Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009917.1 Kokia drynarioides strain JFW-HI SEQ_124657, 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: 213118
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Warning! 108 characters in sequence are not A, C, G, or T
Found at i:543 original size:23 final size:22
Alignment explanation
Indices: 513--613 Score: 94
Period size: 23 Copynumber: 4.5 Consensus size: 22
503 ACGCTAGCGC
513 GCTTACTGTTTCGCACTTTGTGT
1 GCTTACTGTTT-GCACTTTGTGT
536 GCTTACTGTTTCGCACTTTGTGT
1 GCTTACTGTTT-GCACTTTGTGT
* * * * *
559 GCCTATTGATTTGCGCTATGTGC
1 GCTTACTG-TTTGCACTTTGTGT
* * * *
582 GCCTACTGATTGCACTGTGTAT
1 GCTTACTGTTTGCACTTTGTGT
604 GCTTACTGTT
1 GCTTACTGTT
614 AAGTACTTCG
Statistics
Matches: 64, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
22 17 0.27
23 44 0.69
24 3 0.05
ACGTcount: A:0.12, C:0.22, G:0.23, T:0.44
Consensus pattern (22 bp):
GCTTACTGTTTGCACTTTGTGT
Found at i:5245 original size:22 final size:24
Alignment explanation
Indices: 5203--5247 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
5193 ATCGAGATCC
*
5203 AAGATTTACATCAAAGTTTTGGGA
1 AAGATTTACATCAAAGCTTTGGGA
5227 AAGA-TTACAT-AAAGCTTTGGG
1 AAGATTTACATCAAAGCTTTGGG
5248 TACTCGATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 10 0.50
23 6 0.30
24 4 0.20
ACGTcount: A:0.38, C:0.09, G:0.22, T:0.31
Consensus pattern (24 bp):
AAGATTTACATCAAAGCTTTGGGA
Found at i:8011 original size:24 final size:26
Alignment explanation
Indices: 7960--8011 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 26
7950 TTTATTTCTA
7960 AAATTAAAAAGATAAATAAATTATTT
1 AAATTAAAAAGATAAATAAATTATTT
* *
7986 AAATTAAAAA-TTAAA-ACATTATTT
1 AAATTAAAAAGATAAATAAATTATTT
8010 AA
1 AA
8012 CACTTTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 10 0.42
25 4 0.17
26 10 0.42
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (26 bp):
AAATTAAAAAGATAAATAAATTATTT
Found at i:8173 original size:25 final size:25
Alignment explanation
Indices: 8119--8166 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
8109 TAACGCATAA
8119 ATTATATCCATAACATTACAAATAT
1 ATTATATCCATAACATTACAAATAT
* *
8144 ATTATATTCATAATATTACAAAT
1 ATTATATCCATAACATTACAAAT
8167 TAGTTATTAT
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:0.12, G:0.00, T:0.40
Consensus pattern (25 bp):
ATTATATCCATAACATTACAAATAT
Found at i:8309 original size:2 final size:2
Alignment explanation
Indices: 8302--8326 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
8292 TAAAAATAGC
8302 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
8327 TATGGATGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16495 original size:21 final size:21
Alignment explanation
Indices: 16470--16510 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
16460 AACTTAGCTA
16470 ATAAAA-ATAAAAATCTAATTG
1 ATAAAATATAAAAAT-TAATTG
*
16491 ATAAAATATAAACATTAATT
1 ATAAAATATAAAAATTAATT
16511 TCATTATACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (21 bp):
ATAAAATATAAAAATTAATTG
Found at i:17324 original size:46 final size:46
Alignment explanation
Indices: 17257--17348 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
17247 ATATCTGTTC
*
17257 ATACTTTCTTAACACAGCTTGCACACACGTGTGCTCAAACCCGAAT
1 ATACTTTCTTAACACAGCTTGCACACACATGTGCTCAAACCCGAAT
17303 ATACTTTCTTAACACAGCTTGCACACACATGTGCTCAAACCCGAAT
1 ATACTTTCTTAACACAGCTTGCACACACATGTGCTCAAACCCGAAT
17349 CTCCTAAGAT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.32, C:0.30, G:0.12, T:0.26
Consensus pattern (46 bp):
ATACTTTCTTAACACAGCTTGCACACACATGTGCTCAAACCCGAAT
Found at i:17942 original size:6 final size:6
Alignment explanation
Indices: 17928--17996 Score: 74
Period size: 6 Copynumber: 11.8 Consensus size: 6
17918 TTTAATTTAT
* *
17928 TTTAAA TTTAGA TTT-AT TTTAAA TTTAAA -TT-AA TCTTAAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TT-AAA TTTAAA
17975 TTT-AA TTTAAA TTTAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAA
17997 TTCCAAAATT
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
4 2 0.04
5 10 0.19
6 36 0.68
7 2 0.04
8 3 0.06
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:17944 original size:17 final size:17
Alignment explanation
Indices: 17921--17995 Score: 105
Period size: 17 Copynumber: 4.4 Consensus size: 17
17911 CTCCTTTTTT
17921 AATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
*
17938 GATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
* *
17955 AATTAATCTTAAAATTTA
1 AATTTAT-TTTAAATTTA
*
17973 AATTTAATTTAAATTTA
1 AATTTATTTTAAATTTA
17990 AATTTA
1 AATTTA
17996 ATTCCAAAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
17 36 0.72
18 14 0.28
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:17960 original size:11 final size:11
Alignment explanation
Indices: 17946--17998 Score: 54
Period size: 11 Copynumber: 4.6 Consensus size: 11
17936 TAGATTTATT
17946 TTAAATTTAAA
1 TTAAATTTAAA
17957 TT-AATCTTAAAA
1 TTAAAT-TT-AAA
*
17969 TTTAAATTTAAT
1 -TTAAATTTAAA
17981 TTAAATTTAAA
1 TTAAATTTAAA
*
17992 TTTAATT
1 TTAAATT
17999 CCAAAATTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
10 3 0.09
11 20 0.57
12 5 0.14
13 4 0.11
14 3 0.09
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:18009 original size:35 final size:35
Alignment explanation
Indices: 17931--18006 Score: 100
Period size: 35 Copynumber: 2.1 Consensus size: 35
17921 AATTTATTTT
* * *
17931 AAATTTAGATTTATTTTAAATTTAAATTAATCTTA
1 AAATTTAAATTTAATTTAAATTTAAATTAATCTCA
17966 AAATTTAAATTTAATTTAAATTTAAATTTAAT-TCCA
1 AAATTTAAATTTAATTTAAATTTAAA-TTAATCT-CA
18002 AAATT
1 AAATT
18007 AAAAAGTCCA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
35 25 0.69
36 11 0.31
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.49
Consensus pattern (35 bp):
AAATTTAAATTTAATTTAAATTTAAATTAATCTCA
Found at i:18739 original size:3 final size:3
Alignment explanation
Indices: 18718--18780 Score: 90
Period size: 3 Copynumber: 20.3 Consensus size: 3
18708 TTAATATTTT
*
18718 TAA TAG TAA TAA CTAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
18764 TAA TAAA TAT TAA TAA T
1 TAA T-AA TAA TAA TAA T
18781 GGCATTAATT
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
3 48 0.89
4 6 0.11
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:19795 original size:29 final size:29
Alignment explanation
Indices: 19748--20007 Score: 194
Period size: 29 Copynumber: 8.9 Consensus size: 29
19738 CCCTAAAGGT
*
19748 CCCT-GAACTGTCCAAAAATTCCATTTATA
1 CCCTCGAACT-TCCAAAAATTCCATTTTTA
* * *
19777 CCCCCGAACTTCCTAAAATTTCATTTTTGA
1 CCCTCGAACTTCCAAAAATTCCATTTTT-A
** *
19807 CCCTAAAACTTTCAAAAATTCCATTTTTA
