Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014521.1 Kokia drynarioides strain JFW-HI SEQ_129560, 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: 209620
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Warning! 178 characters in sequence are not A, C, G, or T
Found at i:5254 original size:20 final size:18
Alignment explanation
Indices: 5216--5255 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
5206 TGTATTTGGA
*
5216 ATCATTCTCTCGAATGGT
1 ATCATTCTCACGAATGGT
5234 ATCATATCTCACGATATGGT
1 ATCAT-TCTCACGA-ATGGT
5254 AT
1 AT
5256 AAGAAAACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 7 0.37
20 7 0.37
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.38
Consensus pattern (18 bp):
ATCATTCTCACGAATGGT
Found at i:7017 original size:3 final size:3
Alignment explanation
Indices: 7009--7034 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
6999 CACAATTGAA
7009 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
7035 ACCCAACCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:19960 original size:109 final size:110
Alignment explanation
Indices: 19763--19981 Score: 259
Period size: 109 Copynumber: 2.0 Consensus size: 110
19753 CGAAACTTGG
* * *
19763 CCCCATTGATTCGGTCGAATTATCTTTCAAGCCTTTAACATTTATAATTTTATAATAATAAAATG
1 CCCCATTGATTCGGTCGAATTATCTTTCAAGCCCTTAACATTTATAATTTCATAATAATAAAAAG
*
19828 GTAAATTTTTTACTTTGTCCCCCTAAA-ATTTTACAATTCAATTTT
66 GTAAA-TTTTTACTTTGTACCCCTAAATATTTTACAATTCAATTTT
* * * * * *
19873 CCCC-TTGATTTGGTGGGATTATCTTTTAGGCCCTTAACATTTGTAATTTCATAATTAATAAAAA
1 CCCCATTGATTCGGTCGAATTATCTTTCAAGCCCTTAACATTTATAATTTCATAA-TAATAAAAA
*
19937 GGATGAAA-TTTT-CTTT-TAACCCCTAAATATTTTACAATTTAATTT
65 GG-T-AAATTTTTACTTTGT-ACCCCTAAATATTTTACAATTCAATTT
19982 CAACTCTTTC
Statistics
Matches: 93, Mismatches: 11, Indels: 10
0.82 0.10 0.09
Matches are distributed among these distances:
108 1 0.01
109 54 0.58
110 34 0.37
111 1 0.01
112 3 0.03
ACGTcount: A:0.32, C:0.16, G:0.09, T:0.43
Consensus pattern (110 bp):
CCCCATTGATTCGGTCGAATTATCTTTCAAGCCCTTAACATTTATAATTTCATAATAATAAAAAG
GTAAATTTTTACTTTGTACCCCTAAATATTTTACAATTCAATTTT
Found at i:21248 original size:26 final size:23
Alignment explanation
Indices: 21203--21257 Score: 83
Period size: 26 Copynumber: 2.3 Consensus size: 23
21193 TCTTTCCATG
21203 AATTTTTTAAATTTTAAAGTTTC
1 AATTTTTTAAATTTTAAAGTTTC
21226 AATTTTTTGAAAGTATTTAAAGTTTC
1 AATTTTTT-AAA-T-TTTAAAGTTTC
21252 AATTTT
1 AATTTT
21258 GATCTAAACG
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
23 8 0.28
24 3 0.10
25 1 0.03
26 17 0.59
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.55
Consensus pattern (23 bp):
AATTTTTTAAATTTTAAAGTTTC
Found at i:21727 original size:24 final size:24
Alignment explanation
Indices: 21700--21750 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
21690 TAAAAAGTTA
* * *
21700 AAGGTTAAATTGATTAAAAAGAAT
1 AAGGTGAAAATGATAAAAAAGAAT
21724 AAGGTGAAAATGATAAAAAAGAAT
1 AAGGTGAAAATGATAAAAAAGAAT
21748 AAG
1 AAG
21751 TATTAGGGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.20, T:0.22
Consensus pattern (24 bp):
AAGGTGAAAATGATAAAAAAGAAT
Found at i:26749 original size:2 final size:2
Alignment explanation
Indices: 26742--26767 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
26732 TATCATGTAC
26742 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
26768 ATGCCTCCAG
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:31178 original size:17 final size:16
Alignment explanation
Indices: 31158--31203 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
31148 TGTTTATGTA
31158 TAATAAATATATAAAAT
1 TAATAAATAT-TAAAAT
31175 TAATAAATATTAAAA-
1 TAATAAATATTAAAAT
31190 TATATAAA-ATTAAA
1 TA-ATAAATATTAAA
31204 CTTTAATGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.29
16 10 0.36
17 10 0.36
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
TAATAAATATTAAAAT
Found at i:35338 original size:2 final size:2
Alignment explanation
Indices: 35331--35361 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
35321 TGTCCTTTGG
35331 AT AT 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 AT AT A
