTATCGGTAGAAAGGAGACT
Found at i:50021 original size:17 final size:19
Alignment explanation
Indices: 49990--50029 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
49980 TAAAAATAAA
*
49990 TTTTCATTTCAATTCT-AT
1 TTTTCATATCAATTCTCAT
50008 TTTTCATATC-ATTCTCAT
1 TTTTCATATCAATTCTCAT
50026 TTTT
1 TTTT
50030 GTCCCATCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.20, C:0.17, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTCATATCAATTCTCAT
Found at i:51808 original size:24 final size:23
Alignment explanation
Indices: 51781--51825 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
51771 GTTAGATCCA
* *
51781 AATTAATTTTAAAAAGATAATTAG
1 AATTAAATATAAAAA-ATAATTAG
51805 AATTAAATATAAAAAATAATT
1 AATTAAATATAAAAAATAATT
51826 CTCTAATTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (23 bp):
AATTAAATATAAAAAATAATTAG
Found at i:60195 original size:34 final size:34
Alignment explanation
Indices: 60152--60225 Score: 103
Period size: 34 Copynumber: 2.2 Consensus size: 34
60142 GTAATAAAAA
60152 TATTAATGAAAAGTCTCGAATTGTATGGACCGAT
1 TATTAATGAAAAGTCTCGAATTGTATGGACCGAT
* * * **
60186 TATTAATGAAAAGTCTTGACTTTTATGGATTGAT
1 TATTAATGAAAAGTCTCGAATTGTATGGACCGAT
60220 TATTAA
1 TATTAA
60226 AGTTTTTATT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.39
Consensus pattern (34 bp):
TATTAATGAAAAGTCTCGAATTGTATGGACCGAT
Found at i:64686 original size:3 final size:3
Alignment explanation
Indices: 64672--64701 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
64662 TGTTTCAGAT
*
64672 GAA GAT GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
64702 ATAGGCTTGA
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:0.63, C:0.00, G:0.33, T:0.03
Consensus pattern (3 bp):
GAA
Found at i:68584 original size:20 final size:22
Alignment explanation
Indices: 68545--68584 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
68535 TGAATTTTAA
*
68545 AACACTTATTTTTCGAGTAGTG
1 AACACTTATATTTCGAGTAGTG
68567 AACACTTA-ATTT-GAGTAG
1 AACACTTATATTTCGAGTAG
68585 CTCTGCCGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 3 0.18
22 8 0.47
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (22 bp):
AACACTTATATTTCGAGTAGTG
Found at i:69807 original size:3 final size:3
Alignment explanation
Indices: 69799--69828 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
69789 ATAGTGAATA
69799 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
69829 GGTGGTGATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:72972 original size:7 final size:7
Alignment explanation
Indices: 72962--73016 Score: 74
Period size: 7 Copynumber: 7.9 Consensus size: 7
72952 AAACGGAAAA
72962 CGGGTAG
1 CGGGTAG
*
72969 CGGGTAA
1 CGGGTAG
*
72976 CGGGTAA
1 CGGGTAG
*
72983 CGGGTAA
1 CGGGTAG
72990 CGGGTAG
1 CGGGTAG
72997 CGGGTAG
1 CGGGTAG
*
73004 CAGGTAG
1 CGGGTAG
73011 CGGGTA
1 CGGGTA
73017 ACGGAAGAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 44 1.00
ACGTcount: A:0.22, C:0.15, G:0.49, T:0.15
Consensus pattern (7 bp):
CGGGTAG
Found at i:72977 original size:14 final size:14
Alignment explanation
Indices: 72960--73020 Score: 95
Period size: 14 Copynumber: 4.4 Consensus size: 14
72950 GAAAACGGAA
72960 AACGGGTAGCGGGT
1 AACGGGTAGCGGGT
*
72974 AACGGGTAACGGGT
1 AACGGGTAGCGGGT
72988 AACGGGTAGCGGGT
1 AACGGGTAGCGGGT
* *
73002 AGCAGGTAGCGGGT
1 AACGGGTAGCGGGT
73016 AACGG
1 AACGG
73021 AAGAAAGGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 41 1.00
ACGTcount: A:0.25, C:0.15, G:0.48, T:0.13
Consensus pattern (14 bp):
AACGGGTAGCGGGT
Found at i:72977 original size:21 final size:21
Alignment explanation
Indices: 72953--73022 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
72943 GGTAACGGAA
72953 AACGGAAAACGGGTAGCGGGT
1 AACGGAAAACGGGTAGCGGGT
** *
72974 AACGGGTAACGGGTAACGGGT
1 AACGGAAAACGGGTAGCGGGT
* ** * *
72995 AGCGGGTAGCAGGTAGCGGGT
1 AACGGAAAACGGGTAGCGGGT
73016 AACGGAA
1 AACGGAA
73023 GAAAGGAAAA
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.30, C:0.14, G:0.44, T:0.11
Consensus pattern (21 bp):
AACGGAAAACGGGTAGCGGGT
Found at i:78865 original size:15 final size:17
Alignment explanation
Indices: 78830--78864 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
78820 ACTTAAACAC
*
78830 AAATCTAATCTTTAAAA
1 AAATATAATCTTTAAAA
78847 AAATATAATC-TTAAAA
1 AAATATAATCTTTAAAA
78863 AA
1 AA
78865 TTATTTCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.31
Consensus pattern (17 bp):
AAATATAATCTTTAAAA
Found at i:95753 original size:30 final size:30
Alignment explanation