1 CCCTCGAACTTCCAAAAATTCCATTTTTA
*
19836 -CCTCGAACTTCCAAAAATTTCA-TTTTA
1 CCCTCGAACTTCCAAAAATTCCATTTTTA
* ** *
19863 ACCTTTAAATTCCAAAAAATTCC-TTTTTAA
1 CCCTCGAACTTCC-AAAAATTCCATTTTT-A
* * *
19893 CCC-CAAACTTTCAAAAATTCTATTTTTGA
1 CCCTCGAACTTCCAAAAATTCCATTTTT-A
* * *
19922 CCC-CAAAACTTCCAAACATTCAATTTTTTA
1 CCCTC-GAACTTCCAAAAATTCCA-TTTTTA
* *
19952 CCC-CGAAACTTCCAAAATTTCAATTTTTA
1 CCCTCG-AACTTCCAAAAATTCCATTTTTA
*
19981 CCCTCGAACCTCC-AAAATCTCCATTTT
1 CCCTCGAACTTCCAAAAAT-TCCATTTT
20008 CGACCTCAAA
Statistics
Matches: 185, Mismatches: 34, Indels: 24
0.76 0.14 0.10
Matches are distributed among these distances:
27 5 0.03
28 39 0.21
29 68 0.37
30 68 0.37
31 5 0.03
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.35
Consensus pattern (29 bp):
CCCTCGAACTTCCAAAAATTCCATTTTTA
Found at i:19825 original size:30 final size:29
Alignment explanation
Indices: 19753--19984 Score: 161
Period size: 30 Copynumber: 7.9 Consensus size: 29
19743 AAGGTCCCTG
* * ***
19753 AACTGTCCAAAAATTCCATTTATACCCCCG
1 AACT-TCCAAAAATTTCATTTTTACCCTAA
*
19783 AACTTCCTAAAATTTCATTTTTGACCCTAA
1 AACTTCCAAAAATTTCATTTTT-ACCCTAA
* * **
19813 AACTTTCAAAAATTCCATTTTTA-CCTCG
1 AACTTCCAAAAATTTCATTTTTACCCTAA
* * *
19841 AACTTCCAAAAATTTCATTTTAACCTTTA
1 AACTTCCAAAAATTTCATTTTTACCCTAA
* * *
19870 AA-TTCCAAAAAATTCCTTTTTAACCC-CA
1 AACTTCCAAAAATTTCATTTTT-ACCCTAA
* *
19898 AACTTTCAAAAA-TTCTATTTTTGACCCCAA
1 AACTTCCAAAAATTTC-ATTTTT-ACCCTAA
* **
19928 AACTTCCAAACA-TTCAATTTTTTACCCCGA
1 AACTTCCAAAAATTTC-A-TTTTTACCCTAA
19958 AACTTCC-AAAATTTCAATTTTTACCCT
1 AACTTCCAAAAATTTC-ATTTTTACCCT
19985 CGAACCTCCA
Statistics
Matches: 162, Mismatches: 32, Indels: 17
0.77 0.15 0.08
Matches are distributed among these distances:
28 45 0.28
29 52 0.32
30 60 0.37
31 5 0.03
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.36
Consensus pattern (29 bp):
AACTTCCAAAAATTTCATTTTTACCCTAA
Found at i:25927 original size:17 final size:16
Alignment explanation
Indices: 25905--25938 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
25895 GTTTTAGATC
*
25905 ATTATTTTTATTTATTT
1 ATTATTATTATTT-TTT
25922 ATTATTATTATTTTTT
1 ATTATTATTATTTTTT
25938 A
1 A
25939 ATTTAGTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
ATTATTATTATTTTTT
Found at i:26100 original size:25 final size:26
Alignment explanation
Indices: 26055--26107 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
26045 TTTCAAGAAT
26055 TTTTTTTTAAAAATTATAATT-TTTA
1 TTTTTTTTAAAAATTATAATTATTTA
*
26080 TTTTTTTT-AAAATTTTAAATTATTTA
1 TTTTTTTTAAAAATTAT-AATTATTTA
26106 TT
1 TT
26108 GATGTAACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 7 0.28
25 12 0.48
26 6 0.24
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (26 bp):
TTTTTTTTAAAAATTATAATTATTTA
Found at i:31218 original size:4 final size:4
Alignment explanation
Indices: 31211--31236 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
31201 TGTGTATTTA
31211 TTGT TTGT TTGT TTGT TTGT TTGT TT
1 TTGT TTGT TTGT TTGT TTGT TTGT TT
31237 ATTGTTCATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.23, T:0.77
Consensus pattern (4 bp):
TTGT
Found at i:33574 original size:14 final size:15
Alignment explanation
Indices: 33541--33577 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
33531 CACACATCTC
33541 ATTTTTTTATGTATA
1 ATTTTTTTATGTATA
*
33556 ATTTTTTTAT-T-TT
1 ATTTTTTTATGTATA
33569 ATTTTTTTA
1 ATTTTTTTA
33578 CTACTTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 10 0.48
14 1 0.05
15 10 0.48
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.76
Consensus pattern (15 bp):
ATTTTTTTATGTATA
Found at i:36994 original size:19 final size:20
Alignment explanation
Indices: 36971--37020 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
36961 TTATAAAAAA
36971 AATAAAAAATAGTAAAAGTT
1 AATAAAAAATAGTAAAAGTT
* * **
36991 -ATAAAAATTATTAAACTTT
1 AATAAAAAATAGTAAAAGTT
37010 AATAAAAAATA
1 AATAAAAAATA
37021 TAATAAATAT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (20 bp):
AATAAAAAATAGTAAAAGTT
Found at i:36995 original size:9 final size:9
Alignment explanation
Indices: 36956--37125 Score: 81
Period size: 9 Copynumber: 17.6 Consensus size: 9
36946 ACATGTAGTA
36956 AAAAATTAT
1 AAAAATTAT
**
36965 AAAAAAAAT
1 AAAAATTAT
*
36974 AAAAAATAGT
1 AAAAATTA-T
*
36984 AAAAGTTAT
1 AAAAATTAT
36993 AAAAATTATT
1 AAAAATTA-T
**
37003 AAACTTTAAT
1 AAAAATT-AT
*
37013 AAAAAATAT
1 AAAAATTAT
*
37022 AATAAATATTT
1 AA-AAAT-TAT
**
37033 AAATTTTATT
1 AAAAATTA-T
*
37043 ACAAA-TAT
1 AAAAATTAT
*
37051 AAAAATTGT
1 AAAAATTAT
37060 AAAAATATAT
1 AAAAAT-TAT
*
37070 AAAAAAATTGT
1 --AAAAATTAT
37081 AAAAATTTAT
1 AAAAA-TTAT
*
37091 AAAAATCAT
1 AAAAATTAT
*
37100 AAAAAATAT
1 AAAAATTAT
37109 ATAAAATGTAT
1 A-AAAAT-TAT
37120 CAAAAA
1 -AAAAA
37126 GGTCTTTTAA
Statistics
Matches: 119, Mismatches: 28, Indels: 26
0.69 0.16 0.15
Matches are distributed among these distances:
8 5 0.04
9 53 0.45
10 40 0.34
11 14 0.12
12 7 0.06
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (9 bp):
AAAAATTAT
Found at i:37022 original size:29 final size:29
Alignment explanation
Indices: 36990--37057 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
36980 TAGTAAAAGT
36990 TATAAAAATTA-TTAAACTTTAATAAAAAA
1 TATAAAAATTATTTAAA-TTTAATAAAAAA
* * *
37019 TATAATAAA-TATTTAAATTTTATTACAAA
1 TATAA-AAATTATTTAAATTTAATAAAAAA
37048 TATAAAAATT
1 TATAAAAATT
37058 GTAAAAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
28 3 0.09
29 22 0.67
30 8 0.24
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (29 bp):
TATAAAAATTATTTAAATTTAATAAAAAA
Found at i:37077 original size:21 final size:21
Alignment explanation
Indices: 37051--37095 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
37041 TTACAAATAT
37051 AAAAATTGTAAAAATATATAA
1 AAAAATTGTAAAAATATATAA
*
37072 AAAAATTGTAAAAATTTATAA
1 AAAAATTGTAAAAATATATAA
37093 AAA
1 AAA
37096 TCATAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (21 bp):
AAAAATTGTAAAAATATATAA
Found at i:37297 original size:2 final size:2
Alignment explanation
Indices: 37292--37328 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
37282 TATGATAATT
37292 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
37329 TAAAAATTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:37449 original size:26 final size:24
Alignment explanation
Indices: 37414--37465 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
37404 TTTCTATGTT
37414 TTATAATTTTCAATAAAATTTTAATA
1 TTATAATTTT-AATAAAA-TTTAATA
* *
37440 TTATATTTTTATTAAAATTTAATA
1 TTATAATTTTAATAAAATTTAATA
37464 TT
1 TT
37466 TTTATAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 9 0.38