35362 AATAGGATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:36138 original size:39 final size:39
Alignment explanation
Indices: 36084--36166 Score: 148
Period size: 39 Copynumber: 2.1 Consensus size: 39
36074 TGAGTTATTC
*
36084 GAGTTATTTGAGTCCACTTAAATAAGTAATTCAAGTTTT
1 GAGTTATTTGAGTCCACTCAAATAAGTAATTCAAGTTTT
*
36123 GAGTTATTTGAGTCCACTCAAATAAGTAATTCGAGTTTT
1 GAGTTATTTGAGTCCACTCAAATAAGTAATTCAAGTTTT
36162 GAGTT
1 GAGTT
36167 CAAATTGAGT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.40
Consensus pattern (39 bp):
GAGTTATTTGAGTCCACTCAAATAAGTAATTCAAGTTTT
Found at i:39187 original size:31 final size:32
Alignment explanation
Indices: 39138--39269 Score: 111
Period size: 32 Copynumber: 4.3 Consensus size: 32
39128 AAAAAGGCTT
39138 AGGTACCAAATTAGGAAAAAA-TGTCAAGTTC
1 AGGTACCAAATTAGGAAAAAAGTGTCAAGTTC
*
39169 AGGTACCCAAATTA-GAAAAAAGTGTCAAGTTT
1 AGGTA-CCAAATTAGGAAAAAAGTGTCAAGTTC
* * * *
39201 AGGTTCCAAATTGGGTCAAAAA-----AAGTTT
1 AGGTACCAAATTAGG-AAAAAAGTGTCAAGTTC
* *
39229 AGGTACCAAATTAGG--AAAAGTATAAAGTTC
1 AGGTACCAAATTAGGAAAAAAGTGTCAAGTTC
*
39259 AAGTACCAAAT
1 AGGTACCAAAT
39270 GTTATATTAA
Statistics
Matches: 84, Mismatches: 8, Indels: 19
0.76 0.07 0.17
Matches are distributed among these distances:
25 4 0.05
28 19 0.23
30 15 0.18
31 19 0.23
32 22 0.26
33 5 0.06
ACGTcount: A:0.45, C:0.12, G:0.19, T:0.24
Consensus pattern (32 bp):
AGGTACCAAATTAGGAAAAAAGTGTCAAGTTC
Found at i:50200 original size:12 final size:12
Alignment explanation
Indices: 50179--50210 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
50169 AATCATTACA
50179 CATACATGCATG
1 CATACATGCATG
*
50191 CATGCATGCATG
1 CATACATGCATG
50203 CATACATG
1 CATACATG
50211 TTAGAGATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (12 bp):
CATACATGCATG
Found at i:54206 original size:54 final size:52
Alignment explanation
Indices: 54030--54277 Score: 263
Period size: 52 Copynumber: 4.8 Consensus size: 52
54020 ATTTCACTTC
* * * ** *
54030 ATTCATATACTCACGATGACACATAGCCACCGGACCTTATAATCCA-CGAGGG
1 ATTCATATACTCACGATGACACTTAGTCATCGGACCTT-TAATCCATAAAAGG
* *
54082 ATTCATACACTCACGATGACA--TAGAATCATCGGACCTCTTAATCCGT-AAAGG
1 ATTCATATACTCACGATGACACTTAG--TCATCGGACCT-TTAATCCATAAAAGG
* *
54134 ATCCATATACTCACGATGACACTTAGTCAGCGGACCTTTAAATCCATAAAAGG
1 ATTCATATACTCACGATGACACTTAGTCATCGGACCTTT-AATCCATAAAAGG
* * * * *
54187 ATTTCTTATACTCACGATGACACTTAATCATTGGACCTCTAATCCGTAAAA-G
1 A-TTCATATACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAAGG
*
54239 ATTCATTTACTCACGATGACACTTAGTCATCGGACCTTT
1 ATTCATATACTCACGATGACACTTAGTCATCGGACCTTT
54278 TTTTTCATTT
Statistics
Matches: 165, Mismatches: 22, Indels: 19
0.80 0.11 0.09
Matches are distributed among these distances:
50 3 0.02
51 35 0.21
52 75 0.45
53 17 0.10
54 35 0.21
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (52 bp):
ATTCATATACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAAGG
Found at i:54259 original size:105 final size:105
Alignment explanation
Indices: 54030--54277 Score: 315
Period size: 105 Copynumber: 2.4 Consensus size: 105
54020 ATTTCACTTC
* * ** *
54030 ATTCATATACTCACGATGACACATAGCCACCGGACC-TTATAATCCACGAGGGATTCATACACTC
1 ATTCATATACTCACGATGACACTTAGTCACCGGACCTTTATAATCCAAAAAGGATTCATACACTC
*
54094 ACGATGACATAGAATCATCGGACCTCTTAATCCGTAAAGG
66 ACGATGACATAGAATCATCGGACCTCTTAATCCGTAAAAG
* * * *
54134 ATCCATATACTCACGATGACACTTAGTCAGCGGACCTTTA-AATCCATAAAAGGATTTCTTATAC
1 ATTCATATACTCACGATGACACTTAGTCACCGGACCTTTATAATCCA-AAAAGGA-TTCATACAC
* *
54198 TCACGATGACACT-TAATCATTGGACCTC-TAATCCGTAAAAG
64 TCACGATGACA-TAGAATCATCGGACCTCTTAATCCGTAAAAG
* *
54239 ATTCATTTACTCACGATGACACTTAGTCATCGGACCTTT
1 ATTCATATACTCACGATGACACTTAGTCACCGGACCTTT
54278 TTTTTCATTT
Statistics
Matches: 125, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
104 38 0.30
105 55 0.44
106 31 0.25
107 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (105 bp):
ATTCATATACTCACGATGACACTTAGTCACCGGACCTTTATAATCCAAAAAGGATTCATACACTC
ACGATGACATAGAATCATCGGACCTCTTAATCCGTAAAAG
Found at i:56132 original size:21 final size:22
Alignment explanation
Indices: 56085--56143 Score: 77