Indices: 95713--95769 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
95703 TGTAGAGCCA
95713 TCAAGATTGAGCATAGAGAGTAAACAACCT
1 TCAAGATTGAGCATAGAGAGTAAACAACCT
*
95743 TCAAGGTTGAGCATAGAGAGTAAACAA
1 TCAAGATTGAGCATAGAGAGTAAACAA
95770 AAGGTGGTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.44, C:0.14, G:0.23, T:0.19
Consensus pattern (30 bp):
TCAAGATTGAGCATAGAGAGTAAACAACCT
Found at i:104423 original size:20 final size:21
Alignment explanation
Indices: 104398--104445 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 21
104388 CAGTTTGATT
104398 AAATAAATTATTT-AAAAATA
1 AAATAAATTATTTAAAAAATA
*
104418 AAATAAAATATTTAAAAAATA
1 AAATAAATTATTTAAAAAATA
104439 AAA-AAAT
1 AAATAAAT
104446 CAATTTAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (21 bp):
AAATAAATTATTTAAAAAATA
Found at i:108509 original size:22 final size:20
Alignment explanation
Indices: 108479--108518 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
108469 AAAACTTTTG
108479 GTATGATTTGATAGTTTTTGAA
1 GTATGATTT--TAGTTTTTGAA
*
108501 GTATTATTTTAGTTTTTG
1 GTATGATTTTAGTTTTTG
108519 CCATTTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
22 8 0.47
ACGTcount: A:0.23, C:0.00, G:0.20, T:0.57
Consensus pattern (20 bp):
GTATGATTTTAGTTTTTGAA
Found at i:117294 original size:21 final size:23
Alignment explanation
Indices: 117270--117314 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 23
117260 TTTTGAAGAT
117270 ATTTTTATTTTTT-T-AATTATA
1 ATTTTTATTTTTTATGAATTATA
*
117291 ATTTTTTTTTTTTATGAATTATA
1 ATTTTTATTTTTTATGAATTATA
117314 A
1 A
117315 GAGGAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 12 0.57
22 1 0.05
23 8 0.38
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (23 bp):
ATTTTTATTTTTTATGAATTATA
Found at i:117303 original size:23 final size:23
Alignment explanation
Indices: 117271--117314 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
117261 TTTGAAGATA
* *
117271 TTTTTATTTTTTTAATTATAATT
1 TTTTTATTTTATGAATTATAATT
*
117294 TTTTTTTTTTATGAATTATAA
1 TTTTTATTTTATGAATTATAA
117315 GAGGAAAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.70
Consensus pattern (23 bp):
TTTTTATTTTATGAATTATAATT
Found at i:124088 original size:17 final size:17
Alignment explanation
Indices: 124047--124091 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
124037 TTAAATGATA
*
124047 TTTATTTAATTTTATTT
1 TTTATTTAATTTAATTT
** *
124064 ACTGTTTAATTTAATTT
1 TTTATTTAATTTAATTT
124081 TTTATTTAATT
1 TTTATTTAATT
124092 AAATGTGACA
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (17 bp):
TTTATTTAATTTAATTT
Found at i:124530 original size:21 final size:20
Alignment explanation
Indices: 124512--124549 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
124502 ATATAATAAT
124512 AATTTT-AATTTTTAAAATA
1 AATTTTAAATTTTTAAAATA
124531 AATTTTAAAATTTTTAAAA
1 AATTTT-AAATTTTTAAAA
124550 AATTACTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.35
21 11 0.65
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
AATTTTAAATTTTTAAAATA
Found at i:132987 original size:17 final size:17
Alignment explanation
Indices: 132949--132990 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
132939 AAGTATACAT
*
132949 AATAAAAACAATACATA
1 AATAAAAACAATACAAA
*
132966 CATAAAATACAATA-AAA
1 AATAAAA-ACAATACAAA
132983 AATAAAAA
1 AATAAAAA
132991 ATATACATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
16 1 0.05
17 14 0.67
18 6 0.29
ACGTcount: A:0.74, C:0.10, G:0.00, T:0.17
Consensus pattern (17 bp):
AATAAAAACAATACAAA
Found at i:133079 original size:29 final size:28
Alignment explanation
Indices: 133042--133255 Score: 146
Period size: 30 Copynumber: 7.3 Consensus size: 28
133032 CTTTAAAATC
*
133042 GGGTTAAATTTGAATTTTTAAAAACTTTA
1 GGGTCAAATTTGAATTTTTAAAAA-TTTA
*** *
133071 GGGTCAAATCAAAATTTTTGAAAAGTTTGA
1 GGGTCAAATTTGAATTTTT-AAAAATTT-A
* **
133101 GGGTCAAATTGGAACTTTTGGAAAATTTA
1 GGGTCAAATTTGAA-TTTTTAAAAATTTA
* * *
133130 GGGGTCAAA-TTCAAATTTCAAGAAAGTTTA
1 -GGGTCAAATTTGAATTTTTAA-AAA-TTTA
* *
133160 GGG--ATTATTTGAAATTTTGAAAAATTTGA
1 GGGTCA-AATTTG-AATTTTTAAAAATTT-A
* *
133189 GGGTTAAATTTGAATTTTTAGAAATTTTA
1 GGGTCAAATTTGAATTTTTA-AAAATTTA
*
133218 GGGGTCAAATTTGAATTTTTAGAAATTTTA
1 -GGGTCAAATTTGAATTTTTA-AAAATTTA
133248 GGGTCAAA
1 GGGTCAAA
133256 AAACAATTTT
Statistics
Matches: 147, Mismatches: 24, Indels: 28
0.74 0.12 0.14
Matches are distributed among these distances:
27 1 0.01
28 8 0.05
29 53 0.36
30 80 0.54
31 5 0.03
ACGTcount: A:0.37, C:0.05, G:0.20, T:0.38
Consensus pattern (28 bp):
GGGTCAAATTTGAATTTTTAAAAATTTA