25 6 0.25
26 9 0.38
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (24 bp):
TTATAATTTTAATAAAATTTAATA
Found at i:38545 original size:17 final size:17
Alignment explanation
Indices: 38516--38548 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
38506 GAGCTTGTGA
38516 GAAAACTATCCACAAAC
1 GAAAACTATCCACAAAC
38533 GAAAATCTA-CCACAAA
1 GAAAA-CTATCCACAAA
38549 GACAAACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.55, C:0.27, G:0.06, T:0.12
Consensus pattern (17 bp):
GAAAACTATCCACAAAC
Found at i:39366 original size:26 final size:27
Alignment explanation
Indices: 39331--39387 Score: 73
Period size: 26 Copynumber: 2.1 Consensus size: 27
39321 TCTATATAAT
* *
39331 TATAATTAAATCAAATT-ATTA-CAAAA
1 TATAAATAAAT-AAATTGATAATCAAAA
39357 TATAAATAAATAAATTGATAATCAAAA
1 TATAAATAAATAAATTGATAATCAAAA
39384 TATA
1 TATA
39388 TTCAGATCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 5 0.19
26 13 0.48
27 9 0.33
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (27 bp):
TATAAATAAATAAATTGATAATCAAAA
Found at i:39845 original size:23 final size:23
Alignment explanation
Indices: 39801--39847 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
39791 TTTGTGTTAA
* *
39801 TTTGGTGTTGTTTTGGTATTGTT
1 TTTGATGTTGTTCTGGTATTGTT
* *
39824 TTTGATGTTGTTCTGTTGTTGTT
1 TTTGATGTTGTTCTGGTATTGTT
39847 T
1 T
39848 CGCAGCTGTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.04, C:0.02, G:0.28, T:0.66
Consensus pattern (23 bp):
TTTGATGTTGTTCTGGTATTGTT
Found at i:42437 original size:2 final size:2
Alignment explanation
Indices: 42428--42460 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
42418 ACAATAAAAA
42428 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42461 TAAAAAAGCC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:43082 original size:28 final size:28
Alignment explanation
Indices: 43042--43095 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
43032 ATTTTTTTTC
43042 GATTTCTTATTCTCAAA-TATCAATTCTT
1 GATTTCTTATTCT-AAATTATCAATTCTT
* *
43070 GATTTTTTATTCTAAATTCTCAATTC
1 GATTTCTTATTCTAAATTATCAATTC
43096 CCAATTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 3 0.13
28 20 0.87
ACGTcount: A:0.28, C:0.17, G:0.04, T:0.52
Consensus pattern (28 bp):
GATTTCTTATTCTAAATTATCAATTCTT
Found at i:45141 original size:19 final size:19
Alignment explanation
Indices: 45119--45161 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
45109 AAAAAACTCA
* *
45119 CAGTTTATAGAAGAGTTCG
1 CAGTTTATAGAACAGCTCG
*
45138 CAGTTTGTAGAACAGCTCG
1 CAGTTTATAGAACAGCTCG
45157 CAGTT
1 CAGTT
45162 CGCAGTTCCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (19 bp):
CAGTTTATAGAACAGCTCG
Found at i:47544 original size:3 final size:3
Alignment explanation
Indices: 47536--47579 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
47526 TTCAAATTAA
47536 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
47580 GTTCATGATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:51296 original size:27 final size:27
Alignment explanation
Indices: 51235--51308 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 27
51225 AAAGAAATCT
*
51235 TTTATGGCGGATCAT-AGAATTAACGCC
1 TTTATGGC-GATCATGAGAATGAACGCC
**
51262 TTCGTGGCGACTCATGA-AATGAACGCC
1 TTTATGGCGA-TCATGAGAATGAACGCC
*
51289 TTTATGGCAAATCATGAGAA
1 TTTATGGC-GATCATGAGAA
51309 AGGATAACCT
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
26 2 0.05
27 31 0.84
28 4 0.11
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (27 bp):
TTTATGGCGATCATGAGAATGAACGCC
Found at i:56094 original size:45 final size:45
Alignment explanation
Indices: 56044--56134 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
56034 TAATTATAAG
56044 TATGATAACTATGTGTGATTGAATGAAATTTAGTATAAAGAAGCA
1 TATGATAACTATGTGTGATTGAATGAAATTTAGTATAAAGAAGCA
56089 TATGATAACTATGTGTGATTGAATGAAATTTAGTATAAAGAAGCA
1 TATGATAACTATGTGTGATTGAATGAAATTTAGTATAAAGAAGCA
56134 T
1 T
56135 GAGAAAGAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.42, C:0.04, G:0.20, T:0.34
Consensus pattern (45 bp):
TATGATAACTATGTGTGATTGAATGAAATTTAGTATAAAGAAGCA
Found at i:59376 original size:18 final size:18
Alignment explanation
Indices: 59353--59389 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
59343 ACAATTCATA
59353 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* *
59371 TCACTTTCACTTTCAATT
1 TCACTTTCAATTCCAATT
59389 T
1 T
59390 TGATCACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:61211 original size:51 final size:51
Alignment explanation
Indices: 61135--61238 Score: 208
Period size: 51 Copynumber: 2.0 Consensus size: 51
61125 TGGTTAAAAA
61135 ACGTGGATGTTACAATTCTTCTTCCCTAAAAAAATTTCGTCCACGAAATTT
1 ACGTGGATGTTACAATTCTTCTTCCCTAAAAAAATTTCGTCCACGAAATTT
61186 ACGTGGATGTTACAATTCTTCTTCCCTAAAAAAATTTCGTCCACGAAATTT
1 ACGTGGATGTTACAATTCTTCTTCCCTAAAAAAATTTCGTCCACGAAATTT
61237 AC
1 AC
61239 CTGCAACGAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.35
Consensus pattern (51 bp):
ACGTGGATGTTACAATTCTTCTTCCCTAAAAAAATTTCGTCCACGAAATTT
Found at i:63744 original size:9 final size:9
Alignment explanation
Indices: 63693--63778 Score: 61
Period size: 9 Copynumber: 9.2 Consensus size: 9
63683 GTGATACATG
63693 ATAAAAAAT
1 ATAAAAAAT
63702 GAT-AAAAAT
1 -ATAAAAAAT
* *
63711 ATTAAAATT
1 ATAAAAAAT
63720 A-AAAAAATT
1 ATAAAAAA-T
63729 ATAAAAAAAT
1 AT-AAAAAAT
*
63739 ATAAAAACT
1 ATAAAAAAT
63748 ACT-AAAAAT
1 A-TAAAAAAT
*
63757 TTATAAAAAT
1 ATA-AAAAAT
63767 ATAGAAAAAT
1 ATA-AAAAAT
63777 AT
1 AT
63779 TTAAATTTTA
Statistics
Matches: 61, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
8 7 0.11
9 26 0.43
10 22 0.36
11 6 0.10
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (9 bp):
ATAAAAAAT
Found at i:63753 original size:20 final size:18
Alignment explanation
Indices: 63695--63778 Score: 71
Period size: 18 Copynumber: 4.5 Consensus size: 18
63685 GATACATGAT
63695 AAAAAATGATAAAAATAT-
1 AAAAAAT-ATAAAAATATA
* * *
63713 TAAAATTAAAAAAATTATA
1 AAAAAATATAAAAA-TATA
63732 AAAAAATATAAAAACTACTA
1 AAAAAATATAAAAA-TA-TA
**
63752 AAAATTTATAAAAATATA
1 AAAAAATATAAAAATATA
*
63770 GAAAAATAT
1 AAAAAATAT
63779 TTAAATTTTA
Statistics
Matches: 51, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
17 6 0.12
18 16 0.31
19 15 0.29
20 14 0.27
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.26
Consensus pattern (18 bp):
AAAAAATATAAAAATATA
Found at i:63766 original size:28 final size:27
Alignment explanation
Indices: 63693--63774 Score: 83
Period size: 28 Copynumber: 2.9 Consensus size: 27
63683 GTGATACATG
* * * *
63693 ATAAAAAATGATAAAAATATTAAAATT