Period size: 21 Copynumber: 2.7 Consensus size: 22
56075 TATAATAGGG
*
56085 AAACAACAA-GAAAATAGTGACA
1 AAACAACAACAAAAATAGTGA-A
56107 AAACAACAACAAAAATAGTG-A
1 AAACAACAACAAAAATAGTGAA
*
56128 AAACAACAGCAAAAAT
1 AAACAACAACAAAAAT
56144 CATCAATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 16 0.47
22 9 0.26
23 9 0.26
ACGTcount: A:0.66, C:0.15, G:0.10, T:0.08
Consensus pattern (22 bp):
AAACAACAACAAAAATAGTGAA
Found at i:59350 original size:60 final size:60
Alignment explanation
Indices: 59265--59383 Score: 166
Period size: 60 Copynumber: 2.0 Consensus size: 60
59255 ATTTGTTACC
* * ** *
59265 TGAATTTGACATTTTTTTTAATTTGGTACCTAAACTTTTTTTTTGACTCAATTTGGCACT
1 TGAACTTGACACTTTTCCTAATTTGGTACCTAAACTTTTTTTTAGACTCAATTTGGCACT
* * *
59325 TGAACTTGACACTTTTCCTAATTTGGTACCTAAGCTTTTTTTTAGATTCGATTTGGCAC
1 TGAACTTGACACTTTTCCTAATTTGGTACCTAAACTTTTTTTTAGACTCAATTTGGCAC
59384 CTAAATTTAT
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 51 1.00
ACGTcount: A:0.23, C:0.16, G:0.13, T:0.48
Consensus pattern (60 bp):
TGAACTTGACACTTTTCCTAATTTGGTACCTAAACTTTTTTTTAGACTCAATTTGGCACT
Found at i:59643 original size:93 final size:90
Alignment explanation
Indices: 59530--59725 Score: 248
Period size: 93 Copynumber: 2.1 Consensus size: 90
59520 TTAGAAAAGA
** *
59530 TTAGGTACCAAATTAAGAAAAAGAGTCAAGTTCAAGTACCAAATTGGACCCCAAAAAGTTTAAGT
1 TTAGGTACCAAATTAAGAAAAAGAGTCAAGTTCAAGTACCAAATTGGACCAAAAAAAATTTAAGT
*
59595 ACCAACTTAAAAAAAAAAAGTGTCAAGT
66 ACCAAATT---AAAAAAAAGTGTCAAGT
* * ** * *
59623 TTAGGTACCAAATTAGGAAAAAGTGTCAAGTTTGAGTACCAAATTGGACTAAAAAAAATTTAGGT
1 TTAGGTACCAAATTAAGAAAAAGAGTCAAGTTCAAGTACCAAATTGGACCAAAAAAAATTTAAGT
**
59688 ACCAAATTAGGAAAAAGTGTCAAGT
66 ACCAAATTAAAAAAAAGTGTCAAGT
*
59713 TCAGGTACCAAAT
1 TTAGGTACCAAAT
59726 ATTATATTAA
Statistics
Matches: 90, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
90 27 0.30
93 63 0.70
ACGTcount: A:0.46, C:0.13, G:0.17, T:0.23
Consensus pattern (90 bp):
TTAGGTACCAAATTAAGAAAAAGAGTCAAGTTCAAGTACCAAATTGGACCAAAAAAAATTTAAGT
ACCAAATTAAAAAAAAGTGTCAAGT
Found at i:59647 original size:31 final size:31
Alignment explanation
Indices: 59609--59725 Score: 138
Period size: 31 Copynumber: 3.9 Consensus size: 31
59599 ACTTAAAAAA
59609 AAAAAGTGTCAAGTTTAGGTACCAAATTAGG
1 AAAAAGTGTCAAGTTTAGGTACCAAATTAGG
59640 AAAAAGTGTCAAGTTT-GAGTACCAAATT-GG
1 AAAAAGTGTCAAGTTTAG-GTACCAAATTAGG
* *
59670 ACTAAAA----AAAATTTAGGTACCAAATTAGG
1 A--AAAAGTGTCAAGTTTAGGTACCAAATTAGG
*
59699 AAAAAGTGTCAAGTTCAGGTACCAAAT
1 AAAAAGTGTCAAGTTTAGGTACCAAAT
59726 ATTATATTAA
Statistics
Matches: 72, Mismatches: 5, Indels: 18
0.76 0.05 0.19
Matches are distributed among these distances:
27 4 0.06
28 15 0.21
29 4 0.06
30 4 0.06
31 41 0.57
32 4 0.06
ACGTcount: A:0.44, C:0.11, G:0.20, T:0.25
Consensus pattern (31 bp):
AAAAAGTGTCAAGTTTAGGTACCAAATTAGG
Found at i:66132 original size:26 final size:26
Alignment explanation
Indices: 66077--66142 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
66067 AATTTTTATT
** *
66077 TTTGTACTAATTTTGAATTTTAAAAT
1 TTTGTACTAATTTTGAAAATTAAAAC
* *
66103 TTTGTACTTATTTTGAAAATTCAAAC
1 TTTGTACTAATTTTGAAAATTAAAAC
66129 TTTGT-CTGAATTTT
1 TTTGTACT-AATTTT
66143 TAGGGTAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
25 2 0.06
26 31 0.94
ACGTcount: A:0.30, C:0.08, G:0.09, T:0.53
Consensus pattern (26 bp):
TTTGTACTAATTTTGAAAATTAAAAC
Found at i:67967 original size:30 final size:30
Alignment explanation
Indices: 67933--67996 Score: 71
Period size: 30 Copynumber: 2.1 Consensus size: 30
67923 GGGGTGTGCA
67933 AATTTTGAGTAA-AATCT-ATTTAATCGAATT
1 AATTTTGAGTAACAAT-TGA-TTAATCGAATT
*
67963 AA-TTTGATTAATCAATTGATTAATCGAATT
1 AATTTTGAGTAA-CAATTGATTAATCGAATT
67993 AATT
1 AATT
67997 CGATCGGGAG
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
29 8 0.28
30 16 0.55
31 5 0.17
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (30 bp):
AATTTTGAGTAACAATTGATTAATCGAATT
Found at i:68982 original size:24 final size:25
Alignment explanation
Indices: 68948--68997 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
68938 CGCATATTTA
* *
68948 ACGGCCTCGACCACGTCCACG-CCC