Found at i:133242 original size:88 final size:89
Alignment explanation
Indices: 133042--133255 Score: 243
Period size: 88 Copynumber: 2.4 Consensus size: 89
133032 CTTTAAAATC
* * *
133042 GGGTTAAATTTGAATTTTTAAAAACTTTAGGGTCAAATCAAAATTTTTGAAAAGTTTGAGGGTCA
1 GGGTCAAATTTGAATTTTTAGAAACTTTAGGGTCAAATCAAAATTTTTGAAAAATTTGAGGGTCA
*
133107 AATTGGAACTTTTGGAAAATTTAG
66 AATTGGAACTTTTAGAAAATTTAG
** ** * * * ** *
133131 GGGTCAAATTCAAATTTCAAGAAAGTTTAGGGAT-TATTTGAAA-TTTTGAAAAATTTGAGGGTT
1 GGGTCAAATTTGAATTTTTAGAAACTTTAGGG-TCAAATCAAAATTTTTGAAAAATTTGAGGGTC
* * *
133194 AAATTTGAATTTTTAGAAATTTTAG
65 AAATTGGAACTTTTAGAAAATTTAG
*
133219 GGGTCAAATTTGAATTTTTAGAAATTTTAGGGTCAAA
1 GGGTCAAATTTGAATTTTTAGAAACTTTAGGGTCAAA
133256 AAACAATTTT
Statistics
Matches: 99, Mismatches: 24, Indels: 5
0.77 0.19 0.04
Matches are distributed among these distances:
87 1 0.01
88 67 0.68
89 30 0.30
90 1 0.01
ACGTcount: A:0.37, C:0.05, G:0.20, T:0.38
Consensus pattern (89 bp):
GGGTCAAATTTGAATTTTTAGAAACTTTAGGGTCAAATCAAAATTTTTGAAAAATTTGAGGGTCA
AATTGGAACTTTTAGAAAATTTAG
Found at i:133263 original size:29 final size:30
Alignment explanation
Indices: 133201--133265 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
133191 GTTAAATTTG
****
133201 AATTTTTAGAAATTTTAGGGGTCAAATTTG
1 AATTTTTAGAAATTTTAGGGGTCAAAAAAC
133231 AATTTTTAGAAATTTTA-GGGTCAAAAAAC
1 AATTTTTAGAAATTTTAGGGGTCAAAAAAC
133260 AATTTT
1 AATTTT
133266 AAAATAAAGC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 14 0.45
30 17 0.55
ACGTcount: A:0.38, C:0.05, G:0.15, T:0.42
Consensus pattern (30 bp):
AATTTTTAGAAATTTTAGGGGTCAAAAAAC
Found at i:134591 original size:39 final size:39
Alignment explanation
Indices: 134485--134682 Score: 202
Period size: 40 Copynumber: 5.0 Consensus size: 39
134475 TGGCTTTGCG
* * *
134485 GCTTCAATTTGCCCCATGGTCGGGGTAAAAGATTGGATG
1 GCTTCAATCTGCCCCATGGTCAGGGTAAAAGATTGGATT
* *
134524 GTCTTCAATCTGCCCTC-TGATTAGGGTAAAAGATTGGATT
1 G-CTTCAATCTGCCC-CATGGTCAGGGTAAAAGATTGGATT
* * ** *
134564 GCTTCAATCTGCCTCATGGTCAAGGTAAAAGATCAGATG
1 GCTTCAATCTGCCCCATGGTCAGGGTAAAAGATTGGATT
** *
134603 GTCTTCAATCTGCCCTTTGGTCAGGGTAAAAGATTGAATT
1 G-CTTCAATCTGCCCCATGGTCAGGGTAAAAGATTGGATT
* * *
134643 GCTTCAATTTTCCCCATGGTC-GAGGTAAAAGTTTGGATT
1 GCTTCAATCTGCCCCATGGTCAG-GGTAAAAGATTGGATT
134682 G
1 G
134683 TAACTTCGTT
Statistics
Matches: 128, Mismatches: 26, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
38 2 0.02
39 62 0.48
40 63 0.49
41 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (39 bp):
GCTTCAATCTGCCCCATGGTCAGGGTAAAAGATTGGATT
Found at i:134616 original size:79 final size:79
Alignment explanation
Indices: 134485--134673 Score: 279
Period size: 79 Copynumber: 2.4 Consensus size: 79
134475 TGGCTTTGCG
* ** *
134485 GCTTCAATTTGCCCCATGGTCGGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTGATTAGGG
1 GCTTCAATTTGCCCCATGGTCGAGGTAAAAGATCAGATGGTCTTCAATCTGCCCTCTGATCAGGG
*
134550 TAAAAGATTGGATT
66 TAAAAGATTGAATT
* * * * *
134564 GCTTCAATCTGCCTCATGGTCAAGGTAAAAGATCAGATGGTCTTCAATCTGCCCTTTGGTCAGGG
1 GCTTCAATTTGCCCCATGGTCGAGGTAAAAGATCAGATGGTCTTCAATCTGCCCTCTGATCAGGG
134629 TAAAAGATTGAATT
66 TAAAAGATTGAATT
*
134643 GCTTCAATTTTCCCCATGGTCGAGGTAAAAG
1 GCTTCAATTTGCCCCATGGTCGAGGTAAAAG
134674 TTTGGATTGT
Statistics
Matches: 96, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
79 96 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (79 bp):
GCTTCAATTTGCCCCATGGTCGAGGTAAAAGATCAGATGGTCTTCAATCTGCCCTCTGATCAGGG
TAAAAGATTGAATT
Found at i:134826 original size:40 final size:40
Alignment explanation
Indices: 134779--134892 Score: 126
Period size: 40 Copynumber: 2.9 Consensus size: 40
134769 TTACTAATGC
*
134779 GGCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTTG-AT
1 GGCTTCAATATGCCCTCTGGTTAGGGTAAAAGATTTGAAT
* * *
134818 GGTCTTCAATATGCTCTCTAGTCAGGGTAAAAGA-TTGAAT
1 GG-CTTCAATATGCCCTCTGGTTAGGGTAAAAGATTTGAAT
* * *
134858 TGCTTCAATTTGCCC-CATGGTTGGGGTAAAAGATT
1 GGCTTCAATATGCCCTC-TGGTTAGGGTAAAAGATT
134893 GGATTGTAAC
Statistics
Matches: 61, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
38 1 0.02
39 29 0.48
40 31 0.51
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (40 bp):
GGCTTCAATATGCCCTCTGGTTAGGGTAAAAGATTTGAAT
Found at i:134938 original size:216 final size:216
Alignment explanation
Indices: 134564--135001 Score: 626
Period size: 216 Copynumber: 2.0 Consensus size: 216
134554 AGATTGGATT
* * *
134564 GCTTCAATCTGCCTCATGGTCAAGGTAAAAGATCAGATGGTCTTCAATCTGCCCTTTGGTCAGGG
1 GCTTCAATCTGCCTCATGGTCAAGGTAAAAGATCAGATGGTCTTCAATATGCCCTCTAGTCAGGG