1 ATAAAAATTTATAAAAATATAAAAACT
* *
63720 AAAAAAATTATAAAAAAATATAAAAACT
1 ATAAAAATT-TATAAAAATATAAAAACT
63748 ACTAAAAATTTATAAAAATATAGAAAA
1 A-TAAAAATTTATAAAAATATA-AAAA
63775 ATATTTAAAT
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
27 7 0.16
28 26 0.59
29 11 0.25
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (27 bp):
ATAAAAATTTATAAAAATATAAAAACT
Found at i:68750 original size:21 final size:21
Alignment explanation
Indices: 68725--68779 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
68715 CTATCTCCAC
*
68725 CATCGTCTTCATCGTCATCGT
1 CATCGTCTTCATCCTCATCGT
* *
68746 CATCGTCTTCTTCCTCGTCGT
1 CATCGTCTTCATCCTCATCGT
* *
68767 CCTCGTCGTCATC
1 CATCGTCTTCATC
68780 ATCTTCTTCG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.09, C:0.38, G:0.15, T:0.38
Consensus pattern (21 bp):
CATCGTCTTCATCCTCATCGT
Found at i:70309 original size:12 final size:12
Alignment explanation
Indices: 70292--70326 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
70282 GAAAAGAAGT
*
70292 TTGTGGTTGTGG
1 TTGTGGTTGAGG
70304 TTGTGGTTGAGG
1 TTGTGGTTGAGG
*
70316 TTGAGGTTGAG
1 TTGTGGTTGAG
70327 AAGAACCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.09, C:0.00, G:0.49, T:0.43
Consensus pattern (12 bp):
TTGTGGTTGAGG
Found at i:73054 original size:49 final size:48
Alignment explanation
Indices: 73001--73100 Score: 123
Period size: 49 Copynumber: 2.1 Consensus size: 48
72991 TTTAAAGAAA
* *
73001 TTTCATTTTAAAAT-TATGTTTTCTTTCATA-ACAATATTTATTATTATGT
1 TTTCATTTT-AAATCTATATTTTCTTCCATAGA-AATATTTATTATTA-GT
* *
73050 TTTCATTTTAAATCTCTATTTTCTTCCATAGAAATTTTTATTATTAGT
1 TTTCATTTTAAATCTATATTTTCTTCCATAGAAATATTTATTATTAGT
73098 TTT
1 TTT
73101 AAAAAAATCT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
48 9 0.20
49 35 0.78
50 1 0.02
ACGTcount: A:0.28, C:0.10, G:0.04, T:0.58
Consensus pattern (48 bp):
TTTCATTTTAAATCTATATTTTCTTCCATAGAAATATTTATTATTAGT
Found at i:78800 original size:29 final size:29
Alignment explanation
Indices: 78768--79149 Score: 246
Period size: 30 Copynumber: 13.0 Consensus size: 29
78758 TAGATATTCG
78768 GGGGT-AAAATGGTAATTTTTGAAAGTTTC
1 GGGGTAAAAATGG-AATTTTTGAAAGTTTC
* * * * *
78797 GGGGGCAAAAATGAAAATTTTG-GAGGTTC
1 -GGGGTAAAAATGGAATTTTTGAAAGTTTC
*
78826 GAGGGTAAAAATGTAATTTTTGGAAA-TTTC
1 G-GGGTAAAAATGGAATTTTT-GAAAGTTTC
* * * * *
78856 GAGGTTGAAAATTGAATTTTTAAAAGATT-
1 G-GGGTAAAAATGGAATTTTTGAAAGTTTC
* *
78885 GGGGTAAAAATGGAATTTTAG-AAGTTTT
1 GGGGTAAAAATGGAATTTTTGAAAGTTTC
* * *
78913 GGGGTCAAAAATGAAATTTTTGGAAGTTTTA
1 GGGGT-AAAAATGGAATTTTTGAAAG-TTTC
* *
78944 GGGTTGAAAATGGAATTTTT-AGAAG-TTC
1 GGGGTAAAAATGGAATTTTTGA-AAGTTTC
*
78972 GGCGGT-AAAATGGAATTTTCGAAAGTTTC
1 GG-GGTAAAAATGGAATTTTTGAAAGTTTC
* * *
79001 AGAGTCAAAAATGGAATTTTTGGAAG-TTC
1 GGGGT-AAAAATGGAATTTTTGAAAGTTTC
* ** * *
79030 AAGGGCCAAAATGGAATTTTTTGGAAG-TTA
1 -GGGGTAAAAATGGAA-TTTTTGAAAGTTTC
*
79060 GAGGGTTAAAAATGGAATTTTTGGAAGTTTC
1 G-GGG-TAAAAATGGAATTTTTGAAAGTTTC
* *
79091 AGGGTAGAAAATGGAATTTTTGGAAG-TTC
1 GGGGTA-AAAATGGAATTTTTGAAAGTTTC
* *
79120 GGGGGCAAAAATGAAATTTTTGAACAGTTT
1 -GGGGTAAAAATGGAATTTTTGAA-AGTTT
79150 AGAGACCTCC
Statistics
Matches: 279, Mismatches: 49, Indels: 47
0.74 0.13 0.13
Matches are distributed among these distances:
27 5 0.02
28 43 0.15
29 78 0.28
30 126 0.45
31 27 0.10
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.33
Consensus pattern (29 bp):
GGGGTAAAAATGGAATTTTTGAAAGTTTC
Found at i:78811 original size:59 final size:60
Alignment explanation
Indices: 78743--78933 Score: 175
Period size: 59 Copynumber: 3.2 Consensus size: 60
78733 GTTAGAGGTT
*
78743 AAAAGATGAAATTTTTAGATATTCGGGGGT-AAAATGGTAATTTTTGAAAGTTTCGGGGGC
1 AAAA-ATGAAATTTTTAGAGATTCGGGGGTAAAAATGGTAATTTTTGAAAGTTTCGGGGGC
* * * * *
78803 AAAAATGAAAATTTTGGAGGTTCGAGGGTAAAAAT-GTAATTTTTGGAAA-TTTCGAGGTTG-
1 AAAAATGAAATTTTTAGAGATTCGGGGGTAAAAATGGTAATTTTT-GAAAGTTTCG-GG-GGC
* * * * *
78863 AAAATTG-AATTTTTAAAAGATT--GGGGTAAAAATGG-AATTTTAG-AAGTTTTGGGGTC
1 AAAAATGAAATTTTT-AGAGATTCGGGGGTAAAAATGGTAATTTTTGAAAGTTTCGGGGGC
78919 AAAAATGAAATTTTT
1 AAAAATGAAATTTTT
78934 GGAAGTTTTA
Statistics
Matches: 105, Mismatches: 17, Indels: 21
0.73 0.12 0.15
Matches are distributed among these distances:
56 10 0.10
57 12 0.11
58 16 0.15
59 41 0.39
60 25 0.24
61 1 0.01
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.35
Consensus pattern (60 bp):
AAAAATGAAATTTTTAGAGATTCGGGGGTAAAAATGGTAATTTTTGAAAGTTTCGGGGGC
Found at i:78923 original size:87 final size:88
Alignment explanation
Indices: 78827--79115 Score: 261
Period size: 87 Copynumber: 3.3 Consensus size: 88
78817 TGGAGGTTCG
* *
78827 AGGGT-AAAAATGTAATTTTTGGAAATTTCGA-GGTTGAAAATTGAATTTTTAAAAGATT-GG-G
1 AGGGTCAAAAATGAAATTTTTGGAAATTT-GAGGGTTGAAAATGGAATTTTTAAAAG-TTCGGCG
*
78888 GTAAAAATGGAATTTTAG-AAGTTTT
64 GT-AAAATGGAATTTTAGAAAGTTTC
* * * *
78913 GGGGTCAAAAATGAAATTTTTGGAAGTTTTAGGGTTGAAAATGGAATTTTTAGAAGTTCGGCGGT
1 AGGGTCAAAAATGAAATTTTTGGAAATTTGAGGGTTGAAAATGGAATTTTTAAAAGTTCGGCGGT
*
78978 AAAATGGAATTTTCGAAAGTTTC
66 AAAATGGAATTTTAGAAAGTTTC
* * * ** ** ** *
79001 AGAGTCAAAAATGGAATTTTTGGAAGTTCAAGGG-CCAAAATGGAATTTTTTGGAAGTTAGAG-G
1 AGGGTCAAAAATGAAATTTTTGGAAATTTGAGGGTTGAAAATGGAA-TTTTTAAAAGTTCG-GCG
* *
79064 GTTAAAAATGGAATTTTTGGAAGTTTC
64 G-T-AAAATGGAATTTTAGAAAGTTTC
*
79091 AGGGT-AGAAAATGGAATTTTTGGAA
1 AGGGTCA-AAAATGAAATTTTTGGAA
79116 GTTCGGGGGC
Statistics
Matches: 173, Mismatches: 20, Indels: 16
0.83 0.10 0.08
Matches are distributed among these distances:
86 7 0.04
87 68 0.39
88 52 0.30
89 3 0.02
90 43 0.25
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.34
Consensus pattern (88 bp):
AGGGTCAAAAATGAAATTTTTGGAAATTTGAGGGTTGAAAATGGAATTTTTAAAAGTTCGGCGGT
AAAATGGAATTTTAGAAAGTTTC
Found at i:79079 original size:60 final size:58
Alignment explanation
Indices: 78773--79141 Score: 259
Period size: 59 Copynumber: 6.3 Consensus size: 58
78763 ATTCGGGGGT
* * * * *
78773 AAAATGGTAATTTTTGAAAGTTTCGGGGGCAAAAATGAAAATTTTGGAGGTTCGAGGG-TA
1 AAAATGG-AATTTTTGGAAG-TTC-AGGGCAAAAATGGAATTTTTGGAAGTTCGAGGGTTA
* * *** * **
78833 AAAATGTAATTTTTGGAAATTTCGAGGTTGAAAATTGAATTTTTAAAAGATT-G-GGG-TA
1 AAAATGGAATTTTTGG-AAGTTC-AGGGCAAAAATGGAATTTTTGGAAG-TTCGAGGGTTA
* ** * ** *
78891 AAAATGGAA-TTTTAGAAGTTTTGGGGTCAAAAATGAAATTTTTGGAAGTTTTAGGGTTG
1 AAAATGGAATTTTTGGAAG-TTCAGGG-CAAAAATGGAATTTTTGGAAGTTCGAGGGTTA
* ** * * * *
78950 AAAATGGAATTTTTAGAAGTTC-GGCGGTAAAATGGAATTTTCGAAAGTTTC-AGAGTCA
1 AAAATGGAATTTTTGGAAGTTCAGG-GCAAAAATGGAATTTTTGGAAG-TTCGAGGGTTA
* *
79008 AAAATGGAATTTTTGGAAGTTCAAGGGCCAAAATGGAATTTTTTGGAAGTTAGAGGGTTA
1 AAAATGGAATTTTTGGAAGTTC-AGGGCAAAAATGGAA-TTTTTGGAAGTTCGAGGGTTA
* **