1 ACGGCCCCGACCACGACCACGTCCC
*
68972 ACGGCCCCGACCCCGACCACGTCCC
1 ACGGCCCCGACCACGACCACGTCCC
68997 A
1 A
68998 AAGGCCTCCC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.18, C:0.56, G:0.20, T:0.06
Consensus pattern (25 bp):
ACGGCCCCGACCACGACCACGTCCC
Found at i:69635 original size:23 final size:23
Alignment explanation
Indices: 69592--69636 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
69582 TCAATGAACA
* **
69592 ATTCGTGAACATGTTTGTTTAAT
1 ATTCATGAACATGTTCATTTAAT
69615 ATTCATGAACATGTTCATTTAA
1 ATTCATGAACATGTTCATTTAA
69637 CTTAAATGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.31, C:0.11, G:0.13, T:0.44
Consensus pattern (23 bp):
ATTCATGAACATGTTCATTTAAT
Found at i:71981 original size:3 final size:3
Alignment explanation
Indices: 71973--72000 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
71963 CCTTCTTTAC
71973 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
72001 ATATTTTTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:73865 original size:13 final size:13
Alignment explanation
Indices: 73847--73872 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
73837 CTAATAAGAC
73847 TTAAAAAAACAAA
1 TTAAAAAAACAAA
73860 TTAAAAAAACAAA
1 TTAAAAAAACAAA
73873 AGAATAAGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (13 bp):
TTAAAAAAACAAA
Found at i:82716 original size:14 final size:15
Alignment explanation
Indices: 82699--82747 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
82689 GTTAACTATA
82699 ATTTATTAA-AAAAT
1 ATTTATTAATAAAAT
82713 A-TT-TTAATTAAAAT
1 ATTTATTAA-TAAAAT
*
82727 ATTATTTTAATAAAAT
1 ATT-TATTAATAAAAT
82743 ATTTA
1 ATTTA
82748 AATTTCACAT
Statistics
Matches: 29, Mismatches: 1, Indels: 9
0.74 0.03 0.23
Matches are distributed among these distances:
12 4 0.14
13 2 0.07
14 7 0.24
15 2 0.07
16 10 0.34
17 4 0.14
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATTTATTAATAAAAT
Found at i:82744 original size:16 final size:17
Alignment explanation
Indices: 82703--82745 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
82693 ACTATAATTT
*
82703 ATTAAAA-AATATTTTA
1 ATTAAAATATTATTTTA
82719 ATTAAAATATTATTTTA
1 ATTAAAATATTATTTTA
82736 A-TAAAATATT
1 ATTAAAATATT
82746 TAAATTTCAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 16 0.64
17 9 0.36
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATTAAAATATTATTTTA
Found at i:85183 original size:20 final size:21
Alignment explanation
Indices: 85146--85185 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
85136 TTCAAAATTA
*
85146 AAAAATTATAAAATAATAAAT
1 AAAAATAATAAAATAATAAAT
*
85167 AAAAATAATAATA-AATAAA
1 AAAAATAATAAAATAATAAA
85186 AGAATATTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (21 bp):
AAAAATAATAAAATAATAAAT
Found at i:98941 original size:24 final size:23
Alignment explanation
Indices: 98914--98963 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 23
98904 TGAATAATTT
98914 ATTTTATAAA-TAATTTATTATAAA
1 ATTTTATAAACT-ATTT-TTATAAA
*
98938 ATTTTATAAACTATTTTTCTAAA
1 ATTTTATAAACTATTTTTATAAA
98961 ATT
1 ATT
98964 AGAATTGTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 9 0.38
24 14 0.58
25 1 0.04
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (23 bp):
ATTTTATAAACTATTTTTATAAA
Found at i:121536 original size:31 final size:31
Alignment explanation
Indices: 121501--121564 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
121491 ATAAAATAGA
* * *
121501 CACTAAATTATTCAATAGTTTTCATTTAAGT
1 CACTAAACTATTCAAAAGTTTTCAATTAAGT
*
121532 CACTAAACTATTCAAAAGTTTTTAATTAAGT
1 CACTAAACTATTCAAAAGTTTTCAATTAAGT
121563 CA
1 CA
121565 TTGGGTGGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.39, C:0.14, G:0.06, T:0.41
Consensus pattern (31 bp):
CACTAAACTATTCAAAAGTTTTCAATTAAGT
Found at i:126912 original size:6 final size:6
Alignment explanation
Indices: 126901--126950 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
126891 AAAAACATTC
*
126901 ATAAAT ATAAAT ATAAAT ATAAAT GTAAAGTCT ATAAAT A-AAAT A-AAAT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAA---T ATAAAT ATAAAT ATAAAT
126950 A
1 A
126951 ACATAATTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