* * **
134629 TAAAAGATTGAATTGCTTCAATTTTCCCCATGGTCGAGGTAAAAGTTTGGATTGTAACTTCGTTC
66 TAAAAGATTGAATTGCTTCAATTTGCCCCATGGTCGAGGTAAAAGATTGGATTGTAACTTCACTC
* * * *
134694 CATTTTAGCTTTAGAAGTATAAGATTCATACTTACAACTTCAATCTGCCTCTCTACGGCTTTAGG
131 CATTTTAGCTTCAGAAGTATAAGATTCATACTTACAACTTCAATCTGCCCCTCTACAGCTTTAAG
* *
134759 TGAATGAGATTTACTAATGCG
196 TGAATGAGATTTACCAATACG
* * ** *
134780 GCTTCAATCTGCCCTC-TGGTTAGGGTAAAAGATTTGATGGTCTTCAATATGCTCTCTAGTCAGG
1 GCTTCAATCTG-CCTCATGGTCAAGGTAAAAGATCAGATGGTCTTCAATATGCCCTCTAGTCAGG
* *
134844 GTAAAAGATTGAATTGCTTCAATTTGCCCCATGGTTGGGGTAAAAGATTGGATTGTAACTTCACT
65 GTAAAAGATTGAATTGCTTCAATTTGCCCCATGGTCGAGGTAAAAGATTGGATTGTAACTTCACT
* * * * *
134909 CCATTTTAGCTTCAGGAGTATAAGATTCATCCTTGCGACTTTAATCTGCCCCTCTACAGCTTTAA
130 CCATTTTAGCTTCAGAAGTATAAGATTCATACTTACAACTTCAATCTGCCCCTCTACAGCTTTAA
*
134974 GTGAATGAGATTTGCCAATACG
195 GTGAATGAGATTTACCAATACG
134996 GCTTCA
1 GCTTCA
135002 GTCCACCCCT
Statistics
Matches: 195, Mismatches: 26, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
216 191 0.98
217 4 0.02
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.34
Consensus pattern (216 bp):
GCTTCAATCTGCCTCATGGTCAAGGTAAAAGATCAGATGGTCTTCAATATGCCCTCTAGTCAGGG
TAAAAGATTGAATTGCTTCAATTTGCCCCATGGTCGAGGTAAAAGATTGGATTGTAACTTCACTC
CATTTTAGCTTCAGAAGTATAAGATTCATACTTACAACTTCAATCTGCCCCTCTACAGCTTTAAG
TGAATGAGATTTACCAATACG
Found at i:135067 original size:50 final size:50
Alignment explanation
Indices: 134957--135079 Score: 138
Period size: 50 Copynumber: 2.5 Consensus size: 50
134947 CTTTAATCTG
* * * * *
134957 CCCCTCTACAGCTTTAAGTGAATGAGATTTGCCAATACGGCTTCAGTCCA
1 CCCCTCTATAGCTTTAGGTGTATGAGATTTACCAATACGGCTTCAATCCA
* * * *
135007 CCCCTTTATAGCTTTAGGTGTATGAGATTTACCATTGCGGCTTCAATCCG
1 CCCCTCTATAGCTTTAGGTGTATGAGATTTACCAATACGGCTTCAATCCA
** *
135057 TTCCTCTATAGCTTTAGGGGTAT
1 CCCCTCTATAGCTTTAGGTGTAT
135080 AGGATTTGTC
Statistics
Matches: 60, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
50 60 1.00
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (50 bp):
CCCCTCTATAGCTTTAGGTGTATGAGATTTACCAATACGGCTTCAATCCA
Found at i:139839 original size:31 final size:30
Alignment explanation
Indices: 139795--139870 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 30
139785 TTTCTTCAAA
* * *
139795 TTTT-AATGTATGAAAATGCAATGTGAAACT
1 TTTTGAATGCATGAAAATGCAATG-CAAAAT
* *
139825 TTTTGAATGCATGAAAATTCGATGCAAAAT
1 TTTTGAATGCATGAAAATGCAATGCAAAAT
139855 TTTATGAATGCATGAA
1 TTT-TGAATGCATGAA
139871 TGCATATGTA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
30 11 0.28
31 28 0.72
ACGTcount: A:0.39, C:0.08, G:0.17, T:0.36
Consensus pattern (30 bp):
TTTTGAATGCATGAAAATGCAATGCAAAAT
Found at i:141833 original size:16 final size:18
Alignment explanation
Indices: 141812--141847 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
141802 TTTACAAGTG
141812 TACATA-ATAAAA-ACAA
1 TACATACATAAAATACAA
141828 TACATACATAAAATACAA
1 TACATACATAAAATACAA
141846 TA
1 TA
141848 AAAAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 6 0.33
18 6 0.33
ACGTcount: A:0.64, C:0.14, G:0.00, T:0.22
Consensus pattern (18 bp):
TACATACATAAAATACAA
Found at i:141946 original size:30 final size:28
Alignment explanation
Indices: 141908--142124 Score: 166
Period size: 30 Copynumber: 7.3 Consensus size: 28
141898 CATTAAAATC
*
141908 GGGTCAAATTTGAATTTTTGAAAACTTTA
1 GGGTCAAATTAGAATTTTTGAAAA-TTTA
* * *
141937 GGAGTCAAATCAAAATTTTTGGAAAGTTTA
1 GG-GTCAAATTAGAATTTTT-GAAAATTTA
* *
141967 GGGGTCAAATCAAAATTTTTGGAAAATTTA
1 -GGGTCAAATTAGAATTTTT-GAAAATTTA
* *
141997 AGGTCAAATTCA-AATTTTTAAAAAGTTTA
1 GGGTCAAATT-AGAATTTTTGAAAA-TTTA
*
142026 GGGATCAAATTTGAATTTTTGGAAAATTTGA
1 GGG-TCAAATTAGAATTTTT-GAAAATTT-A
* * *
142057 GGGTTAAATTAGAATTTTTGGAAATTTT
1 GGGTCAAATTAGAATTTTTGAAAATTTA
* * *
142085 GTAGGTCAATTTTGAATTTTTAGAAATTTTA
1 G--GGTCAAATTAGAATTTTT-GAAAATTTA
142116 GGGGTCAAA
1 -GGGTCAAA
142125 AACTAATTTT
Statistics
Matches: 153, Mismatches: 22, Indels: 25
0.76 0.11 0.12
Matches are distributed among these distances:
28 5 0.03
29 30 0.20
30 97 0.63
31 20 0.13
32 1 0.01
ACGTcount: A:0.37, C:0.05, G:0.19, T:0.39
Consensus pattern (28 bp):
GGGTCAAATTAGAATTTTTGAAAATTTA
Found at i:142024 original size:59 final size:60
Alignment explanation
Indices: 141920--142054 Score: 168
Period size: 59 Copynumber: 2.3 Consensus size: 60
141910 GTCAAATTTG
* ** *
141920 AATTTTT-GAAAACTTTAGGAGTCAAATCAAAATTTTTGGAAAGTTTAGGGGTCAAATCAA
1 AATTTTTGGAAAA-TTTAAGAGTCAAATCAAAATTTTTAAAAAGTTTAGGGATCAAATCAA
***
141980 AATTTTTGGAAAATTTAAG-GTCAAATTC-AAATTTTTAAAAAGTTTAGGGATCAAATTTG
