Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015337.1 Kokia drynarioides strain JFW-HI SEQ_130384, 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: 210647
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Warning! 276 characters in sequence are not A, C, G, or T
Found at i:319 original size:18 final size:19
Alignment explanation
Indices: 286--321 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
276 AATCATTGGT
*
286 TTAATTTAGTAATATTATC
1 TTAATTGAGTAATATTATC
305 TTAATTGAG-AATATTAT
1 TTAATTGAGTAATATTAT
322 TATTTTTAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.39, C:0.03, G:0.08, T:0.50
Consensus pattern (19 bp):
TTAATTGAGTAATATTATC
Found at i:5220 original size:21 final size:20
Alignment explanation
Indices: 5183--5221 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
5173 AGATAAATTT
* *
5183 AAATGTTTAATATTCTTGTC
1 AAATGTTTAAAAATCTTGTC
5203 AAATGATTTAAAAATCTTG
1 AAATG-TTTAAAAATCTTG
5222 AATTTAAATC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.44
Consensus pattern (20 bp):
AAATGTTTAAAAATCTTGTC
Found at i:6209 original size:30 final size:30
Alignment explanation
Indices: 6174--6262 Score: 106
Period size: 30 Copynumber: 2.9 Consensus size: 30
6164 AGATTTAATG
*
6174 TGCAATTGTATACTTGAAACTTTAATTTGA
1 TGCAATTATATACTTGAAACTTTAATTTGA
* * *
6204 TGCAATTATACACGTGAAACTCTAATTCTGA
1 TGCAATTATATACTTGAAACTTTAATT-TGA
* * *
6235 TTCAAATATATACTTAAAACTTTAATTT
1 TGCAATTATATACTTGAAACTTTAATTT
6263 TAATTTAACC
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
30 24 0.50
31 24 0.50
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.40
Consensus pattern (30 bp):
TGCAATTATATACTTGAAACTTTAATTTGA
Found at i:6255 original size:31 final size:30
Alignment explanation
Indices: 6182--6262 Score: 99
Period size: 31 Copynumber: 2.7 Consensus size: 30
6172 TGTGCAATTG
*
6182 TATACTTGAAACTTTAATTTGATGCAATTA
1 TATACTTGAAACTTTAATTTGATGCAAATA
* * * *
6212 TACACGTGAAACTCTAATTCTGATTCAAATA
1 TATACTTGAAACTTTAATT-TGATGCAAATA
*
6243 TATACTTAAAACTTTAATTT
1 TATACTTGAAACTTTAATTT
6263 TAATTTAACC
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
30 17 0.41
31 24 0.59
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (30 bp):
TATACTTGAAACTTTAATTTGATGCAAATA
Found at i:6576 original size:29 final size:29
Alignment explanation
Indices: 6501--6588 Score: 86
Period size: 29 Copynumber: 3.0 Consensus size: 29
6491 GATTAAATCA
* * * *
6501 AAATTAAAGTTTCAAGTATATATTTGAACC
1 AAATTAAA-ATTCATGTATATAATTGCACC
* * *
6531 ACAATTAGAGTTGATGTATATAATTGCACC
1 A-AATTAAAATTCATGTATATAATTGCACC
*
6561 AAATTAAAATTCATGTATACAATTGCAC
1 AAATTAAAATTCATGTATATAATTGCAC
6589 ATTAAATCAA
Statistics
Matches: 47, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
29 23 0.49
30 18 0.38
31 6 0.13
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.34
Consensus pattern (29 bp):
AAATTAAAATTCATGTATATAATTGCACC
Found at i:8324 original size:21 final size:21
Alignment explanation
Indices: 8298--8354 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
8288 AAGTGTAAGC
** *
8298 GATTTATCTTCAACTATGAGT
1 GATTTATCCACAACGATGAGT
8319 GATTTATCCACAACGATGAGT
1 GATTTATCCACAACGATGAGT
* *
8340 GGTTCATCCACAACG
1 GATTTATCCACAACG
8355 TATTGGCAGC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.32
Consensus pattern (21 bp):
GATTTATCCACAACGATGAGT
Found at i:23257 original size:31 final size:31
Alignment explanation
Indices: 23216--23281 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
23206 TCACATTTTG
* * *
23216 GTCATTGAACTATTTAAAAGTTTTTATTTAA
1 GTCAATGAACTATTCAAAAATTTTTATTTAA
23247 GTCAATGAACTATTCAAAAATTTTTATTTAA
1 GTCAATGAACTATTCAAAAATTTTTATTTAA
23278 GTCA
1 GTCA
23282 CTAAGTTGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.44
Consensus pattern (31 bp):
GTCAATGAACTATTCAAAAATTTTTATTTAA
Found at i:25370 original size:116 final size:117
Alignment explanation
Indices: 25137--25363 Score: 341
Period size: 116 Copynumber: 1.9 Consensus size: 117
25127 GTTAGCCATA
* *
25137 TGATACTAATATAAGATACCCCAAAGGTAAGGGTGAGTATTCGATTGAGTCGAGTCGAATCAAAT
1 TGATACTAATATAAGATACCCCAAAGGTAAGGGTGAGTATTCAATTGAGTC--G-CAAATCAAAT
25202 CGAGTAAAAAAATTTCAAGTTAGTCGAATTGACGAATCCTATTTTAGTAACCGTG
63 CGAGTAAAAAAATTTCAAGTTAGTCGAATTGACGAATCCTATTTTAGTAACCGTG
* *
25257 TGATACTAATATAAGATACCCCAAAGG-AAGGGGTGAGTATTCAATTGAGTC-CAAATCGAGTCG
1 TGATACTAATATAAGATACCCCAAAGGTAA-GGGTGAGTATTCAATTGAGTCGCAAATCAAATCG
** *
25320 AGTAAAAAAATTTTGAGTTAGTCGAGTTGACGAATCCTATTTTA
65 AGTAAAAAAATTTCAAGTTAGTCGAATTGACGAATCCTATTTTA
25364 AGAACCGAAT
Statistics
Matches: 99, Mismatches: 7, Indels: 6
0.88 0.06 0.05
Matches are distributed among these distances:
116 50 0.51
119 2 0.02
120 47 0.47
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.29
Consensus pattern (117 bp):