79068 AAAATGGAATTTTTGGAAGTTTCAGGGTAGAAAATGGAATTTTTGGAAGTTCG-GGGGCA
1 AAAATGGAATTTTTGGAAG-TTCAGGGCA-AAAATGGAATTTTTGGAAGTTCGAGGGTTA
*
79127 AAAATGAAATTTTTG
1 AAAATGGAATTTTTG
79142 AACAGTTTAG
Statistics
Matches: 242, Mismatches: 51, Indels: 33
0.74 0.16 0.10
Matches are distributed among these distances:
56 6 0.02
57 22 0.09
58 59 0.24
59 73 0.30
60 70 0.29
61 12 0.05
ACGTcount: A:0.36, C:0.04, G:0.27, T:0.33
Consensus pattern (58 bp):
AAAATGGAATTTTTGGAAGTTCAGGGCAAAAATGGAATTTTTGGAAGTTCGAGGGTTA
Found at i:81283 original size:12 final size:11
Alignment explanation
Indices: 81277--81340 Score: 51
Period size: 11 Copynumber: 5.7 Consensus size: 11
81267 TTTAATTTTG
81277 AAATTAAATTT
1 AAATTAAATTT
81288 AAATTTAAGA-TT
1 AAA-TTAA-ATTT
*
81300 AATTTAAATTT
1 AAATTAAATTT
* *
81311 AAAATAAATCT
1 AAATTAAATTT
*
81322 AAATTTAAA-AT
1 AAA-TTAAATTT
81333 AAATTAAA
1 AAATTAAA
81341 AAAAAGGGGG
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
10 6 0.14
11 24 0.56
12 12 0.28
13 1 0.02
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (11 bp):
AAATTAAATTT
Found at i:81305 original size:17 final size:17
Alignment explanation
Indices: 81267--81337 Score: 88
Period size: 17 Copynumber: 4.1 Consensus size: 17
81257 TAATTGGATT
* *
81267 TTTAATTTTGAAATTAAA
1 TTTAAATTT-AAAATAAA
* *
81285 TTTAAATTTAAGATTAA
1 TTTAAATTTAAAATAAA
81302 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
*
81319 TCTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
81336 TT
1 TT
81338 AAAAAAAAGG
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
17 37 0.82
18 8 0.18
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:81332 original size:7 final size:6
Alignment explanation
Indices: 81267--81330 Score: 55
Period size: 6 Copynumber: 11.0 Consensus size: 6
81257 TAATTGGATT
*
81267 TTTAAT TTTGAAA -TTAAA TTTAAA TTTAAGA -TT-AA TTTAAA TTTAAA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA
* *
81314 -ATAAA TCTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA
81331 ATAAATTAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
4 1 0.02
5 10 0.21
6 34 0.71
7 3 0.06
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (6 bp):
TTTAAA
Found at i:81726 original size:21 final size:23
Alignment explanation
Indices: 81682--81726 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
81672 TAGTCATTAA
*
81682 TTTATAATTTCTTATATTTATTT
1 TTTATAATTTCTTATATATATTT
*
81705 TTTA-AATTTTTTATA-ATATTT
1 TTTATAATTTCTTATATATATTT
81726 T
1 T
81727 ATAATTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 6 0.30
22 10 0.50
23 4 0.20
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (23 bp):
TTTATAATTTCTTATATATATTT
Found at i:87444 original size:22 final size:22
Alignment explanation
Indices: 87419--87465 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
87409 CAATTTGTTT
* *
87419 TTTTATTTATTTTCGAATTAAA
1 TTTTATTTATTTTCAAACTAAA
*
87441 TTTTATTTTTTTTCAAACTAAA
1 TTTTATTTATTTTCAAACTAAA
87463 TTT
1 TTT
87466 GGGTTTTGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.62
Consensus pattern (22 bp):
TTTTATTTATTTTCAAACTAAA
Found at i:89150 original size:18 final size:19
Alignment explanation
Indices: 89111--89151 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
89101 AAAATTACAA
* *
89111 AAAATTTAAAATAATTTTT
1 AAAATTCAAAATAATTTAT
89130 AAAATTCAAAAT-ATTTAT
1 AAAATTCAAAATAATTTAT
89148 AAAA
1 AAAA
89152 ATACCAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAATTCAAAATAATTTAT
Found at i:89152 original size:19 final size:19
Alignment explanation
Indices: 89110--89166 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 19
89100 AAAAATTACA
*
89110 AAAAATTTAAAATAATTT-T
1 AAAAATTCAAAAT-ATTTAT
*
89129 TAAAATTCAAAATATTTAT
1 AAAAATTCAAAATATTTAT
* *
89148 AAAAATACCAAAT-TTTAT
1 AAAAATTCAAAATATTTAT
89166 A
1 A
89167 TATTTTTAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
18 10 0.31
19 22 0.69
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAAATTCAAAATATTTAT
Found at i:90986 original size:18 final size:18
Alignment explanation
Indices: 90963--91006 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
90953 ACACACCTAT
* *
90963 AATAAATCTTTTAATATA
1 AATAAATATTTTAAAATA
*
90981 AATAAAAATTTTAAAATA
1 AATAAATATTTTAAAATA
*
90999 TATAAATA
1 AATAAATA
91007 ATCTATTTTG
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (18 bp):
AATAAATATTTTAAAATA
Found at i:92212 original size:30 final size:30
Alignment explanation
Indices: 92172--92369 Score: 210
Period size: 29 Copynumber: 6.6 Consensus size: 30
92162 CTGGGGTGAG
*
92172 ATGGTAATTTTGGGAAATTTTAGGGTTAAAA
1 ATGG-AATTTTGGGAAGTTTTAGGGTTAAAA
*
92203 ATGGAATTTTTGGG-AGTTTTAGGGTCAAAA
1 ATGGAA-TTTTGGGAAGTTTTAGGGTTAAAA
*
92233 ATGGAAATTTT-GGAAG--TTAGGGGGTAAAA
1 ATGG-AATTTTGGGAAGTTTTA-GGGTTAAAA
* * *
92262 ATGGAATTTT-AGAAGTTTTGGGGTCAAAA
1 ATGGAATTTTGGGAAGTTTTAGGGTTAAAA
*
92291 ATGGAATTTTGGGAAGTTTGAGGG-TAAAA
1 ATGGAATTTTGGGAAGTTTTAGGGTTAAAA
* * *
92320 ATAGAATTTTTGGAAGTTTTGAGGGGTAAAA
1 ATGGAATTTTGGGAAGTTTT-AGGGTTAAAA
*
92351 ATGGAATTTTTGGAAGTTT
1 ATGGAATTTTGGGAAGTTT
92370 CGGGACCTCT
Statistics
Matches: 142, Mismatches: 16, Indels: 18
0.81 0.09 0.10
Matches are distributed among these distances:
28 13 0.09
29 51 0.36
30 42 0.30
31 36 0.25
ACGTcount: A:0.34, C:0.01, G:0.30, T:0.35
Consensus pattern (30 bp):
ATGGAATTTTGGGAAGTTTTAGGGTTAAAA
Found at i:92284 original size:29 final size:30
Alignment explanation
Indices: 92172--92369 Score: 217
Period size: 30 Copynumber: 6.6 Consensus size: 30
92162 CTGGGGTGAG
* * * *
92172 ATGGTAATTTTGGGAAATTTTAGGGTTAAAA
1 ATGG-AATTTTTGGAAGTTTTGGGGGTAAAA
* *
92203 ATGGAATTTTTGGGAGTTTT-AGGGTCAAAA
1 ATGGAATTTTTGGAAGTTTTGGGGGT-AAAA
* *
92233 ATGGAAATTTTGGAAG-TTAGGGGGTAAAA
1 ATGGAATTTTTGGAAGTTTTGGGGGTAAAA
*
92262 ATGGAA-TTTTAGAAGTTTT-GGGGTCAAAA
1 ATGGAATTTTTGGAAGTTTTGGGGGT-AAAA
* *
92291 ATGGAATTTTGGGAAG-TTTGAGGGTAAAA
1 ATGGAATTTTTGGAAGTTTTGGGGGTAAAA
*
92320 ATAGAATTTTTGGAAGTTTTGAGGGGTAAAA
1 ATGGAATTTTTGGAAGTTTTG-GGGGTAAAA
92351 ATGGAATTTTTGGAAGTTT
1 ATGGAATTTTTGGAAGTTT
92370 CGGGACCTCT
Statistics
Matches: 141, Mismatches: 18, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
28 13 0.09
29 48 0.34
30 50 0.35
31 30 0.21
ACGTcount: A:0.34, C:0.01, G:0.30, T:0.35
Consensus pattern (30 bp):
ATGGAATTTTTGGAAGTTTTGGGGGTAAAA
Found at i:115293 original size:20 final size:19
Alignment explanation
Indices: 115230--115285 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 19
115220 CAAATAAATC
*
115230 ATAATAA-AC-AAAGTATA
1 ATAATAAGACAAAAGTAAA
* **
115247 ATAAAAACCCAAAAGTAAA
1 ATAATAAGACAAAAGTAAA