5 10 0.26
6 24 0.62
9 5 0.13
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (6 bp):
ATAAAT
Found at i:128732 original size:15 final size:15
Alignment explanation
Indices: 128712--128750 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
128702 TTGAGGGAAA
*
128712 AGAGAGAAACGGTAG
1 AGAGAGAAACGATAG
128727 AGAGAGAAACGATAG
1 AGAGAGAAACGATAG
128742 AGAGAGAAA
1 AGAGAGAAA
128751 ACACAAATGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.54, C:0.05, G:0.36, T:0.05
Consensus pattern (15 bp):
AGAGAGAAACGATAG
Found at i:137307 original size:18 final size:16
Alignment explanation
Indices: 137258--137323 Score: 80
Period size: 18 Copynumber: 4.0 Consensus size: 16
137248 TTTTTAAAAA
137258 ATTTAAAAATA-TTTT
1 ATTTAAAAATATTTTT
**
137273 ATTTAGTAATATTTTT
1 ATTTAAAAATATTTTT
137289 ATTTTAAAAATATTTTTT
1 A-TTTAAAAATA-TTTTT
137307 ACTTTAAAAATATTTTT
1 A-TTTAAAAATATTTTT
137324 GAAAAATAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
15 9 0.21
16 5 0.12
17 13 0.30
18 16 0.37
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (16 bp):
ATTTAAAAATATTTTT
Found at i:137598 original size:13 final size:13
Alignment explanation
Indices: 137580--137604 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
137570 GTCCTAAGTT
137580 CTTTTAATTAATG
1 CTTTTAATTAATG
137593 CTTTTAATTAAT
1 CTTTTAATTAAT
137605 AAATATATTA
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:0.32, C:0.08, G:0.04, T:0.56
Consensus pattern (13 bp):
CTTTTAATTAATG
Found at i:137706 original size:22 final size:22
Alignment explanation
Indices: 137663--137705 Score: 72
Period size: 20 Copynumber: 2.0 Consensus size: 22
137653 TATAAAATCA
137663 AATAATAAATATGTAATTATAT
1 AATAATAAATATGTAATTATAT
137685 AATAA-AAATATGT-ATTATAT
1 AATAATAAATATGTAATTATAT
137705 A
1 A
137706 TTGTTAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 8 0.38
21 8 0.38
22 5 0.24
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.40
Consensus pattern (22 bp):
AATAATAAATATGTAATTATAT
Found at i:137774 original size:23 final size:22
Alignment explanation
Indices: 137744--137806 Score: 83
Period size: 25 Copynumber: 2.7 Consensus size: 22
137734 TCTTTATTTA
137744 TATAAATATATTTATTATTATG
1 TATAAATATATTTATTATTATG
137766 TAATAAATATATATTTATTATTATG
1 T-AT-AA-ATATATTTATTATTATG
137791 T-TAAATATACTTTATT
1 TATAAATATA-TTTATT
137807 TTTTTAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
21 5 0.14
22 9 0.24
23 3 0.08
24 2 0.05
25 18 0.49
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (22 bp):
TATAAATATATTTATTATTATG
Found at i:137783 original size:25 final size:23
Alignment explanation
Indices: 137749--137799 Score: 84
Period size: 25 Copynumber: 2.1 Consensus size: 23
137739 ATTTATATAA
137749 ATATATTTATTATTATGTAATAAAT
1 ATATATTTATTATTATGT--TAAAT
137774 ATATATTTATTATTATGTTAAAT
1 ATATATTTATTATTATGTTAAAT
137797 ATA
1 ATA
137800 CTTTATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 8 0.31
25 18 0.69
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (23 bp):
ATATATTTATTATTATGTTAAAT
Found at i:157144 original size:191 final size:190
Alignment explanation
Indices: 156812--157173 Score: 494
Period size: 191 Copynumber: 1.9 Consensus size: 190
156802 TGGGGCAGCC
*
156812 CTATTGTACTGTTTATATGGGTCCTACGTCCCTACGCTTTTTGGTAAATTTCCTACTAGGTGACT
1 CTATTGTACTGTTTATATGGGTCCTACGTCCCTACGCTTTTTGGTAAATTTCATACTAGGTGACT
* * * * *
156877 AAACTATTACTGAGTTTATCTTTTGGTCATTTAACTTCAAAAAATTATAAAATAATCATTGAACT
66 AAACTATTACTAAATTTATCTTTTGATCATTTAACTTCAAAAAATTATAAAATAATCACTAAACT
*
156942 ATTCAAAAAATTTTCATTTTAAATCACTGAACTGTTAAAAATGCTGTCGTATGATCTTCT
131 ACTCAAAAAATTTTCATTTTAAATCACTGAACTGTTAAAAATGCTGTCGTATGATCTTCT
* * **
157002 CTATTGTACTGTTTATGTGGGTCCTATGTCCCTACTTTTTTTGGGTAAATTTCAT-CTTAGGTGA
1 CTATTGTACTGTTTATATGGGTCCTACGTCCCTACGCTTTTT-GGTAAATTTCATAC-TAGGTGA
* * * * * * * *
157066 CTAAATTGTTAGTAAATTTATGTTTTGATCATTTAATTTTAAAAAGTTATAAAATGATCACTAAA
64 CTAAACTATTACTAAATTTATCTTTTGATCATTTAACTTCAAAAAATTATAAAATAATCACTAAA
**
157131 CTACT-ATAAAAATTTTCATTTTAAATCACTGAGTTGTTAAAAA
129 CTACTCA-AAAAATTTTCATTTTAAATCACTGAACTGTTAAAAA