TGATACTAATATAAGATACCCCAAAGGTAAGGGTGAGTATTCAATTGAGTCGCAAATCAAATCGA
GTAAAAAAATTTCAAGTTAGTCGAATTGACGAATCCTATTTTAGTAACCGTG
Found at i:30089 original size:15 final size:13
Alignment explanation
Indices: 30056--30091 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
30046 GGTTGGAGCC
30056 TGTATATATTGAA
1 TGTATATATTGAA
30069 TGTATATATTGAA
1 TGTATATATTGAA
*
30082 TGCATATATT
1 TGTATATATT
30092 TTTAACATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.36, C:0.03, G:0.14, T:0.47
Consensus pattern (13 bp):
TGTATATATTGAA
Found at i:36322 original size:95 final size:96
Alignment explanation
Indices: 36150--36329 Score: 226
Period size: 95 Copynumber: 1.9 Consensus size: 96
36140 AGGATATTTG
* *
36150 ATTATCTCGATTTGAAGAAAGGTCGCACCTAGTAAGTTAAGGCGCAATATTTCAGAATCGAAGAT
1 ATTATCTCGATTTGAAGAAAGATCGCACCTAGTAAGTTAAGGCACAATATTTCAGAATCGAAGAT
*
36215 AAGGAAACATTGCCTCGATTAAGGGTATTCA
66 AAAGAAACATTGCCTCGATTAAGGGTATTCA
* * *
36246 ATTATTTCGATTTGAGGAAA-ATTGCACCTAGTAAGTTAAGGCACAA-ATTTTC-GAAATTCGAA
1 ATTATCTCGATTTGAAGAAAGATCGCACCTAGTAAGTTAAGGCACAATA-TTTCAG-AA-TCGAA
*
36308 -ATAAA-AGAATATTGCCTCGATT
63 GATAAAGA-AACATTGCCTCGATT
36330 TTAAAGTTTT
Statistics
Matches: 73, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
94 3 0.04
95 47 0.64
96 23 0.32
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.29
Consensus pattern (96 bp):
ATTATCTCGATTTGAAGAAAGATCGCACCTAGTAAGTTAAGGCACAATATTTCAGAATCGAAGAT
AAAGAAACATTGCCTCGATTAAGGGTATTCA
Found at i:36633 original size:29 final size:29
Alignment explanation
Indices: 36554--36900 Score: 236
Period size: 29 Copynumber: 12.0 Consensus size: 29
36544 TTCGGATACC
* *
36554 CGGGGGT-AAAATGGTAATTTTTCGAAAAATT
1 CGGGGGTAAAAATGG-AATTTTT-G-GAAGTT
* * * *
36585 CGAGGTTAAAAATGGGATTTTTGGAAGCT
1 CGGGGGTAAAAATGGAATTTTTGGAAGTT
* *
36614 CAGGGGTAAAATTGGAATTTTTGGAAGTTT
1 CGGGGGTAAAAATGGAATTTTTGGAAG-TT
* * *
36644 TGGGGGTCAAAAATGGGATTTTTAGAAGTT
1 CGGGGGT-AAAAATGGAATTTTTGGAAGTT
36674 CGGGGGTAAAAATGGAATTTTT-G-A---
1 CGGGGGTAAAAATGGAATTTTTGGAAGTT
* * *
36698 ---GGTTAAAAATAGG-GTTTTCGGAAGTT
1 CGGGGGTAAAAAT-GGAATTTTTGGAAGTT
* *
36724 TGAGGGTAAAAATGGAATTTTTGGAAGTT
1 CGGGGGTAAAAATGGAATTTTTGGAAGTT
** * * *
36753 TTGGGATCAATAATGGGATTTTTGGAAGTT
1 CGGGGGT-AAAAATGGAATTTTTGGAAGTT
* *
36783 CGGGGGTAAAAATAGAATTTTTAGAAGTTT
1 CGGGGGTAAAAATGGAATTTTTGGAAG-TT
*
36813 C-GGTGTCAAAAAT-GAGATTTTTGGAAGTT
1 CGGGGGT-AAAAATGGA-ATTTTTGGAAGTT
*
36842 C-GAGGTAAAAATGGAATTTTTGGAAGTTT
1 CGGGGGTAAAAATGGAATTTTTGGAAG-TT
* *
36871 CGAGGTTAAAAATAGG-ATTTTTGGACAGTT
1 CGGGGGTAAAAAT-GGAATTTTTGGA-AGTT
36901 TAGGGACCTT
Statistics
Matches: 250, Mismatches: 44, Indels: 45
0.74 0.13 0.13
Matches are distributed among these distances:
21 13 0.05
22 3 0.01
23 1 0.00
27 1 0.00
28 20 0.08
29 96 0.38
30 77 0.31
31 32 0.13
32 7 0.03
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.34
Consensus pattern (29 bp):
CGGGGGTAAAAATGGAATTTTTGGAAGTT
Found at i:36633 original size:60 final size:59
Alignment explanation
Indices: 36556--36695 Score: 163
Period size: 60 Copynumber: 2.3 Consensus size: 59
36546 CGGATACCCG
* *
36556 GGGGTAAAATGGTAATTTTTCGAAAAATTCGAGGTTAAAAATGGGATTTTTGGAAGCTCA
1 GGGGTAAAATGG-AATTTTTCGAAAAATTCGAGGTCAAAAATGGGATTTTTAGAAGCTCA
* *** * * * *
36616 GGGGTAAAATTGGAATTTTTGGAAGTTTTGGGGGTCAAAAATGGGATTTTTAGAAGTTCG
1 GGGGTAAAA-TGGAATTTTTCGAAAAATTCGAGGTCAAAAATGGGATTTTTAGAAGCTCA
36676 GGGGTAAAAATGGAATTTTT
1 GGGGT-AAAATGGAATTTTT
36696 GAGGTTAAAA
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
60 61 0.90
61 7 0.10
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.34
Consensus pattern (59 bp):
GGGGTAAAATGGAATTTTTCGAAAAATTCGAGGTCAAAAATGGGATTTTTAGAAGCTCA
Found at i:36790 original size:59 final size:59
Alignment explanation
Indices: 36712--36900 Score: 224
Period size: 59 Copynumber: 3.2 Consensus size: 59
36702 AAAAATAGGG
* * * * * *
36712 TTTTCGGAAGTTTGAGGGTAAAAATGGAATTTTTGGAAGTTTTGG-GATCAATAATGGGA
1 TTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTCGGTG-TCAAAAATGAGA
* *
36771 TTTTTGGAAGTTCGGGGGTAAAAATAGAATTTTTAGAAGTTTCGGTGTCAAAAATGAGA
1 TTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTCGGTGTCAAAAATGAGA
* *
36830 TTTTTGGAAGTTC-GAGGTAAAAATGGAATTTTTGGAAGTTTCGAG-GTTAAAAAT-AGGA
1 TTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTCG-GTGTCAAAAATGA-GA
36888 TTTTTGGACAGTT
1 TTTTTGGA-AGTT
36901 TAGGGACCTT
Statistics
Matches: 114, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
57 1 0.01
58 45 0.39
59 67 0.59
60 1 0.01
ACGTcount: A:0.32, C:0.04, G:0.28, T:0.36
Consensus pattern (59 bp):
TTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTCGGTGTCAAAAATGAGA
Found at i:38045 original size:12 final size:12
Alignment explanation
Indices: 38028--38083 Score: 55
Period size: 11 Copynumber: 4.8 Consensus size: 12