1 AATTTTTGGAAAATTTAAGAGTCAAA-TCAAAATTTTTAAAAAGTTTAGGGATCAAATCAA
142039 AATTTTTGGAAAATTT
1 AATTTTTGGAAAATTT
142055 GAGGGTTAAA
Statistics
Matches: 66, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
59 47 0.71
60 14 0.21
61 5 0.08
ACGTcount: A:0.40, C:0.06, G:0.16, T:0.38
Consensus pattern (60 bp):
AATTTTTGGAAAATTTAAGAGTCAAATCAAAATTTTTAAAAAGTTTAGGGATCAAATCAA
Found at i:142096 original size:59 final size:58
Alignment explanation
Indices: 141909--142124 Score: 188
Period size: 60 Copynumber: 3.6 Consensus size: 58
141899 ATTAAAATCG
* * *
141909 GGTCAAATTTGAATTTTT-GAAAACTTTAGGAGTCAAATCAAAATTTTTGGAAAGTTTAG-G
1 GGTCAAATTTGAATTTTTGGAAAA-TTTAGG-GTCAAAT-TAAATTTTTGGAAA-TTTTGTA
*** * * **
141969 GGTCAAATCAAAATTTTTGGAAAATTTAAGGTCAAATTCAAATTTTT-AAAAAGTT-TA
1 GGTCAAATTTGAATTTTTGGAAAATTTAGGGTCAAATT-AAATTTTTGGAAATTTTGTA
*
142026 GGGATCAAATTTGAATTTTTGGAAAATTTGAGGGTTAAATTAGAATTTTTGGAAATTTTGTA
1 -GG-TCAAATTTGAATTTTTGGAAAATTT-AGGGTCAAATTA-AATTTTTGGAAATTTTGTA
* * *
142088 GGTCAATTTTGAATTTTTAGAAATTTTAGGGGTCAAA
1 GGTCAAATTTGAATTTTTGGAAAATTTA-GGGTCAAA
142125 AACTAATTTT
Statistics
Matches: 124, Mismatches: 22, Indels: 20
0.75 0.13 0.12
Matches are distributed among these distances:
57 1 0.01
58 5 0.04
59 39 0.31
60 65 0.52
61 12 0.10
62 2 0.02
ACGTcount: A:0.37, C:0.05, G:0.19, T:0.39
Consensus pattern (58 bp):
GGTCAAATTTGAATTTTTGGAAAATTTAGGGTCAAATTAAATTTTTGGAAATTTTGTA
Found at i:142946 original size:51 final size:50
Alignment explanation
Indices: 142865--142966 Score: 186
Period size: 51 Copynumber: 2.0 Consensus size: 50
142855 CGATCGCGAC
142865 GACGGCACGGGCGTGGGCATGCTCGCAGTGGCGACAGATCTAAGGCTAGG
1 GACGGCACGGGCGTGGGCATGCTCGCAGTGGCGACAGATCTAAGGCTAGG
*
142915 NGACGGCACGGGCGTGGGCATGCTCGTAGTGGCGACAGATCTAAGGCTAGG
1 -GACGGCACGGGCGTGGGCATGCTCGCAGTGGCGACAGATCTAAGGCTAGG
142966 G
1 G
142967 TTAGGGTTTT
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
50 1 0.02
51 49 0.98
ACGTcount: A:0.20, C:0.23, G:0.42, T:0.15
Consensus pattern (50 bp):
GACGGCACGGGCGTGGGCATGCTCGCAGTGGCGACAGATCTAAGGCTAGG
Found at i:143415 original size:16 final size:16
Alignment explanation
Indices: 143394--143431 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
143384 TTAATAAAAA
143394 TAAATTTAAC-AATATT
1 TAAATTTAACGAA-ATT
143410 TAAA-TTAACGAAATT
1 TAAATTTAACGAAATT
143425 TAAATTT
1 TAAATTT
143432 GCTTATTACC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (16 bp):
TAAATTTAACGAAATT
Found at i:172536 original size:43 final size:43
Alignment explanation
Indices: 172475--172563 Score: 151
Period size: 43 Copynumber: 2.1 Consensus size: 43
172465 GCCATTTAAT
172475 TTTAGAAGAATTTCACTCCCTTCACCTCTATATAAAGCATTCA
1 TTTAGAAGAATTTCACTCCCTTCACCTCTATATAAAGCATTCA
* * *
172518 TTTAGAATATTTTCACTCCTTTCACCTCTATATAAAGCATTCA
1 TTTAGAAGAATTTCACTCCCTTCACCTCTATATAAAGCATTCA
172561 TTT
1 TTT
172564 GTTGTTTGGG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.30, C:0.24, G:0.06, T:0.40
Consensus pattern (43 bp):
TTTAGAAGAATTTCACTCCCTTCACCTCTATATAAAGCATTCA
Found at i:183563 original size:18 final size:18
Alignment explanation
Indices: 183540--183577 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
183530 TTATTAGAGT
183540 AAGTTTTTTCAACCTATA
1 AAGTTTTTTCAACCTATA
183558 AAGTTTTTTCAACCTATA
1 AAGTTTTTTCAACCTATA
183576 AA
1 AA
183578 TAGATGTAGT
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:0.37, C:0.16, G:0.05, T:0.42
Consensus pattern (18 bp):
AAGTTTTTTCAACCTATA
Found at i:186992 original size:45 final size:44
Alignment explanation
Indices: 186912--187077 Score: 154
Period size: 45 Copynumber: 3.7 Consensus size: 44
186902 GACCCTAAAG
* * *
186912 GATATATTGAACTGGCTCGGTAA-AGCAGTATACTGTACTAGGAGC
1 GATATACTGAACTGGCTC-GTAAGAGCAATACACTGTACT-GGAGC
* *
186957 GATATACTAAACTGGCTCGTGAGAGCAATACACTGTACTGGAAGC
1 GATATACTGAACTGGCTCGTAAGAGCAATACACTGTACTGG-AGC
* * * * * * **
187002 GATATACTGGACTGGATCATAAGAGCAATATATTATACTGGGAAT
1 GATATACTGAACTGGCTCGTAAGAGCAATACACTGTACT-GGAGC
* *
187047 GATATACTGAATTGGCTCGTAAGAGCGATAC
1 GATATACTGAACTGGCTCGTAAGAGCAATAC
187078 TGGATCGTAA
Statistics
Matches: 97, Mismatches: 21, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
44 5 0.05
45 90 0.93
46 2 0.02
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.26
Consensus pattern (44 bp):
GATATACTGAACTGGCTCGTAAGAGCAATACACTGTACTGGAGC
Found at i:187781 original size:25 final size:25
Alignment explanation
Indices: 187732--187782 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