157174 CGTTGTGCAC
Statistics
Matches: 148, Mismatches: 21, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
190 40 0.27
191 108 0.73
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (190 bp):
CTATTGTACTGTTTATATGGGTCCTACGTCCCTACGCTTTTTGGTAAATTTCATACTAGGTGACT
AAACTATTACTAAATTTATCTTTTGATCATTTAACTTCAAAAAATTATAAAATAATCACTAAACT
ACTCAAAAAATTTTCATTTTAAATCACTGAACTGTTAAAAATGCTGTCGTATGATCTTCT
Found at i:157883 original size:5 final size:5
Alignment explanation
Indices: 157873--157907 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
157863 GAAAAGCTGT
157873 ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA
157908 TTTGTCATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:162100 original size:6 final size:6
Alignment explanation
Indices: 162089--162113 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
162079 CCATAATATA
162089 TAATTT TAATTT TAATTT TAATTT T
1 TAATTT TAATTT TAATTT TAATTT T
162114 TTTAGTCGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TAATTT
Found at i:164593 original size:6 final size:6
Alignment explanation
Indices: 164582--164610 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
164572 TTATTATAAA
164582 AAACCT AAACCT AAACCT AAACCT AAACC
1 AAACCT AAACCT AAACCT AAACCT AAACC
164611 GTTCAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.34, G:0.00, T:0.14
Consensus pattern (6 bp):
AAACCT
Found at i:172310 original size:12 final size:13
Alignment explanation
Indices: 172295--172323 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
172285 TGAAATCGTG
172295 AAATAAATAAA-T
1 AAATAAATAAATT
172307 AAATAAATAAATT
1 AAATAAATAAATT
172320 AAAT
1 AAAT
172324 TAAGAATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAATAAATAAATT
Found at i:174127 original size:25 final size:24
Alignment explanation
Indices: 174078--174123 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
174068 TTTTATATTA
174078 ATATTAATATTAATTAAAAATAATT
1 ATATTAATATTAA-TAAAAATAATT
174103 ATATTAATATTAA-AAAAATAA
1 ATATTAATATTAATAAAAATAA
174124 AATTCCCTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 8 0.38
25 13 0.62
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
ATATTAATATTAATAAAAATAATT
Found at i:174834 original size:43 final size:42
Alignment explanation
Indices: 174769--174857 Score: 148
Period size: 43 Copynumber: 2.2 Consensus size: 42
174759 TCCAATGAGA
174769 TTTTT-TTTTTTTT--AAAAAAAAAATGAGGGTCTAATTAAT
1 TTTTTATTTTTTTTAAAAAAAAAAAATGAGGGTCTAATTAAT
174808 TTTTTATNTTTTTTTAAAAAAAAAAAATGAGGGTCTAATTAAT
1 TTTTTAT-TTTTTTTAAAAAAAAAAAATGAGGGTCTAATTAAT
174851 TTTTTAT
1 TTTTTAT
174858 GAGATTAACG
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
39 5 0.11
40 1 0.02
41 7 0.15
43 33 0.72
ACGTcount: A:0.38, C:0.02, G:0.09, T:0.49
Consensus pattern (42 bp):
TTTTTATTTTTTTTAAAAAAAAAAAATGAGGGTCTAATTAAT
Found at i:175931 original size:2 final size:2
Alignment explanation
Indices: 175924--175958 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
175914 TGTAATTGAG
175924 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT
175959 TTAAAATAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:178970 original size:33 final size:31
Alignment explanation
Indices: 178896--178972 Score: 84
Period size: 32 Copynumber: 2.4 Consensus size: 31
178886 GATACTTGGG
178896 AAAGTAAGAATATTGAGAATCTCATATTCAAA
1 AAAGTAA-AATATTGAGAATCTCATATTCAAA
* *
178928 ATAGTTAAAATATTGAGAAT-TCAAATATTTTAAA
1 AAAG-TAAAATATTGAGAATCTC--ATA-TTCAAA
178962 AAAGTAAAATA
1 AAAGTAAAATA
178973 GTTGTAATTC
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
31 2 0.05
32 15 0.39
33 13 0.34
34 8 0.21
ACGTcount: A:0.53, C:0.05, G:0.10, T:0.31
Consensus pattern (31 bp):
AAAGTAAAATATTGAGAATCTCATATTCAAA
Found at i:181727 original size:2 final size:2
Alignment explanation
Indices: 181722--181763 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
181712 TTATATTAAT
*
181722 TA TA TA TG T- 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
181763 T
1 T
181764 TAAATCACTA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:194767 original size:7 final size:7