115266 ATAATAAGACAAAA-TAAA
1 ATAATAAGACAAAAGTAAA
115284 AT
1 AT
115286 GAAATAAGTC
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
17 6 0.19
18 7 0.23
19 18 0.58
ACGTcount: A:0.68, C:0.09, G:0.05, T:0.18
Consensus pattern (19 bp):
ATAATAAGACAAAAGTAAA
Found at i:116515 original size:66 final size:66
Alignment explanation
Indices: 116438--116569 Score: 228
Period size: 66 Copynumber: 2.0 Consensus size: 66
116428 AGTAGAAAAT
* * *
116438 ACCAAAGAATGTATTTGAGGTACGAAGTTTTCTTGGTTTAGTTGAGTATTGTAGAAGATTTGTAA
1 ACCAAAGAATGTATCTGAGGTACGAAGTTTTCTTGGTTTAGCTGAGTATTATAGAAGATTTGTAA
116503 A
66 A
*
116504 ACCAAAGAATGTATCTGAGGTACGAAGTTTTCTTGGTTTAGCTGGGTATTATAGAAGATTTGTAA
1 ACCAAAGAATGTATCTGAGGTACGAAGTTTTCTTGGTTTAGCTGAGTATTATAGAAGATTTGTAA
116569 A
66 A
116570 TGGATTTTCG
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 62 1.00
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.36
Consensus pattern (66 bp):
ACCAAAGAATGTATCTGAGGTACGAAGTTTTCTTGGTTTAGCTGAGTATTATAGAAGATTTGTAA
A
Found at i:119133 original size:20 final size:21
Alignment explanation
Indices: 119108--119157 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 21
119098 ATATATATAT
*
119108 AAGAAATAAAAGAATA-AAGA-
1 AAGAAAAAAAAGAA-ACAAGAG
119128 AAGAAAAAAAAGAAACAAGAG
1 AAGAAAAAAAAGAAACAAGAG
119149 AAGAAAAAA
1 AAGAAAAAA
119158 CAGAGGCTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 1 0.04
20 17 0.63
21 9 0.33
ACGTcount: A:0.78, C:0.02, G:0.16, T:0.04
Consensus pattern (21 bp):
AAGAAAAAAAAGAAACAAGAG
Found at i:123237 original size:11 final size:11
Alignment explanation
Indices: 123218--123254 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
123208 AGATCGATGC
*
123218 TTTTCCTTTTT
1 TTTTTCTTTTT
123229 TTTTTC-TTTT
1 TTTTTCTTTTT
123239 TTTTTCTTTTT
1 TTTTTCTTTTT
123250 TTTTT
1 TTTTT
123255 TGTATTTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 10 0.42
11 14 0.58
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:123262 original size:22 final size:22
Alignment explanation
Indices: 123218--123263 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
123208 AGATCGATGC
*
123218 TTTTCCTTTTTTTTTTCTTTTT
1 TTTTCCTTTTTTTTTTCTATTT
* *
123240 TTTTCTTTTTTTTTTTGTATTT
1 TTTTCCTTTTTTTTTTCTATTT
123262 TT
1 TT
123264 CCGTAAGCCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.02, C:0.09, G:0.02, T:0.87
Consensus pattern (22 bp):
TTTTCCTTTTTTTTTTCTATTT
Found at i:123263 original size:11 final size:10
Alignment explanation
Indices: 123225--123253 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
123215 TGCTTTTCCT
123225 TTTTTTTTTC
1 TTTTTTTTTC
123235 TTTTTTTTTC
1 TTTTTTTTTC
123245 TTTTTTTTT
1 TTTTTTTTT
123254 TTGTATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:123263 original size:13 final size:12
Alignment explanation
Indices: 123218--123255 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
123208 AGATCGATGC
*
123218 TTTTCCTTTTTT
1 TTTTCTTTTTTT
123230 TTTTC--TTTTT
1 TTTTCTTTTTTT
123240 TTTTCTTTTTTT
1 TTTTCTTTTTTT
123252 TTTT
1 TTTT
123256 GTATTTTTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 10 0.42
12 14 0.58
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (12 bp):
TTTTCTTTTTTT
Found at i:125551 original size:20 final size:21
Alignment explanation
Indices: 125511--125551 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
125501 TAATGGTTTT
*
125511 TTTTTTTTTCCTTAATTAAAA
1 TTTTTTTTTCCTTAATGAAAA
*
125532 TTTTTTTTTCTTTAA-GAAAA
1 TTTTTTTTTCCTTAATGAAAA
125552 CATGATTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.61
Consensus pattern (21 bp):
TTTTTTTTTCCTTAATGAAAA
Found at i:137984 original size:39 final size:39
Alignment explanation
Indices: 137881--137985 Score: 183
Period size: 39 Copynumber: 2.7 Consensus size: 39
137871 TATGCACTCA
* *
137881 ATGGACACCTTTTGAAGAGTCACAACCCTTTCAAATTTG
1 ATGGACACCTATTGAAGAGTCACAATCCTTTCAAATTTG
137920 ATGGACACCTATTGAAGAGTCACAATCCTTTCAAATTTG
1 ATGGACACCTATTGAAGAGTCACAATCCTTTCAAATTTG
*
137959 ATGGACACCTATTGAAGAGTGACAATC
1 ATGGACACCTATTGAAGAGTCACAATC
137986 TTTTTCATAT
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 63 1.00
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (39 bp):
ATGGACACCTATTGAAGAGTCACAATCCTTTCAAATTTG
Found at i:139574 original size:12 final size:13
Alignment explanation
Indices: 139559--139613 Score: 51
Period size: 12 Copynumber: 4.1 Consensus size: 13
139549 TTGTAAATTC
139559 TAAT-TTATTTTT
1 TAATATTATTTTT
139571 TAATATTATTTTT
1 TAATATTATTTTT
*
139584 AATAAATATTA-TTTA
1 --T-AATATTATTTTT
139599 TAATATTATTATTT
1 TAATATTATT-TTT
139613 T
1 T
139614 TCACTCCTAC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
12 11 0.31
13 10 0.29
14 3 0.09
15 4 0.11
16 7 0.20
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TAATATTATTTTT
Found at i:139593 original size:16 final size:15
Alignment explanation
Indices: 139559--139614 Score: 64
Period size: 16 Copynumber: 3.9 Consensus size: 15
139549 TTGTAAATTC
139559 TAAT-TTATTTTT--
1 TAATATTATTTTTAA
139571 TAATATTATTTTTAA
1 TAATATTATTTTTAA
*
139586 TAAATATTATTTATAA
1 T-AATATTATTTTTAA
*
139602 TATTATTATTTTT
1 TAATATTATTTTT
139615 CACTCCTACA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
12 4 0.11
13 8 0.22
15 11 0.30
16 14 0.38
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TAATATTATTTTTAA
Found at i:140743 original size:29 final size:29
Alignment explanation
Indices: 140692--140747 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
140682 GGTTGGATGG
140692 GAGAGGAGTAAAAGTTTTAGGAGGAAAGT
1 GAGAGGAGTAAAAGTTTTAGGAGGAAAGT
*
140721 GAGAGAGAGTAAATGTTTT-GGAGGAAA
1 GAGAG-GAGTAAAAGTTTTAGGAGGAAA
140748 ATAAAGAGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 13 0.52
30 12 0.48
ACGTcount: A:0.41, C:0.00, G:0.38, T:0.21
Consensus pattern (29 bp):
GAGAGGAGTAAAAGTTTTAGGAGGAAAGT
Found at i:142967 original size:39 final size:39
Alignment explanation
Indices: 142847--142946 Score: 173
Period size: 39 Copynumber: 2.6 Consensus size: 39
142837 TATTACAGAT
142847 TATAACGAGATCCAACATTTGTTGCAGATCCCCGGGTAA
1 TATAACGAGATCCAACATTTGTTGCAGATCCCCGGGTAA
** *
142886 TATAACGAGATTTAGCATTTGTTGCAGATCCCCGGGTAA
1 TATAACGAGATCCAACATTTGTTGCAGATCCCCGGGTAA
142925 TATAACGAGATCCAACATTTGT
1 TATAACGAGATCCAACATTTGT
142947 CATGAATTCT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 55 1.00
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (39 bp):
TATAACGAGATCCAACATTTGTTGCAGATCCCCGGGTAA
Found at i:143170 original size:20 final size:18
Alignment explanation
Indices: 143141--143181 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 18