187722 GCAGGGTGTA
*
187732 CACGAGCTGAGACACGATCGAGTGG
1 CACGAGCTGAGACACGACCGAGTGG
* * *
187757 CACGGGCTGAGACACGGCCGTGTGG
1 CACGAGCTGAGACACGACCGAGTGG
187782 C
1 C
187783 CTTAATTCGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.22, C:0.27, G:0.39, T:0.12
Consensus pattern (25 bp):
CACGAGCTGAGACACGACCGAGTGG
Found at i:189321 original size:26 final size:26
Alignment explanation
Indices: 189272--189331 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
189262 ACAAGCCCAC
*
189272 TACAGTGTATCGCTCTTAAAAGCCAA
1 TACAGTATATCGCTCTTAAAAGCCAA
* ** *
189298 TTCAGTATATCGCTCTTACGAGCCAG
1 TACAGTATATCGCTCTTAAAAGCCAA
189324 TACAGTAT
1 TACAGTAT
189332 CTTAAAGTCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (26 bp):
TACAGTATATCGCTCTTAAAAGCCAA
Found at i:189373 original size:19 final size:19
Alignment explanation
Indices: 189349--189420 Score: 117
Period size: 19 Copynumber: 3.8 Consensus size: 19
189339 TCTCCAGTAA
*
189349 ATCGCTCTTACGAGCTAGT
1 ATCGCTCTTACGAGCCAGT
*
189368 ATCGCTCTTATGAGCCAGT
1 ATCGCTCTTACGAGCCAGT
*
189387 ATCGCTCTTATGAGCCAGT
1 ATCGCTCTTACGAGCCAGT
189406 ATCGCTCTTACGAGC
1 ATCGCTCTTACGAGC
189421 TAGTGAAGTA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 50 1.00
ACGTcount: A:0.21, C:0.28, G:0.21, T:0.31
Consensus pattern (19 bp):
ATCGCTCTTACGAGCCAGT
Found at i:194001 original size:19 final size:18
Alignment explanation
Indices: 193977--194017 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
193967 TCAATATATG
193977 ATTTCAAAAAATTATTAAA
1 ATTTC-AAAAATTATTAAA
*
193996 ATTTCAATAATTATTAAA
1 ATTTCAAAAATTATTAAA
194014 ATTT
1 ATTT
194018 TATTTTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTTCAAAAATTATTAAA
Found at i:199764 original size:18 final size:17
Alignment explanation
Indices: 199721--199762 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
199711 ATATTTATAT
199721 TAATTTTTATTTAAAAA
1 TAATTTTTATTTAAAAA
199738 TAATTTTTATTTAAAAA
1 TAATTTTTATTTAAAAA
199755 TAATTTTT
1 TAATTTTT
199763 TAAAAATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TAATTTTTATTTAAAAA
Found at i:199766 original size:14 final size:16
Alignment explanation
Indices: 199725--199770 Score: 69
Period size: 17 Copynumber: 2.9 Consensus size: 16
199715 TTATATTAAT
199725 TTTTATTTAAAAATAA
1 TTTTATTTAAAAATAA
199741 TTTTTATTTAAAAATAA
1 -TTTTATTTAAAAATAA
199758 -TTT-TTTAAAAATA
1 TTTTATTTAAAAATA
199771 TAATACAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
14 10 0.34
15 3 0.10
17 16 0.55
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTTATTTAAAAATAA
Found at i:199922 original size:40 final size:40
Alignment explanation
Indices: 199818--199904 Score: 131
Period size: 40 Copynumber: 2.2 Consensus size: 40
199808 TAAAAAATAT
**
199818 TTATATT-AAAAACACTATCATAAATATAATAAATATTTTA
1 TTATATTAAAAAACAC-AAAATAAATATAATAAATATTTTA
199858 TTATATTAAAAAACACAAAATAAATATAATAAATATTTTA
1 TTATATTAAAAAACACAAAATAAATATAATAAATATTTTA
*
199898 TTGTATT
1 TTATATT
199905 GAATATAACA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
40 35 0.81
41 8 0.19
ACGTcount: A:0.53, C:0.06, G:0.01, T:0.40
Consensus pattern (40 bp):
TTATATTAAAAAACACAAAATAAATATAATAAATATTTTA
Found at i:211560 original size:45 final size:45
Alignment explanation
Indices: 211507--211598 Score: 175
Period size: 45 Copynumber: 2.0 Consensus size: 45
211497 CAAAAGCGTG
*
211507 TTAACATGGAAGTGCTTTACAAAAAAGGTCCACGTGAGAGTGTTT
1 TTAACATGGAAGTGCTTTACAAAAAAAGTCCACGTGAGAGTGTTT
211552 TTAACATGGAAGTGCTTTACAAAAAAAGTCCACGTGAGAGTGTTT
1 TTAACATGGAAGTGCTTTACAAAAAAAGTCCACGTGAGAGTGTTT
211597 TT
1 TT
211599 CAGATTTTTA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.30
Consensus pattern (45 bp):
TTAACATGGAAGTGCTTTACAAAAAAAGTCCACGTGAGAGTGTTT
Found at i:223059 original size:19 final size:19
Alignment explanation
Indices: 223010--223059 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
223000 AGATGCTCAA
*
223010 ACAAGCTGACACTGCTTAC
1 ACAAGCTGACATTGCTTAC
* *
223029 ACAAACTAACATTGCTTAC
1 ACAAGCTGACATTGCTTAC
223048 ACAAGCTGACAT
1 ACAAGCTGACAT
223060 CGTATCAAGG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.38, C:0.28, G:0.12, T:0.22
Consensus pattern (19 bp):
ACAAGCTGACATTGCTTAC
Found at i:223523 original size:43 final size:43
Alignment explanation
Indices: 223475--223603 Score: 249
Period size: 43 Copynumber: 3.0 Consensus size: 43
223465 ATTACCTGGC
223475 AAAACAACAAACGAACACTTTAAAGACTAATAAACAAATTTAT
1 AAAACAACAAACGAACACTTTAAAGACTAATAAACAAATTTAT
223518 AAAACAACAAACGAACACTTTAAAGACTAATAAACAAATTTAT