Alignment explanation
Indices: 194750--194841 Score: 55
Period size: 7 Copynumber: 12.9 Consensus size: 7
194740 TTTTTATAAT
194750 TTTTGAAA
1 TTTT-AAA
194758 TTTTAAA
1 TTTTAAA
194765 TTTTAAA
1 TTTTAAA
*
194772 ATTT-AA
1 TTTTAAA
*
194778 TCTTTATA
1 T-TTTAAA
194786 TTTT-AA
1 TTTTAAA
194792 TTTTCAAAA
1 TTTT--AAA
* *
194801 ATTTAATT
1 TTTTAA-A
**
194809 TTTTATT
1 TTTTAAA
194816 TTTTAAA
1 TTTTAAA
*
194823 TTTCAAA
1 TTTTAAA
194830 TTTT-AA
1 TTTTAAA
194836 TTTTAA
1 TTTTAA
194842 TTATCATTAA
Statistics
Matches: 65, Mismatches: 12, Indels: 15
0.71 0.13 0.16
Matches are distributed among these distances:
6 13 0.20
7 37 0.57
8 10 0.15
9 5 0.08
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (7 bp):
TTTTAAA
Found at i:194811 original size:22 final size:22
Alignment explanation
Indices: 194785--194841 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
194775 TAATCTTTAT
194785 ATTTTAATTTTCAAAAATTT-AA
1 ATTTTAATTTT-AAAAATTTCAA
* * **
194807 TTTTTTATTTTTTAAATTTCAA
1 ATTTTAATTTTAAAAATTTCAA
194829 ATTTTAATTTTAA
1 ATTTTAATTTTAA
194842 TTATCATTAA
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
21 6 0.23
22 20 0.77
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.60
Consensus pattern (22 bp):
ATTTTAATTTTAAAAATTTCAA
Found at i:194820 original size:30 final size:29
Alignment explanation
Indices: 194746--194839 Score: 109
Period size: 29 Copynumber: 3.2 Consensus size: 29
194736 TTTTTTTTTA
* * *
194746 TAATTTTTGAAATTTTAAATTTTAAAATT
1 TAATTTTTTATATTTTAAATTTCAAAATT
* *
194775 TAA-TCTTTATATTTTAATTTTCAAAAATT
1 TAATTTTTTATATTTTAAATTTC-AAAATT
* *
194804 TAATTTTTTATTTTTTAAATTTCAAATTT
1 TAATTTTTTATATTTTAAATTTCAAAATT
194833 TAATTTT
1 TAATTTT
194840 AATTATCATT
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
28 14 0.26
29 24 0.44
30 16 0.30
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (29 bp):
TAATTTTTTATATTTTAAATTTCAAAATT
Found at i:194851 original size:16 final size:15
Alignment explanation
Indices: 194832--194867 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
194822 ATTTCAAATT
*
194832 TTAATTTTAATTATCA
1 TTAAATTTAATT-TCA
194848 TTAAATTTAATTTCA
1 TTAAATTTAATTTCA
194863 TTAAA
1 TTAAA
194868 ACATCAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.53
Consensus pattern (15 bp):
TTAAATTTAATTTCA
Found at i:200841 original size:36 final size:36
Alignment explanation
Indices: 200788--200939 Score: 180
Period size: 36 Copynumber: 4.2 Consensus size: 36
200778 ACTCCACTGG
* *
200788 ATCTTCGGCCTCATCTTCATGTGCACGTCAGGA-TTA
1 ATCTTCGGCCTCGTCTTCATGTGCACGT-TGGAGTTA
*
200824 ATCTTCGGCCTTGTCTTCATGTGCACGTTGGAGTTA
1 ATCTTCGGCCTCGTCTTCATGTGCACGTTGGAGTTA
*
200860 ATCTTCGGCCTCGTCTTCATGTGCACGTTGGAGTGA
1 ATCTTCGGCCTCGTCTTCATGTGCACGTTGGAGTTA
* * * * * * *
200896 ATCTTCAGTCTTGTCTTCACGTGCATGTCGGAGTTG
1 ATCTTCGGCCTCGTCTTCATGTGCACGTTGGAGTTA
*
200932 ACCTTCGG
1 ATCTTCGG
200940 TCTCATCTCC
Statistics
Matches: 100, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
35 3 0.03
36 97 0.97
ACGTcount: A:0.15, C:0.25, G:0.24, T:0.36
Consensus pattern (36 bp):
ATCTTCGGCCTCGTCTTCATGTGCACGTTGGAGTTA
Found at i:200877 original size:72 final size:72
Alignment explanation
Indices: 200788--200947 Score: 205
Period size: 72 Copynumber: 2.2 Consensus size: 72
200778 ACTCCACTGG
* * *
200788 ATCTTCGGCCTCATCTTCATGTGCACGTCAGGA-TTAATCTTCGGCCTTGTCTTCATGTGCACGT
1 ATCTTCGGCCTCATCTTCATGTGCACGT-AGGAGTGAATCTTCAGCCTTGTCTTCACGTGCACGT
*
200852 TGGAGTTA
65 CGGAGTTA
* * * *
200860 ATCTTCGGCCTCGTCTTCATGTGCACGTTGGAGTGAATCTTCAGTCTTGTCTTCACGTGCATGTC
1 ATCTTCGGCCTCATCTTCATGTGCACGTAGGAGTGAATCTTCAGCCTTGTCTTCACGTGCACGTC
*
200925 GGAGTTG
66 GGAGTTA
* *
200932 ACCTTCGGTCTCATCT
1 ATCTTCGGCCTCATCT
200948 CCTTCCTCCG
Statistics
Matches: 75, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
71 3 0.04
72 72 0.96
ACGTcount: A:0.15, C:0.26, G:0.23, T:0.36
Consensus pattern (72 bp):
ATCTTCGGCCTCATCTTCATGTGCACGTAGGAGTGAATCTTCAGCCTTGTCTTCACGTGCACGTC
GGAGTTA
Found at i:201251 original size:63 final size:63
Alignment explanation
Indices: 201179--201332 Score: 168