38018 ATAATAATTT
38028 TAAATTTGAAA-A
1 TAAATTT-AAACA
*
38040 TAAATTTAAACT
1 TAAATTTAAACA
**
38052 TAAA-TTAAATT
1 TAAATTTAAACA
38063 TAAATTTAAA-A
1 TAAATTTAAACA
38074 TAAATTTAAA
1 TAAATTTAAA
38084 TTATAAAACA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
11 23 0.59
12 16 0.41
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (12 bp):
TAAATTTAAACA
Found at i:38054 original size:6 final size:6
Alignment explanation
Indices: 38026--38090 Score: 64
Period size: 6 Copynumber: 11.0 Consensus size: 6
38016 TTATAATAAT
* *
38026 TTTAAA TTTGAAA -ATAAA TTTAAA CTTAAA -TTAAA TTTAAA TTTAAA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
38073 -ATAAA TTTAAA TTATAAA
1 TTTAAA TTTAAA TT-TAAA
38091 ACAAATTTAA
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
5 12 0.24
6 30 0.61
7 7 0.14
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (6 bp):
TTTAAA
Found at i:38062 original size:17 final size:17
Alignment explanation
Indices: 38008--38118 Score: 134
Period size: 17 Copynumber: 6.4 Consensus size: 17
37998 AATTTTATTT
* *
38008 ATTTTAATTTATAATAA
1 ATTTAAATTTAAAATAA
*
38025 TTTTAAATTTGAAAATAA
1 ATTTAAATTT-AAAATAA
* *
38043 ATTTAAACTTAAATTAA
1 ATTTAAATTTAAAATAA
38060 ATTTAAATTTAAAATAA
1 ATTTAAATTTAAAATAA
*
38077 ATTTAAATTATAAAACAA
1 ATTTAAATT-TAAAATAA
38095 ATTT-AATCTTAAAATAA
1 ATTTAAAT-TTAAAATAA
38112 ATTTAAA
1 ATTTAAA
38119 ATGAGTTTGA
Statistics
Matches: 80, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
17 52 0.65
18 28 0.35
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:38065 original size:35 final size:35
Alignment explanation
Indices: 38026--38118 Score: 127
Period size: 35 Copynumber: 2.7 Consensus size: 35
38016 TTATAATAAT
**
38026 TTTAAATTTGAAAATAAATTTAAACT-TAAATTAAA
1 TTTAAATTT-AAAATAAATTTAAACTATAAAACAAA
*
38061 TTTAAATTTAAAATAAATTTAAATTATAAAACAAA
1 TTTAAATTTAAAATAAATTTAAACTATAAAACAAA
38096 TTT-AATCTTAAAATAAATTTAAA
1 TTTAAAT-TTAAAATAAATTTAAA
38119 ATGAGTTTGA
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
34 18 0.34
35 35 0.66
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (35 bp):
TTTAAATTTAAAATAAATTTAAACTATAAAACAAA
Found at i:38070 original size:52 final size:52
Alignment explanation
Indices: 38008--38118 Score: 152
Period size: 52 Copynumber: 2.1 Consensus size: 52
37998 AATTTTATTT
* * * * *
38008 ATTTTAATTTATAATAATTTTAAATT-TGAAAATAAATTTAAACTTAAATTAA
1 ATTTAAATTTAAAATAAATTTAAATTAT-AAAACAAATTTAAACTTAAAATAA
*
38060 ATTTAAATTTAAAATAAATTTAAATTATAAAACAAATTTAATCTTAAAATAA
1 ATTTAAATTTAAAATAAATTTAAATTATAAAACAAATTTAAACTTAAAATAA
38112 ATTTAAA
1 ATTTAAA
38119 ATGAGTTTGA
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
52 51 0.98
53 1 0.02
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (52 bp):
ATTTAAATTTAAAATAAATTTAAATTATAAAACAAATTTAAACTTAAAATAA
Found at i:39798 original size:22 final size:21
Alignment explanation
Indices: 39756--39798 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
39746 AGCACTAAAC
*
39756 AATAAATAAAAAAACATTTTA
1 AATAAATAAAAAAACAATTTA
* *
39777 AATACAATATAAAAATAATTTA
1 AATA-AATAAAAAAACAATTTA
39799 TCCAGAGTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (21 bp):
AATAAATAAAAAAACAATTTA
Found at i:40059 original size:13 final size:14
Alignment explanation
Indices: 40041--40071 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
40031 ATGTCTTTTC
40041 TTTTA-TTTTATTT
1 TTTTATTTTTATTT
40054 TTTTATTTTTATTT
1 TTTTATTTTTATTT
40068 TTTT
1 TTTT
40072 TATGATTAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (14 bp):
TTTTATTTTTATTT
Found at i:40069 original size:15 final size:15
Alignment explanation
Indices: 40036--40074 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
40026 AATTCATGTC
40036 TTTTCTTTTA-TTTTA
1 TTTT-TTTTATTTTTA
40051 -TTTTTTTATTTTTA
1 TTTTTTTTATTTTTA
40065 TTTTTTTTAT
1 TTTTTTTTAT
40075 GATTAGCCAG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 5 0.23
14 8 0.36
15 9 0.41
ACGTcount: A:0.13, C:0.03, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTTTTTTATTTTTA
Found at i:59273 original size:30 final size:31
Alignment explanation
Indices: 59192--59276 Score: 97
Period size: 29 Copynumber: 2.9 Consensus size: 31
59182 TCAAAAACGA
*
59192 AATTTTTG-GACATTCGGGGGT-AAAAGGGT
1 AATTTTTGAGACATTTGGGGGTCAAAAGGGT
* * *
59221 AATTTTTGA-ACGTTTCGGGGTCAAAATGG-
1 AATTTTTGAGACATTTGGGGGTCAAAAGGGT
*
59250 AATTTTGGAGACATTTGGGGGTCAAAA
1 AATTTTTGAGACATTTGGGGGTCAAAA
59277 ACATAATTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
29 25 0.54
30 21 0.46
ACGTcount: A:0.29, C:0.08, G:0.31, T:0.32
Consensus pattern (31 bp):
AATTTTTGAGACATTTGGGGGTCAAAAGGGT
Found at i:59315 original size:30 final size:30
Alignment explanation
Indices: 59238--59315 Score: 86
Period size: 31 Copynumber: 2.6 Consensus size: 30