1 AAAACAACAAACGAACACTTTAAAGACTAATAAACAAATTTAT
*
223561 AAAACAACAAATGAACACTTTAAAGACTAATAAACAAATTTAT
1 AAAACAACAAACGAACACTTTAAAGACTAATAAACAAATTTAT
223604 CTTTTCCTCG
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
43 85 1.00
ACGTcount: A:0.58, C:0.16, G:0.05, T:0.22
Consensus pattern (43 bp):
AAAACAACAAACGAACACTTTAAAGACTAATAAACAAATTTAT
Found at i:238354 original size:16 final size:17
Alignment explanation
Indices: 238322--238355 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
238312 TATGACAGGG
*
238322 AAGAAATGATATGGCTT
1 AAGAAATAATATGGCTT
238339 AAGAAATAAT-TGGCTT
1 AAGAAATAATATGGCTT
238355 A
1 A
238356 GGAATTTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.44, C:0.06, G:0.21, T:0.29
Consensus pattern (17 bp):
AAGAAATAATATGGCTT
Found at i:241719 original size:12 final size:12
Alignment explanation
Indices: 241704--241728 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
241694 ATCTTGAAAA
241704 ATAAAAAAAATT
1 ATAAAAAAAATT
241716 ATAAAAAAAATT
1 ATAAAAAAAATT
241728 A
1 A
241729 AAATAAATTT
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
ATAAAAAAAATT
Found at i:241758 original size:22 final size:21
Alignment explanation
Indices: 241698--241750 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 21
241688 TAAAAAATCT
241698 TGAAAAATAAAAAAAATTATA
1 TGAAAAATAAAAAAAATTATA
** * *
241719 AAAAAAATTAAAATAAATTTTA
1 TGAAAAA-TAAAAAAAATTATA
241741 TGAAAAATAA
1 TGAAAAATAA
241751 TAAGAAATCT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 8 0.32
22 17 0.68
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (21 bp):
TGAAAAATAAAAAAAATTATA
Found at i:244770 original size:5 final size:5
Alignment explanation
Indices: 244760--244786 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
244750 GGGCAAACCC
244760 AAGAA AAGAA AAGAA AAGAA AAGAA AA
1 AAGAA AAGAA AAGAA AAGAA AAGAA AA
244787 ACCCCCAGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:253825 original size:14 final size:14
Alignment explanation
Indices: 253806--253834 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
253796 TTGTTGGCTA
253806 AGTATAAGCCAGTG
1 AGTATAAGCCAGTG
253820 AGTATAAGCCAGTG
1 AGTATAAGCCAGTG
253834 A
1 A
253835 AGGTTGATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.14, G:0.28, T:0.21
Consensus pattern (14 bp):
AGTATAAGCCAGTG
Found at i:262242 original size:108 final size:108
Alignment explanation
Indices: 262130--262336 Score: 290
Period size: 108 Copynumber: 1.9 Consensus size: 108
262120 CAATGTTCTT
* * * * *
262130 TTATTTAGGGAATTCGAGAAATTGTGCTCAAACGGTACTGCATATGA-TTTTTTCTTTGAATCTA
1 TTATTTAGGAAATTCAAAAAATTGTGCTCAAA-GATACTGCATATGATTTTTTTCTTTGAACCTA
*
262194 AATAATCGAATATCCTATTTAAAGTCCATAAATGTTAGATGTTC
65 AATAATCGAATATCCTATTTAAAATCCATAAATGTTAGATGTTC
* *
262238 TTATTTAGGAAATTCAAAAAATTGTGCTCAAATATACTGGATATGATTTTTTTCTTTGAACCTAA
1 TTATTTAGGAAATTCAAAAAATTGTGCTCAAAGATACTGCATATGATTTTTTTCTTTGAACCTAA
* * * *
262303 GTAGTTGAATATCCTATTTAAAATCGATAAATGT
66 ATAATCGAATATCCTATTTAAAATCCATAAATGT
262337 CCTTAATCTT
Statistics
Matches: 86, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
107 11 0.13
108 75 0.87
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (108 bp):
TTATTTAGGAAATTCAAAAAATTGTGCTCAAAGATACTGCATATGATTTTTTTCTTTGAACCTAA
ATAATCGAATATCCTATTTAAAATCCATAAATGTTAGATGTTC
Found at i:263128 original size:3 final size:3
Alignment explanation
Indices: 263120--263157 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
263110 AATTTAACTT
263120 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
263158 GTTTTGGTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:269062 original size:22 final size:22
Alignment explanation
Indices: 269041--269081 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
269031 CCATCCATAT
269041 TAGTTTT-TTTTAATATTTATA
1 TAGTTTTATTTTAATATTTATA
*
269062 TGGTTTTATTTTAATATTTA
1 TAGTTTTATTTTAATATTTA
269082 ATAATTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.66
Consensus pattern (22 bp):
TAGTTTTATTTTAATATTTATA
Found at i:277146 original size:44 final size:45
Alignment explanation
Indices: 277075--277162 Score: 108
Period size: 44 Copynumber: 2.0 Consensus size: 45
277065 TAGTGCCGAG
* * *
277075 TTAAGAGTTAGAATATGTGGTTAAAATAA-AAAGATTAGGAAAAA
1 TTAAGAATTAGAATATGTAGTTAAAATAAGAAAGATTAAGAAAAA
* *
277119 TTAAGAATTAGAATGTGTAGTCT-AAATAAGAAAGGTTAAGAAAA
1 TTAAGAATTAGAATATGTAGT-TAAAATAAGAAAGATTAAGAAAA
277163 TTCAAGGATT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
44 24 0.65
45 13 0.35
ACGTcount: A:0.51, C:0.01, G:0.20, T:0.27