Period size: 63 Copynumber: 2.4 Consensus size: 63
201169 AAAATATTGA
* * * *
201179 GCATCTTATGTTGTTTGTGTAAAATAAATCGGGGATGACTGTGTTGGTG-TAGAGAATGATTAC
1 GCATGTTATGTTGTTTGTGTAAAATAAATCGGGGATGACAGTGTTGGTGCAAG-GAATGAATAC
* * * * *
201242 GCATGTTATGGTT-CTTGTGTAAAATAAATTGGTGATGAGAGTGTTGGTGCAAGGAATGAATGC
1 GCATGTTAT-GTTGTTTGTGTAAAATAAATCGGGGATGACAGTGTTGGTGCAAGGAATGAATAC
* * *
201305 GCCTGTTATGGTGTTGGTGTAAAATAAA
1 GCATGTTATGTTGTTTGTGTAAAATAAA
201333 CTGATACGTG
Statistics
Matches: 75, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
62 2 0.03
63 68 0.91
64 5 0.07
ACGTcount: A:0.28, C:0.07, G:0.30, T:0.35
Consensus pattern (63 bp):
GCATGTTATGTTGTTTGTGTAAAATAAATCGGGGATGACAGTGTTGGTGCAAGGAATGAATAC
Found at i:204593 original size:17 final size:17
Alignment explanation
Indices: 204571--204625 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 17
204561 GAGGAGTTTA
204571 GGGGTTTGTTTACTAAT
1 GGGGTTTGTTTACTAAT
** * * *
204588 GGGG-TT-CATCCAAAA
1 GGGGTTTGTTTACTAAT
204603 GGGGTTTGTTTACTAAT
1 GGGGTTTGTTTACTAAT
204620 GGGGTT
1 GGGGTT
204626 CATTGGTATG
Statistics
Matches: 26, Mismatches: 10, Indels: 4
0.65 0.25 0.10
Matches are distributed among these distances:
15 8 0.31
16 4 0.15
17 14 0.54
ACGTcount: A:0.20, C:0.09, G:0.33, T:0.38
Consensus pattern (17 bp):
GGGGTTTGTTTACTAAT
Found at i:209356 original size:21 final size:21
Alignment explanation
Indices: 209322--209393 Score: 80
Period size: 20 Copynumber: 3.5 Consensus size: 21
209312 ATTATATTGT
*
209322 TGTTATGG-TGCTTTTTTTAA
1 TGTTTTGGTTGCTTTTTTTAA
209342 TGTTTTGGTTGC-TTTTTT-A
1 TGTTTTGGTTGCTTTTTTTAA
*
209361 TGTTTTTGTGTTG-TTTTTTTAT
1 TG-TTTTG-GTTGCTTTTTTTAA
209383 TGTTTTGGTTG
1 TGTTTTGGTTG
209394 TTATTTTGGT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
19 3 0.07
20 22 0.49
21 18 0.40
22 2 0.04
ACGTcount: A:0.07, C:0.03, G:0.22, T:0.68
Consensus pattern (21 bp):
TGTTTTGGTTGCTTTTTTTAA
Found at i:209394 original size:20 final size:19
Alignment explanation
Indices: 209333--209400 Score: 82
Period size: 21 Copynumber: 3.3 Consensus size: 19
209323 GTTATGGTGC
209333 TTTTTTTAATGTTTTGGTTG
1 TTTTTTT-ATGTTTTGGTTG
*
209353 CTTTTTTATGTTTTTGTGTTG
1 TTTTTTTATG-TTTTG-GTTG
209374 TTTTTTTATTGTTTTGGTTG
1 TTTTTTTA-TGTTTTGGTTG
209394 TTATTTT
1 TT-TTTT
209401 GGTGCTATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
19 3 0.07
20 17 0.40
21 20 0.48
22 2 0.05
ACGTcount: A:0.07, C:0.01, G:0.18, T:0.74
Consensus pattern (19 bp):
TTTTTTTATGTTTTGGTTG
Found at i:209400 original size:21 final size:19
Alignment explanation
Indices: 209333--209400 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 19
209323 GTTATGGTGC
209333 TTTTTTTAATGTTTTGGTTG
1 TTTTTTT-ATGTTTTGGTTG
*
209353 CTTTTTTATGTTTTTGTGTTG
1 TTTTTTTATG-TTTTG-GTTG
209374 TTTTTTTATTGTTTTGGTTG
1 TTTTTTTA-TGTTTTGGTTG
*
209394 TTATTTT
1 TTTTTTT
209401 GGTGCTATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
19 3 0.07
20 21 0.50
21 16 0.38
22 2 0.05
ACGTcount: A:0.07, C:0.01, G:0.18, T:0.74
Consensus pattern (19 bp):
TTTTTTTATGTTTTGGTTG
Found at i:209452 original size:24 final size:24
Alignment explanation
Indices: 209417--209473 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
209407 ATTTTTTTAA
209417 ATTTTTAG-TGCTATTTTTGCTGTT
1 ATTTTT-GTTGCTATTTTTGCTGTT
*
209441 ATTTTTGTTGCTATTTTTGTTGTT
1 ATTTTTGTTGCTATTTTTGCTGTT
*
209465 -GTTTTGTTG
1 ATTTTTGTTG
209474 TTAATTTTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
23 9 0.30
24 21 0.70
ACGTcount: A:0.09, C:0.05, G:0.19, T:0.67
Consensus pattern (24 bp):
ATTTTTGTTGCTATTTTTGCTGTT
Found at i:209469 original size:12 final size:12
Alignment explanation
Indices: 209428--209481 Score: 65
Period size: 12 Copynumber: 4.6 Consensus size: 12
209418 TTTTTAGTGC
*
209428 TATTTTTGCTGT
1 TATTTTTGTTGT
*
209440 TATTTTTGTTGC
1 TATTTTTGTTGT
209452 TATTTTTGTTGT
1 TATTTTTGTTGT
*
209464 T-GTTTTGTTGT
1 TATTTTTGTTGT
*
209475 TAATTTT
1 TATTTTT
209482 ACTACTGTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
11 10 0.28
12 26 0.72
ACGTcount: A:0.09, C:0.04, G:0.17, T:0.70
Consensus pattern (12 bp):
TATTTTTGTTGT
Done.