143131 GAATATGGTA
*
143141 TGAAATGAATTATGTGAAAT
1 TGAAAAGAATT-TGT-AAAT
143161 TGAAAAGAATTTGTAAAT
1 TGAAAAGAATTTGTAAAT
143179 TGA
1 TGA
143182 TAAATGTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 7 0.35
19 3 0.15
20 10 0.50
ACGTcount: A:0.46, C:0.00, G:0.20, T:0.34
Consensus pattern (18 bp):
TGAAAAGAATTTGTAAAT
Found at i:146319 original size:6 final size:6
Alignment explanation
Indices: 146308--146350 Score: 68
Period size: 6 Copynumber: 7.2 Consensus size: 6
146298 CAGTTTTCGG
* *
146308 TCCAAC TCCAAC TCCAAC TCCAAC TCCGAC TCCGAC TCCAAC T
1 TCCAAC TCCAAC TCCAAC TCCAAC TCCAAC TCCAAC TCCAAC T
146351 ACATTTTCTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.28, C:0.49, G:0.05, T:0.19
Consensus pattern (6 bp):
TCCAAC
Found at i:148125 original size:14 final size:15
Alignment explanation
Indices: 148089--148131 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
148079 GTGAAATGAA
148089 ATTCGAGTCAAATTG
1 ATTCGAGTCAAATTG
* *
148104 AATCGAGTGAAATTG
1 ATTCGAGTCAAATTG
*
148119 -TTCGAGTTAAATT
1 ATTCGAGTCAAATT
148132 AAAAAATTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (15 bp):
ATTCGAGTCAAATTG
Found at i:148386 original size:9 final size:9
Alignment explanation
Indices: 148370--148399 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
148360 TTCTTTAGAA
148370 TTTT-TAAT
1 TTTTATAAT
148378 TTTTATAAT
1 TTTTATAAT
148387 TTTTATAAT
1 TTTTATAAT
148396 TTTT
1 TTTT
148400 TTTCAAAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 4 0.19
9 17 0.81
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (9 bp):
TTTTATAAT
Found at i:148444 original size:19 final size:19
Alignment explanation
Indices: 148420--148484 Score: 80
Period size: 19 Copynumber: 3.4 Consensus size: 19
148410 TAGATTTTAA
148420 AATTTTTATAAA-TATTTTG
1 AATTTTTA-AAATTATTTTG
*
148439 AATTTTAAAAATTATTTT-
1 AATTTTTAAAATTATTTTG
148457 AATTTTTGAAAATTATTTTG
1 AATTTTT-AAAATTATTTTG
148477 AACTTTTT
1 AA-TTTTT
148485 TTTTTTTGTA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
18 9 0.22
19 24 0.60
20 2 0.05
21 5 0.12
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.57
Consensus pattern (19 bp):
AATTTTTAAAATTATTTTG
Found at i:148695 original size:12 final size:13
Alignment explanation
Indices: 148672--148696 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
148662 AAACTCGAAA
148672 TTCAATTTTTTTT
1 TTCAATTTTTTTT
148685 TTCAATTTTTTT
1 TTCAATTTTTTT
148697 AGTTGAATCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (13 bp):
TTCAATTTTTTTT
Found at i:150978 original size:23 final size:22
Alignment explanation
Indices: 150947--150998 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 22
150937 AATTAAATTG
* * *
150947 TAATATTTAATAGTATATTTTTA
1 TAATTTTTAATAGGATA-ATTTA
150970 TAATTTTT-ATAGGATAATTTA
1 TAATTTTTAATAGGATAATTTA
150991 -AATTTTTA
1 TAATTTTTA
150999 TCATTTTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
20 7 0.28
21 4 0.16
22 7 0.28
23 7 0.28
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (22 bp):
TAATTTTTAATAGGATAATTTA
Found at i:159558 original size:37 final size:37
Alignment explanation
Indices: 159338--159550 Score: 264
Period size: 37 Copynumber: 5.8 Consensus size: 37
159328 GTTCTTGGAT
* *
159338 CACCGGCACAAAGCCTGCTAGGGACACAGCCTGATTA
1 CACCGGCACAAAGCCTGCTAGGCACACAGCCTGAATA
* ** *
159375 CACTGGCATGAAGCCTGTTAGGCACACAGCCTGAATA
1 CACCGGCACAAAGCCTGCTAGGCACACAGCCTGAATA
* * * * *
159412 CACCGGCACTAAGCTTGTTAGACACATAGCCTGAATA
1 CACCGGCACAAAGCCTGCTAGGCACACAGCCTGAATA
* * * *
159449 CACTGGCACAAAACCTGCTAGGCACATAACCTGAATA
1 CACCGGCACAAAGCCTGCTAGGCACACAGCCTGAATA
* **
159486 CAGCGGCATGAAGCCTGCTAGGCACACAGCCTGAATA
1 CACCGGCACAAAGCCTGCTAGGCACACAGCCTGAATA
159523 CACCGGCACAAAGCCTGCTAGGCACACA
1 CACCGGCACAAAGCCTGCTAGGCACACA
159551 ACTTGAATTT
Statistics
Matches: 147, Mismatches: 29, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 147 1.00
ACGTcount: A:0.32, C:0.31, G:0.22, T:0.15
Consensus pattern (37 bp):
CACCGGCACAAAGCCTGCTAGGCACACAGCCTGAATA
Found at i:159558 original size:111 final size:111
Alignment explanation
Indices: 159342--159558 Score: 301
Period size: 111 Copynumber: 2.0 Consensus size: 111
159332 TTGGATCACC
* * * * *
159342 GGCACAAAGCCTGCTAGGGACACAGCCTGATTACACTGGCATGAAGCCTGTTAGGCACACAGCCT
1 GGCACAAAACCTGCTAGGCACACAACCTGAATACACTGGCATGAAGCCTGCTAGGCACACAGCCT
* * * * *
159407 GAATACACCGGCACTAAGCTTGTTAGACACATAGCCTGAATACACT
66 GAATACACCGGCACAAAGCCTGCTAGACACACAACCTGAATACACT
*
159453 GGCACAAAACCTGCTAGGCACATAACCTGAATACAGC-GGCATGAAGCCTGCTAGGCACACAGCC
1 GGCACAAAACCTGCTAGGCACACAACCTGAATACA-CTGGCATGAAGCCTGCTAGGCACACAGCC
* *
159517 TGAATACACCGGCACAAAGCCTGCTAGGCACACAACTTGAAT
65 TGAATACACCGGCACAAAGCCTGCTAGACACACAACCTGAAT
159559 TTGTAGATGC
Statistics
Matches: 92, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
111 91 0.99
112 1 0.01
ACGTcount: A:0.32, C:0.29, G:0.22, T:0.17
Consensus pattern (111 bp):
GGCACAAAACCTGCTAGGCACACAACCTGAATACACTGGCATGAAGCCTGCTAGGCACACAGCCT
GAATACACCGGCACAAAGCCTGCTAGACACACAACCTGAATACACT
Found at i:160880 original size:23 final size:24
Alignment explanation
Indices: 160840--160920 Score: 62
Period size: 25 Copynumber: 3.4 Consensus size: 24
160830 TAGTAATATA
** *
160840 ATATAAACATTAAAAATATATATAT
1 ATATAAA-ATTATTAATATATAAAT
*
160865 ATATAAAATT-TTAATAAATAAAAAT
1 ATATAAAATTATTAAT--ATATAAAT
160890 ATATAAAATTATTAA-ATATTAAAT
1 ATATAAAATTATTAATATA-TAAAT
160914 -TA-AAAAT
1 ATATAAAAT
160921 GATATAAATG
Statistics
Matches: 47, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
22 5 0.11
23 8 0.17
24 7 0.15
25 23 0.49
26 4 0.09
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (24 bp):
ATATAAAATTATTAATATATAAAT
Found at i:164399 original size:29 final size:29
Alignment explanation
Indices: 164366--164445 Score: 151
Period size: 29 Copynumber: 2.8 Consensus size: 29
164356 TATTTGTCTC
*
164366 ATGTTACATTTTAGTCACTTATATTTGAA
1 ATGTTACGTTTTAGTCACTTATATTTGAA
164395 ATGTTACGTTTTAGTCACTTATATTTGAA
1 ATGTTACGTTTTAGTCACTTATATTTGAA
164424 ATGTTACGTTTTAGTCACTTAT
1 ATGTTACGTTTTAGTCACTTAT
164446 GTTATTATTT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.28, C:0.11, G:0.12, T:0.49
Consensus pattern (29 bp):
ATGTTACGTTTTAGTCACTTATATTTGAA
Found at i:168355 original size:7 final size:7
Alignment explanation
Indices: 168343--168384 Score: 84
Period size: 7 Copynumber: 6.0 Consensus size: 7
168333 TAACAATTGG
168343 TGGTGAC
1 TGGTGAC
168350 TGGTGAC
1 TGGTGAC
168357 TGGTGAC
1 TGGTGAC
168364 TGGTGAC
1 TGGTGAC
168371 TGGTGAC
1 TGGTGAC
168378 TGGTGAC
1 TGGTGAC