59228 GAACGTTTCG
** **
59238 GGGTCAAAATGGAATTTTGGAGACATTTGG
1 GGGTCAAAATATAATTTTGGAGACATTTAA
*
59268 GGGTCAAAAACATAATTTTGGAGA-AGTTTAA
1 GGGTC-AAAATATAATTTTGGAGACA-TTTAA
59299 GGGTCAAAATATAATTT
1 GGGTCAAAATATAATTT
59316 CTAGATAGTT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
30 17 0.43
31 23 0.57
ACGTcount: A:0.37, C:0.06, G:0.26, T:0.31
Consensus pattern (30 bp):
GGGTCAAAATATAATTTTGGAGACATTTAA
Found at i:59590 original size:29 final size:29
Alignment explanation
Indices: 59536--59639 Score: 138
Period size: 30 Copynumber: 3.5 Consensus size: 29
59526 TAAATTGTAA
* *
59536 TAAAAATGTAATTTTTAGAAGTTTTGGGG
1 TAAAAATGGAATTTTTGGAAGTTTTGGGG
*
59565 CTAAAAATGGAATTTTTGGAAGTTTGGGGG
1 -TAAAAATGGAATTTTTGGAAGTTTTGGGG
*
59595 TAAAAACGTGAA-TTTTGGAAGTTTTGGGG
1 TAAAAATG-GAATTTTTGGAAGTTTTGGGG
59624 TCAAAAATGGAATTTT
1 T-AAAAATGGAATTTT
59640 GGAGATGTTT
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
29 27 0.42
30 38 0.58
ACGTcount: A:0.34, C:0.03, G:0.27, T:0.37
Consensus pattern (29 bp):
TAAAAATGGAATTTTTGGAAGTTTTGGGG
Found at i:59668 original size:59 final size:59
Alignment explanation
Indices: 59548--59690 Score: 157
Period size: 59 Copynumber: 2.4 Consensus size: 59
59538 AAAATGTAAT
* *
59548 TTTTAGAAGTTTTGGGG-CTAAAAATGGAATTTTTGGAAGTTTGGGGGTAAAAACGTGAA
1 TTTTGGAAGTTTTGGGGTC-AAAAATGGAATTTTTGGAAGTTTGGGGGTAAAAACATGAA
** *
59607 TTTTGGAAGTTTTGGGGTCAAAAATGGAA-TTTTGGAGATGTTTGTTGGTCAAAACAT-AA
1 TTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTGGA-A-GTTTGGGGGTAAAAACATGAA
**
59666 TTTTGGAGAACTTTGAGGGTCAAAA
1 TTTTGGA-AGTTTTG-GGGTCAAAA
59691 TATAATGTTT
Statistics
Matches: 72, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
58 7 0.10
59 36 0.50
60 20 0.28
61 9 0.12
ACGTcount: A:0.31, C:0.05, G:0.29, T:0.35
Consensus pattern (59 bp):
TTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTTGGGGGTAAAAACATGAA
Found at i:59670 original size:30 final size:30
Alignment explanation
Indices: 59617--59703 Score: 88
Period size: 30 Copynumber: 2.9 Consensus size: 30
59607 TTTTGGAAGT
**
59617 TTTG-GGGTCAAAA-ATGGAATTTTGGAGATG
1 TTTGAGGGTCAAAACAT--AATTTTGGAGAAC
**
59647 TTTGTTGGTCAAAACATAATTTTGGAGAAC
1 TTTGAGGGTCAAAACATAATTTTGGAGAAC
*
59677 TTTGAGGGTCAAAATATAATGTTTGGA
1 TTTGAGGGTCAAAACATAAT-TTTGGA
59704 TAGTTTAGGG
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
30 32 0.67
31 14 0.29
32 2 0.04
ACGTcount: A:0.32, C:0.06, G:0.26, T:0.36
Consensus pattern (30 bp):
TTTGAGGGTCAAAACATAATTTTGGAGAAC
Found at i:60812 original size:3 final size:3
Alignment explanation
Indices: 60806--60895 Score: 67
Period size: 3 Copynumber: 29.7 Consensus size: 3
60796 ATTTTTTTTA
* * * *
60806 TAT TATT TAT TAT TAT TAA TA- AATT TAT TAT TGT TAT TAT TAA TAT
1 TAT TA-T TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT
* * * *
60852 TAT CA- TAT TCAT CAT CAT CAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
60896 ATGTTCATTC
Statistics
Matches: 71, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
2 2 0.03
3 63 0.89
4 6 0.08
ACGTcount: A:0.36, C:0.06, G:0.01, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:61629 original size:17 final size:17
Alignment explanation
Indices: 61604--61640 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
61594 TTTTAATTTT
*
61604 ATTTTAATTTAAAATAA
1 ATTTAAATTTAAAATAA
*
61621 ATTTAAATTTAAAGTAA
1 ATTTAAATTTAAAATAA
61638 ATT
1 ATT
61641 CAAACTCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:73167 original size:30 final size:31
Alignment explanation
Indices: 73133--73196 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
73123 AGTCAATAAT
*
73133 TGACGTTATCAAAAA-TAACAAAACAATCAC
1 TGACGTTATAAAAAAGTAACAAAACAATCAC
* *
73163 TGACGTTATAAAAAAGTGACAAAACAGTCAC
1 TGACGTTATAAAAAAGTAACAAAACAATCAC
73194 TGA
1 TGA
73197 TTAATATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 14 0.47
31 16 0.53
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.20
Consensus pattern (31 bp):
TGACGTTATAAAAAAGTAACAAAACAATCAC
Found at i:90418 original size:37 final size:37
Alignment explanation
Indices: 90368--90464 Score: 167
Period size: 37 Copynumber: 2.6 Consensus size: 37
90358 TACTTATTCA
90368 TAAAATCTAGAATCTTATTTTATTTTTAATTAAAAAG
1 TAAAATCTAGAATCTTATTTTATTTTTAATTAAAAAG
*
90405 TAAAATCTAGAATCCTATTTTATTTTTAATTAAAAAG
1 TAAAATCTAGAATCTTATTTTATTTTTAATTAAAAAG
*
90442 TAAAATCTAGAATCCTTTTTTTA
1 TAAAATCTAGAAT-CTTATTTTA
90465 AAATATGTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
37 49 0.88
38 7 0.12
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.45
Consensus pattern (37 bp):
TAAAATCTAGAATCTTATTTTATTTTTAATTAAAAAG
Found at i:98882 original size:15 final size:14
Alignment explanation
Indices: 98840--98883 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