Consensus pattern (45 bp):
TTAAGAATTAGAATATGTAGTTAAAATAAGAAAGATTAAGAAAAA
Found at i:278968 original size:6 final size:6
Alignment explanation
Indices: 278957--279007 Score: 66
Period size: 6 Copynumber: 8.5 Consensus size: 6
278947 TGATCAAAAT
* * * *
278957 TGAAAG TGAAAG TGAAAG TGAAAG TAAAAG TGAAAT TGGAAT TGAAAG
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG
279005 TGA
1 TGA
279008 TATGAATTGT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.29, T:0.22
Consensus pattern (6 bp):
TGAAAG
Found at i:281458 original size:17 final size:17
Alignment explanation
Indices: 281436--281474 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
281426 AGGTGGAGAA
* *
281436 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
281453 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
281470 CTTGT
1 CTTGT
281475 CAAGGTGGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.13, G:0.26, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:286972 original size:185 final size:185
Alignment explanation
Indices: 286655--287028 Score: 712
Period size: 185 Copynumber: 2.0 Consensus size: 185
286645 AGATCAAGAG
286655 GAAAATAACATAGAGTAACAGTGTGATGAATAAATCCTAGAAGATGGCTATACTTTTAGAATCAT
1 GAAAATAACATAGAGTAACAGTGTGATGAATAAATCCTAGAAGATGGCTATACTTTTAGAATCAT
*
286720 AAATCAATATATGATATAAAACTTAATAAATCATAAATCAAGATCTATCATGTCAAATCATCAAG
66 AAATCAATATATGATATAAAACTTAATAAATCATAAATCAAGATCTATCATGTCAAATCAACAAG
286785 AATAAAACGATAATAAAACTAGATGCGGAAGCATACCTGAATTCATCAATTTCTT
131 AATAAAACGATAATAAAACTAGATGCGGAAGCATACCTGAATTCATCAATTTCTT
* *
286840 GAAAATAACATAGAGTAATAGTGTTATGAATAAATCCTAGAAGATGGCTATACTTTTAGAATCAT
1 GAAAATAACATAGAGTAACAGTGTGATGAATAAATCCTAGAAGATGGCTATACTTTTAGAATCAT
286905 AAATCAATATATGATATAAAACTTAATAAATCATAAATCAAGATCTATCATGTCAAATCAACAAG
66 AAATCAATATATGATATAAAACTTAATAAATCATAAATCAAGATCTATCATGTCAAATCAACAAG
*
286970 AATAAAACGATAATAAAACTAGATGCGGAAGCATACCTGAATTCATCAGTTTCTT
131 AATAAAACGATAATAAAACTAGATGCGGAAGCATACCTGAATTCATCAATTTCTT
287025 GAAA
1 GAAA
287029 TTTACAGATT
Statistics
Matches: 185, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
185 185 1.00
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.28
Consensus pattern (185 bp):
GAAAATAACATAGAGTAACAGTGTGATGAATAAATCCTAGAAGATGGCTATACTTTTAGAATCAT
AAATCAATATATGATATAAAACTTAATAAATCATAAATCAAGATCTATCATGTCAAATCAACAAG
AATAAAACGATAATAAAACTAGATGCGGAAGCATACCTGAATTCATCAATTTCTT
Found at i:287568 original size:17 final size:17
Alignment explanation
Indices: 287543--287624 Score: 94
Period size: 17 Copynumber: 4.8 Consensus size: 17
287533 CTGGGCCCAA
*
287543 TAAACTTAAATTTATTT
1 TAAATTTAAATTTATTT
* *
287560 TAAAATTAAGA-TTATTC
1 TAAATTTAA-ATTTATTT
*
287577 TAAATTTAAATTTAGTT
1 TAAATTTAAATTTATTT
* *
287594 GAAATTTAAATTTATTA
1 TAAATTTAAATTTATTT
287611 TAAATTTAAATTTA
1 TAAATTTAAATTTA
287625 AAATTTATTT
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
16 1 0.02
17 52 0.96
18 1 0.02
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (17 bp):
TAAATTTAAATTTATTT
Found at i:287586 original size:6 final size:6
Alignment explanation
Indices: 287577--287631 Score: 53
Period size: 6 Copynumber: 9.3 Consensus size: 6
287567 AAGATTATTC
* *
287577 TAAATT TAAATT T-AGTT GAAATT TAAATT T--ATT ATAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT -TAAATT TAAATT
287623 TAAAATT TA
1 T-AAATT TA
287632 TTTTAAATGT
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
4 3 0.08
5 4 0.10
6 24 0.60
7 9 0.22
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (6 bp):
TAAATT
Found at i:287609 original size:34 final size:34
Alignment explanation
Indices: 287542--287624 Score: 105
Period size: 34 Copynumber: 2.4 Consensus size: 34
287532 TCTGGGCCCA
* * *
287542 ATAAACTTAAATTTATTTTAAAATTAAGATTATT
1 ATAAATTTAAATTTAGTTGAAAATTAAGATTATT
* *
287576 CTAAATTTAAATTTAGTTGAAATTTAA-ATTTATT
1 ATAAATTTAAATTTAGTTGAAAATTAAGA-TTATT
287610 ATAAATTTAAATTTA
1 ATAAATTTAAATTTA
287625 AAATTTATTT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
33 1 0.02
34 41 0.98
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (34 bp):
ATAAATTTAAATTTAGTTGAAAATTAAGATTATT
Found at i:287633 original size:24 final size:23
Alignment explanation
Indices: 287595--287639 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
287585 AATTTAGTTG
287595 AAATTTAAATTTATTATAAATTT
1 AAATTTAAATTTATTATAAATTT
*
287618 AAATTTAAAATTTATTTTAAAT
1 AAATTT-AAATTTATTATAAAT
287640 GTCTAAGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
AAATTTAAATTTATTATAAATTT
Done.