168385 ATATACATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.14, C:0.14, G:0.43, T:0.29
Consensus pattern (7 bp):
TGGTGAC
Found at i:173072 original size:2 final size:2
Alignment explanation
Indices: 173065--173091 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
173055 TATTATTCTC
173065 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
173092 CAAAATTTAG
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:173448 original size:20 final size:20
Alignment explanation
Indices: 173411--173450 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
173401 ACTTTCTAGA
*
173411 AAATATATATTTATCCAAAT
1 AAATATATAATTATCCAAAT
173431 AAATA-ATAATTATACCAAAT
1 AAATATATAATTAT-CCAAAT
173451 TTAAGTGCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (20 bp):
AAATATATAATTATCCAAAT
Found at i:184764 original size:21 final size:21
Alignment explanation
Indices: 184720--184764 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
184710 ATTTAATTAT
* *
184720 TATAGTATTGAGATAGAATAC
1 TATAATATTGAGATAAAATAC
184741 TATAATATTGAGATTAAAAT-C
1 TATAATATTGAGA-TAAAATAC
184762 TAT
1 TAT
184765 GGTGAAATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.44, C:0.04, G:0.13, T:0.38
Consensus pattern (21 bp):
TATAATATTGAGATAAAATAC
Found at i:185644 original size:2 final size:2
Alignment explanation
Indices: 185637--185662 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
185627 TGGGTTTTTC
185637 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
185663 AAGTTTTAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:189735 original size:14 final size:15
Alignment explanation
Indices: 189716--189744 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
189706 CTTACAATTT
189716 CCAAAACT-AACACA
1 CCAAAACTGAACACA
189730 CCAAAACTGAACACA
1 CCAAAACTGAACACA
189745 TCTGATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.55, C:0.34, G:0.03, T:0.07
Consensus pattern (15 bp):
CCAAAACTGAACACA
Found at i:195994 original size:2 final size:2
Alignment explanation
Indices: 195987--196020 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
195977 AGATATTAAA
195987 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
196021 TGGATAATGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:204044 original size:25 final size:24
Alignment explanation
Indices: 203999--204046 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
203989 GTTCTATAAT
* *
203999 TTTTATAACTTGTAATCATTTTTG
1 TTTTATAACTTCTAATAATTTTTG
*
204023 TTTTATAAGCTTCTATTAATTTTT
1 TTTTATAA-CTTCTAATAATTTTT
204047 AGTAATTTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.25, C:0.08, G:0.06, T:0.60
Consensus pattern (24 bp):
TTTTATAACTTCTAATAATTTTTG
Found at i:204838 original size:20 final size:20
Alignment explanation
Indices: 204822--204859 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
204812 TTTAAAAGTT
204822 ATAAAAATTATAAAAAATTC
1 ATAAAAATTATAAAAAATTC
204842 ATAAAAATTATAAAAAAT
1 ATAAAAATTATAAAAAAT
204860 AGAGTCCACG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (20 bp):
ATAAAAATTATAAAAAATTC
Found at i:204859 original size:10 final size:9
Alignment explanation
Indices: 204804--204857 Score: 65
Period size: 9 Copynumber: 5.8 Consensus size: 9
204794 TGATACACCA
204804 ATAAATAATT
1 ATAAA-AATT
*
204814 -TAAAAGTT
1 ATAAAAATT
204822 ATAAAAATT
1 ATAAAAATT
204831 ATAAAAAATT
1 AT-AAAAATT
204841 CATAAAAATT
1 -ATAAAAATT
204851 ATAAAAA
1 ATAAAAA
204858 ATAGAGTCCA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
8 3 0.08
9 20 0.51
10 14 0.36
11 2 0.05
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (9 bp):
ATAAAAATT
Found at i:212015 original size:18 final size:19
Alignment explanation
Indices: 211984--212019 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
211974 ACCGAACTTG
*
211984 ACTCGGACATGTTGACCGA
1 ACTCGGACACGTTGACCGA
212003 ACTC-GACACGTTGACCG
1 ACTCGGACACGTTGACCG
212020 TTGATAGTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.25, C:0.31, G:0.25, T:0.19
Consensus pattern (19 bp):
ACTCGGACACGTTGACCGA
Found at i:212023 original size:7 final size:7
Alignment explanation
Indices: 212011--212079 Score: 57
Period size: 7 Copynumber: 9.9 Consensus size: 7
212001 GAACTCGACA
212011 CGTTGAC
1 CGTTGAC
*
212018 CGTTGAT
1 CGTTGAC
*
212025 AGTTGAC
1 CGTTGAC
*
212032 CCTTGAC
1 CGTTGAC
*
212039 TGTTGAC
1 CGTTGAC
**
212046 TATTGAC
1 CGTTGAC
*
212053 CGTTGAT
1 CGTTGAC
*
212060 CGTTGAT
1 CGTTGAC
*
212067 CATTGAC
1 CGTTGAC
212074 CGTTGA
1 CGTTGA
212080 TTATTGATCA
Statistics
Matches: 48, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
7 48 1.00
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (7 bp):
CGTTGAC
Found at i:212043 original size:21 final size:20
Alignment explanation
Indices: 212011--212079 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 20
212001 GAACTCGACA
*
212011 CGTTGACCGTTGATAGTTGAC
1 CGTTGACTGTTGATA-TTGAC
*
212032 CCTTGACTGTTGACTATTGAC
1 CGTTGACTGTTGA-TATTGAC
212053 CGTTGA-TCGTTGATCATTGAC
1 CGTTGACT-GTTGAT-ATTGAC
212074 CGTTGA
1 CGTTGA
212080 TTATTGATCA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
20 2 0.05
21 38 0.90
22 2 0.05
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (20 bp):
CGTTGACTGTTGATATTGAC
Found at i:212080 original size:21 final size:21
Alignment explanation
Indices: 212011--212107 Score: 74
Period size: 21 Copynumber: 4.6 Consensus size: 21
212001 GAACTCGACA
* **
212011 CGTTGACCGTTGATAGTTGAC
1 CGTTGATCGTTGATCATTGAC
*
212032 CCTTGACT-GTTGACT-ATTGAC
1 CGTTGA-TCGTTGA-TCATTGAC
212053 CGTTGATCGTTGATCATTGAC
1 CGTTGATCGTTGATCATTGAC
** *
212074 CGTTGATTATTGATCAGTT-AT
1 CGTTGATCGTTGATCA-TTGAC
*
212095 CGTTGAACGTTGA
1 CGTTGATCGTTGA
212108 CCGTTGATTT
Statistics
Matches: 61, Mismatches: 10, Indels: 10
0.75 0.12 0.12
Matches are distributed among these distances:
20 2 0.03
21 56 0.92
22 3 0.05
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.38
Consensus pattern (21 bp):
CGTTGATCGTTGATCATTGAC
Found at i:212097 original size:35 final size:35
Alignment explanation
Indices: 212013--212116 Score: 111
Period size: 35 Copynumber: 3.0 Consensus size: 35
212003 ACTCGACACG
* * * * * *
212013 TTGACCGTTGATAGTTGACCCTTGACTGTTGACTA
1 TTGACAGTTGATCGTTGAACATTGACCGTTGATTA
* *
212048 TTGACCGTTGATCGTTGATCATTGACCGTTGATTA
1 TTGACAGTTGATCGTTGAACATTGACCGTTGATTA
*
212083 TTGATCAGTT-ATCGTTGAACGTTGACCGTTGATT
1 TTGA-CAGTTGATCGTTGAACATTGACCGTTGATT
212117 TAAAATGTTT
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
35 56 0.93
36 4 0.07
ACGTcount: A:0.20, C:0.17, G:0.23, T:0.39
Consensus pattern (35 bp):
TTGACAGTTGATCGTTGAACATTGACCGTTGATTA
Done.