98830 TATATTTTTA
*
98840 ATTAAATTTAAATA
1 ATTAAATTTAAATT
* *
98854 AATAAATTTTAATT
1 ATTAAATTTAAATT
98868 ATTAAATATTAAATT
1 ATTAAAT-TTAAATT
98883 A
1 A
98884 GCTGGATCTA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
14 17 0.71
15 7 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTAAATTTAAATT
Found at i:99992 original size:7 final size:7
Alignment explanation
Indices: 99978--100007 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
99968 AAAAAGAATG
99978 ACATGGC
1 ACATGGC
*
99985 ATATGGC
1 ACATGGC
99992 ACATGGC
1 ACATGGC
99999 ACATGGC
1 ACATGGC
100006 AC
1 AC
100008 GAACCTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.30, C:0.27, G:0.27, T:0.17
Consensus pattern (7 bp):
ACATGGC
Found at i:110405 original size:30 final size:30
Alignment explanation
Indices: 110369--110460 Score: 125
Period size: 30 Copynumber: 3.1 Consensus size: 30
110359 CATCAAAACA
*
110369 GGTTAAATTTTAATTTTTGAAAACTTTAGG
1 GGTTAAATTTGAATTTTTGAAAACTTTAGG
110399 GGTTAAATTTGAATTTTTGGAAAA-TTT-GG
1 GGTTAAATTTGAATTTTT-GAAAACTTTAGG
* * *
110428 GGTGAAATTTGAATTTTTGATAACTTTAAG
1 GGTTAAATTTGAATTTTTGAAAACTTTAGG
110458 GGT
1 GGT
110461 CAAAAAATGA
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
28 4 0.07
29 22 0.40
30 24 0.44
31 5 0.09
ACGTcount: A:0.32, C:0.02, G:0.22, T:0.45
Consensus pattern (30 bp):
GGTTAAATTTGAATTTTTGAAAACTTTAGG
Found at i:111825 original size:18 final size:18
Alignment explanation
Indices: 111787--111835 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
111777 AGCATTAATT
111787 ATAATTTCTTAAA-AAATA
1 ATAATTT-TTAAATAAATA
111805 ATAATTTTTAAATGAAA-A
1 ATAATTTTTAAAT-AAATA
*
111823 AT-ATTTATAAATA
1 ATAATTTTTAAATA
111836 TATATATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
16 1 0.04
17 14 0.50
18 10 0.36
19 3 0.11
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (18 bp):
ATAATTTTTAAATAAATA
Found at i:111849 original size:20 final size:20
Alignment explanation
Indices: 111824--111865 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
111814 AAATGAAAAA
111824 TATTTATAAATATATATATT
1 TATTTATAAATATATATATT
**
111844 TATTTATATTTATATATATT
1 TATTTATAAATATATATATT
111864 TA
1 TA
111866 AGTAGCTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TATTTATAAATATATATATT
Found at i:111852 original size:10 final size:10
Alignment explanation
Indices: 111834--111865 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
111824 TATTTATAAA
111834 TATATATATT
1 TATATATATT
*
111844 TATTTATATT
1 TATATATATT
111854 TATATATATT
1 TATATATATT
111864 TA
1 TA
111866 AGTAGCTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TATATATATT
Found at i:111852 original size:16 final size:16
Alignment explanation
Indices: 111823--111865 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
111813 TAAATGAAAA
**
111823 ATATTTATAAATATAT
1 ATATTTATTTATATAT
*
111839 ATATTTATTTATATTT
1 ATATTTATTTATATAT
*
111855 ATATATATTTA
1 ATATTTATTTA
111866 AGTAGCTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATATTTATTTATATAT
Found at i:116760 original size:6 final size:6
Alignment explanation
Indices: 116749--116787 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
116739 TGGGTCGGTG
116749 AGGGAT AGGGAT AGGGAT AGGGAT AGGGAT AGGGAT AGG
1 AGGGAT AGGGAT AGGGAT AGGGAT AGGGAT AGGGAT AGG
116788 AAGGGAGTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.51, T:0.15
Consensus pattern (6 bp):
AGGGAT
Found at i:130710 original size:31 final size:31
Alignment explanation
Indices: 130665--130725 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
130655 CCAAAAGTGA
*
130665 GCTGTTGTTACTTAGGACATGAATTTAAATT
1 GCTGTTCTTACTTAGGACATGAATTTAAATT
*
130696 GCTGTTCTTTCTTAGGACATGAATTTAAAT
1 GCTGTTCTTACTTAGGACATGAATTTAAAT
130726 CTTCTAGAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.28, C:0.11, G:0.18, T:0.43
Consensus pattern (31 bp):
GCTGTTCTTACTTAGGACATGAATTTAAATT
Found at i:136622 original size:8 final size:8
Alignment explanation
Indices: 136609--136634 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
136599 ATTACAAGTA
136609 AAAAAAAT
1 AAAAAAAT
136617 AAAAAAAT
1 AAAAAAAT
136625 AAAAAAAT
1 AAAAAAAT
136633 AA
1 AA
136635 TACATTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAAAAT
Found at i:141776 original size:11 final size:10
Alignment explanation
Indices: 141755--141796 Score: 52
Period size: 9 Copynumber: 4.3 Consensus size: 10
141745 CATGCTAATA
141755 TTTT-TAAAT
1 TTTTATAAAT
141764 TTTTATGAAAT
1 TTTTAT-AAAT
*
141775 TTTTATAATT
1 TTTTATAAAT
141785 TTTTA-AAAT
1 TTTTATAAAT
141794 TTT
1 TTT
141797 GAATTTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 10 0.34
10 9 0.31
11 10 0.34
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (10 bp):
TTTTATAAAT
Found at i:141778 original size:19 final size:19
Alignment explanation
Indices: 141754--141796 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
141744 TCATGCTAAT
*
141754 ATTTTTA-AATTTTTATGAA
1 ATTTTTATAATTTTT-TAAA
141773 ATTTTTATAATTTTTTAAA
1 ATTTTTATAATTTTTTAAA
141792 ATTTT
1 ATTTT
141797 GAATTTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (19 bp):
ATTTTTATAATTTTTTAAA
Found at i:143031 original size:19 final size:18
Alignment explanation
Indices: 143005--143050 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
142995 TATTAAATTT
143005 ATTA-AATTTTAATAAAA
1 ATTAGAATTTTAATAAAA
* *
143022 ATATATAA-TTTATTAAAA
1 AT-TAGAATTTTAATAAAA
143040 ATTAGAATTTT
1 ATTAGAATTTT
143051 TTTAATGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
17 6 0.25
18 16 0.67
19 2 0.08
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (18 bp):
ATTAGAATTTTAATAAAA
Found at i:143620 original size:6 final size:7
Alignment explanation
Indices: 143593--143619 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
143583 CATAGGCTTA
143593 ATTTTTT
1 ATTTTTT
143600 ATTTTTT
1 ATTTTTT
143607 ATTTTTT
1 ATTTTTT
143614 ATTTTT
1 ATTTTT
143620 AAGTTTGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
ATTTTTT
Found at i:150675 original size:19 final size:19
Alignment explanation
Indices: 150633--150675 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
150623 TATTTTTTTA
* *
150633 ATAAAATTTTTAAAATTTT
1 ATAATATTTTTAAAATATT
*
150652 ATAATATTTTTATAATATT
1 ATAATATTTTTAAAATATT
*
150671 CTAAT
1 ATAAT
150676 GGGTCAAACA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (19 bp):
ATAATATTTTTAAAATATT
Found at i:156205 original size:27 final size:27
Alignment explanation
Indices: 156174--156227 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
156164 CTCAACAACC
*
156174 CGAATCGAATCGAATCAAATC-GTTGAT
1 CGAATCGAATCGAACCAAA-CAGTTGAT
* *
156201 CGAATTGAATTGAACCAAACAGTTGAT
1 CGAATCGAATCGAACCAAACAGTTGAT
156228 TGAACCAAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 1 0.04
27 22 0.96
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.26
Consensus pattern (27 bp):
CGAATCGAATCGAACCAAACAGTTGAT
Found at i:156743 original size:11 final size:10
Alignment explanation
Indices: 156715--156749 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
156705 TGTAATGTTG
156715 TGTTGTGATA
1 TGTTGTGATA
*
156725 TTTTGTGATTA
1 TGTTGTGA-TA
156736 TGTTGTGATA
1 TGTTGTGATA
156746 TGTT
1 TGTT
156750 ATCAATGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.17, C:0.00, G:0.26, T:0.57
Consensus pattern (10 bp):
TGTTGTGATA
Found at i:157387 original size:4 final size:4
Alignment explanation
Indices: 157380--157404 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
157370 TGTGTGTGTG
157380 TGTA TGTA TGTA TGTA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA T
157405 ATGAATGTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TGTA
Found at i:187702 original size:20 final size:21
Alignment explanation
Indices: 187677--187716 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
187667 CATTTTGAAT
187677 GGTTCA-GAGGAAAATGGTGG
1 GGTTCACGAGGAAAATGGTGG
*
187697 GGTTCACGAGGAAATTGGTG
1 GGTTCACGAGGAAAATGGTG
187717 ACAGTTACAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.28, C:0.07, G:0.42, T:0.23
Consensus pattern (21 bp):
GGTTCACGAGGAAAATGGTGG
Found at i:190272 original size:3 final size:3
Alignment explanation
Indices: 190257--190293 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
190247 GCCTCCCACT
*
190257 TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
190294 CTCATCGTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:191241 original size:26 final size:26
Alignment explanation
Indices: 191211--191264 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
191201 GAAAGTAAGT
191211 TGGGAGAGAGAATATGCTTCTTTGTC
1 TGGGAGAGAGAATATGCTTCTTTGTC
191237 TGGGAGAGAGAATATGCTTCTTTGTC
1 TGGGAGAGAGAATATGCTTCTTTGTC
191263 TG
1 TG
191265 AATGGTCACC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.22, C:0.11, G:0.31, T:0.35
Consensus pattern (26 bp):
TGGGAGAGAGAATATGCTTCTTTGTC
Found at i:197921 original size:52 final size:52
Alignment explanation
Indices: 197835--198079 Score: 287
Period size: 52 Copynumber: 4.7 Consensus size: 52
197825 AATGAAAAAG
* * * *
197835 GGTCTGATGATTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTATGA
1 GGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTATAA
* *
197887 GGTCCGATGACTAAGTATCATCGTGAGTATATGAAATCCTTTATGGATT-TAAA
1 GGTCCGATGACTAAGTGTCATCGTGAGTATATG-AATCCTTTACGGATTAT-AA
* *
197940 GGTCCGATGACTAAGTGTCATCGTGAGAATACGAATCCTTTACGGATTA-AGA
1 GGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTATA-A
** * * ***
197992 GGTCCGATGACTCTGTGTCATCGTGAGTATACGAATCCCTCGTGGATTATAA
1 GGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTATAA
* * *
198044 GGTCCGGTGGCTATGTGTCATCGTGAGTATATGAAT
1 GGTCCGATGACTAAGTGTCATCGTGAGTATATGAAT
198080 GAAGTGAAAT
Statistics
Matches: 167, Mismatches: 21, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
51 1 0.01
52 120 0.72
53 46 0.28
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (52 bp):
GGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTATAA
Found at i:198022 original size:105 final size:104
Alignment explanation
Indices: 197835--198079 Score: 314
Period size: 105 Copynumber: 2.3 Consensus size: 104
197825 AATGAAAAAG
* * *
197835 GGTCTGATGATTAAGTGTCATCGTGAGTAA-ATGAATCCTTTACGGATTATGAGGTCCGATGACT
1 GGTCCGATGACTAAGTGTCATCGTGAG-AATATGAATCCTTTACGGATTAAGAGGTCCGATGACT
* * *
197899 AAGTATCATCGTGAGTATATGAAATCCTTTATGGATT-TAAA
65 AAGTATCATCGTGAGTATACG-AATCCCTCATGGATTAT-AA
* *
197940 GGTCCGATGACTAAGTGTCATCGTGAGAATACGAATCCTTTACGGATTAAGAGGTCCGATGACTC
1 GGTCCGATGACTAAGTGTCATCGTGAGAATATGAATCCTTTACGGATTAAGAGGTCCGATGACTA
* * *
198005 TGTGTCATCGTGAGTATACGAATCCCTCGTGGATTATAA
66 AGTATCATCGTGAGTATACGAATCCCTCATGGATTATAA
* * * *
198044 GGTCCGGTGGCTATGTGTCATCGTGAGTATATGAAT
1 GGTCCGATGACTAAGTGTCATCGTGAGAATATGAAT
198080 GAAGTGAAAT
Statistics
Matches: 122, Mismatches: 16, Indels: 5
0.85 0.11 0.03
Matches are distributed among these distances:
104 47 0.39
105 75 0.61
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (104 bp):
GGTCCGATGACTAAGTGTCATCGTGAGAATATGAATCCTTTACGGATTAAGAGGTCCGATGACTA
AGTATCATCGTGAGTATACGAATCCCTCATGGATTATAA
Found at i:202231 original size:11 final size:11
Alignment explanation
Indices: 202217--202272 Score: 58
Period size: 11 Copynumber: 4.9 Consensus size: 11
202207 TTGTTTAAAA
202217 TTTAAATTTAT
1 TTTAAATTTAT
*
202228 TTTAAATTTAAA
1 TTTAAATTT-AT
* *
202240 TTTAAATTAAG
1 TTTAAATTTAT
*
202251 TTTAAAATTAT
1 TTTAAATTTAT
202262 TTTCAAATTTA
1 TTT-AAATTTA
202273 AAATTTAAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
11 21 0.58
12 15 0.42
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:202249 original size:5 final size:6
Alignment explanation
Indices: 202183--202287 Score: 71
Period size: 6 Copynumber: 18.2 Consensus size: 6
202173 CCATACTTCC
* * * *
202183 TTTAAA TTT-AT TTTAAA ATTAAA TTT--G TTTAAAA TTTAAA TTT-AT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA
* * *
202228 TTTAAA TTTAAA TTTAAA -TTAAG TTTAAA ATT-AT TTTCAAA TTTAAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTT-AAA
202276 TTTAAA -TTAAA T
1 TTTAAA TTTAAA T
202288 AAAACCCAAA
Statistics
Matches: 75, Mismatches: 15, Indels: 18
0.69 0.14 0.17
Matches are distributed among these distances:
4 3 0.04
5 20 0.27
6 39 0.52
7 13 0.17
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:202249 original size:17 final size:17
Alignment explanation
Indices: 202183--202279 Score: 113
Period size: 17 Copynumber: 5.6 Consensus size: 17
202173 CCATACTTCC
202183 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* * *
202200 ATTAAATTTGTTTAAAA
1 TTTAAATTTATTTTAAA
202217 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
** *
202234 TTTAAATTTAAATTAAG
1 TTTAAATTTATTTTAAA
*
202251 TTTAAAATTATTTTCAAA
1 TTTAAATTTATTTT-AAA
202269 TTTAAAATTTA
1 TTT-AAATTTA
202280 AATTAAATAA
Statistics
Matches: 64, Mismatches: 14, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
17 53 0.83
18 5 0.08
19 6 0.09
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:202255 original size:34 final size:34
Alignment explanation
Indices: 202183--202287 Score: 131
Period size: 34 Copynumber: 3.0 Consensus size: 34
202173 CCATACTTCC
* **
202183 TTTAAATTTATTTTAAAATTAAATTT-GTTTAAAA
1 TTTAAATTTATTTTAAATTTAAATTTAAATT-AAA
*
202217 TTTAAATTTATTTTAAATTTAAATTTAAATTAAG
1 TTTAAATTTATTTTAAATTTAAATTTAAATTAAA
*
202251 TTTAAAATTATTTTCAAATTTAAAATTTAAATTAAA
1 TTTAAATTTATTTT-AAATTT-AAATTTAAATTAAA
202287 T
1 T
202288 AAAACCCAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
34 40 0.65
35 8 0.13
36 14 0.23
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (34 bp):
TTTAAATTTATTTTAAATTTAAATTTAAATTAAA
Found at i:203041 original size:27 final size:28
Alignment explanation
Indices: 202995--203047 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
202985 AAGTGGGCGG
* *
202995 TTTTTAAAATATTTATTAATAATAATTT
1 TTTTTAAAATATATAATAATAATAATTT
*
203023 TTTTTAAAATA-ATAATAATATTAAT
1 TTTTTAAAATATATAATAATAATAAT
203048 AATATTAATG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 11 0.50
28 11 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (28 bp):
TTTTTAAAATATATAATAATAATAATTT
Found at i:204141 original size:29 final size:29
Alignment explanation
Indices: 204098--204479 Score: 199
Period size: 29 Copynumber: 13.0 Consensus size: 29
204088 TAAGGTCCCT
204098 AAACTTTCCAAAAATTACCATTTTACCCCC
1 AAAC-TTCCAAAAATTACCATTTTACCCCC
* ** *
204128 AAACTT-CAAAAAAT-CTCATTTTTGACATCG
1 AAACTTCCAAAAATTAC-CA-TTTT-ACCCCC
* * *
204158 AACCTT-CTAAAATTATCATTTTACCCCC
1 AAACTTCCAAAAATTACCATTTTACCCCC
* * *
204186 GAACTTCCAAAAA-TCCCATTTTTGA-CCCG
1 AAACTTCCAAAAATTACCA-TTTT-ACCCCC
* *
204215 AACCTTCTAAAAATTACCATTTTACCCCC
1 AAACTTCCAAAAATTACCATTTTACCCCC
* * * *
204244 GAACTTCCAAAAA-TCCCATTTTTGACTCCG
1 AAACTTCCAAAAATTACCA-TTTT-ACCCCC
* *
204274 AACCTTCTAAAAATTACCATTTTACCCCC
1 AAACTTCCAAAAATTACCATTTTACCCCC
* *** *
204303 GAACTT-CAAAAATCTCATTTTTTTACCCCG
1 AAACTTCCAAAAAT-T-ACCATTTTACCCCC
* * *
204333 AACCTTCCGAAAATTACCATTTTACCCCT
1 AAACTTCCAAAAATTACCATTTTACCCCC
* * *
204362 AAACTTCCAAAAA-TCCCATTTTTGACTCCG
1 AAACTTCCAAAAATTACCA-TTTT-ACCCCC
* * * *
204392 AACCTTTCTAAAAATCACCATTTTACCCTC
1 AAAC-TTCCAAAAATTACCATTTTACCCCC
* * * *
204422 GAACTTCCAAAAA-TCCCATTTTTGACTCCG
1 AAACTTCCAAAAATTACCA-TTTT-ACCCCC
* * *
204452 AACCTTCC-AAAACTACCATTTTGCCCCC
1 AAACTTCCAAAAATTACCATTTTACCCCC
204480 GTGCATCTGA
Statistics
Matches: 256, Mismatches: 74, Indels: 46
0.68 0.20 0.12
Matches are distributed among these distances:
27 1 0.00
28 40 0.16
29 107 0.42
30 83 0.32
31 22 0.09
32 3 0.01
ACGTcount: A:0.33, C:0.32, G:0.04, T:0.31
Consensus pattern (29 bp):
AAACTTCCAAAAATTACCATTTTACCCCC
Found at i:204304 original size:59 final size:59
Alignment explanation
Indices: 204107--204480 Score: 542
Period size: 58 Copynumber: 6.4 Consensus size: 59
204097 TAAACTTTCC
* * *
204107 AAAAATTACCATTTTACCCCCAAACTTCAAAAAATCTCATTTTTGACAT-CGAACCTTCT
1 AAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGAC-TCCGAACCTTCT
*
204166 -AAAATTATCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGAC-CCGAACCTTCT
1 AAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACTCCGAACCTTCT
204223 AAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACTCCGAACCTTCT
1 AAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACTCCGAACCTTCT
* * * *
204282 AAAAATTACCATTTTACCCCCGAACTT-CAAAAATCTCATTTTTTTACCCCGAACCTTCC
1 AAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCA-TTTTTGACTCCGAACCTTCT
* **
204341 GAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACTCCGAACCTTTCT
1 AAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACTCCGAACC-TTCT
* *
204401 AAAAATCACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACTCCGAACCTTC-
1 AAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACTCCGAACCTTCT
* * *
204459 CAAAACTACCATTTTGCCCCCG
1 AAAAATTACCATTTTACCCCCG
204481 TGCATCTGAA
Statistics
Matches: 283, Mismatches: 26, Indels: 13
0.88 0.08 0.04
Matches are distributed among these distances:
57 10 0.04
58 114 0.40
59 96 0.34
60 63 0.22
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.31
Consensus pattern (59 bp):
AAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACTCCGAACCTTCT
Found at i:204504 original size:118 final size:116
Alignment explanation
Indices: 204103--204480 Score: 546
Period size: 118 Copynumber: 3.2 Consensus size: 116
204093 TCCCTAAACT
* * *
204103 TTCCAAAAATTACCATTTTACCCCCAAACTTCAAAAAATCTCATTTTTGACAT-CGAACCTTCT-
1 TTCC-AAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGAC-TCCGAACCTTCTA
*
204166 AAAATTATCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCGAACC
64 AAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCGAACC
*
204219 TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACTCCGAACCTTCTAA
1 TTC-CAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACTCCGAACCTTCTAA
* *
204284 AAATTACCATTTTACCCCCGAACTT-CAAAAATCTCATTTTTTTACCCCGAACC
65 AAATTACCATTTTACCCCCGAACTTCCAAAAATCCCA-TTTTTGA-CCCGAACC
**
204337 TTCCGAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACTCCGAACCTTTCTA
1 TTCC-AAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACTCCGAACC-TTCTA
* *
204402 AAAATCACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACTCCGAACC
64 AAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGAC-CCGAACC
* *
204456 TTCCAAAACTACCATTTTGCCCCCG
1 TTCCAAAATTACCATTTTACCCCCG
204481 TGCATCTGAA
Statistics
Matches: 235, Mismatches: 18, Indels: 16
0.87 0.07 0.06
Matches are distributed among these distances:
115 1 0.00
116 66 0.28
117 31 0.13
118 81 0.34
119 46 0.20
120 10 0.04
ACGTcount: A:0.32, C:0.32, G:0.05, T:0.31
Consensus pattern (116 bp):
TTCCAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACTCCGAACCTTCTAAA
AATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCGAACC
Found at i:208136 original size:14 final size:14
Alignment explanation
Indices: 208117--208144 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
208107 AGGAGGGTGT
208117 AATGTTACATTTGA
1 AATGTTACATTTGA
208131 AATGTTACATTTGA
1 AATGTTACATTTGA
208145 TGAACCAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (14 bp):
AATGTTACATTTGA
Done.