Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014145.1 Kokia drynarioides strain JFW-HI SEQ_129178, 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: 260204
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 82 characters in sequence are not A, C, G, or T
Found at i:7130 original size:12 final size:12
Alignment explanation
Indices: 7110--7169 Score: 57
Period size: 12 Copynumber: 4.8 Consensus size: 12
7100 TTCAGCATTC
*
7110 TTTTGAAAAATG
1 TTTTAAAAAATG
*
7122 TTTTAAAAAGTG
1 TTTTAAAAAATG
* *
7134 TTGTAAAAAAGTAA
1 TTTTAAAAAA-T-G
7148 TTTTAAAAAATG
1 TTTTAAAAAATG
*
7160 TTCTAAAAAA
1 TTTTAAAAAA
7170 GTTAAAAATG
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
12 27 0.71
13 2 0.05
14 9 0.24
ACGTcount: A:0.50, C:0.02, G:0.12, T:0.37
Consensus pattern (12 bp):
TTTTAAAAAATG
Found at i:7152 original size:26 final size:26
Alignment explanation
Indices: 7122--7171 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
7112 TTGAAAAATG
* *
7122 TTTTAAAAAGTGTTGTAAAAAAGTAA
1 TTTTAAAAAATGTTCTAAAAAAGTAA
7148 TTTTAAAAAATGTTCTAAAAAAGT
1 TTTTAAAAAATGTTCTAAAAAAGT
7172 TAAAAATGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.50, C:0.02, G:0.12, T:0.36
Consensus pattern (26 bp):
TTTTAAAAAATGTTCTAAAAAAGTAA
Found at i:7771 original size:18 final size:19
Alignment explanation
Indices: 7750--7810 Score: 65
Period size: 18 Copynumber: 3.3 Consensus size: 19
7740 GAAACTTGTA
7750 AAAATTTA-AAAAAATTAG
1 AAAATTTATAAAAAATTAG
**
7768 AAAA-TTATCTAAAATTATG
1 AAAATTTATAAAAAATTA-G
*
7787 AAAGTTTATAAAAAATTA-
1 AAAATTTATAAAAAATTAG
7805 AAAATT
1 AAAATT
7811 ATATCACACG
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
17 3 0.09
18 16 0.47
19 4 0.12
20 11 0.32
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.33
Consensus pattern (19 bp):
AAAATTTATAAAAAATTAG
Found at i:20622 original size:1 final size:1
Alignment explanation
Indices: 20576--20603 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
20566 GGTAAAATTT
20576 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
20604 NNNNNNNNNN
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:23791 original size:9 final size:9
Alignment explanation
Indices: 23777--23806 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
23767 TACATATTCC
23777 TTTTCTTTT
1 TTTTCTTTT
23786 TTTTC-TTT
1 TTTTCTTTT
23794 TTTTCTTTT
1 TTTTCTTTT
23803 TTTT
1 TTTT
23807 TGTGAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (9 bp):
TTTTCTTTT
Found at i:26311 original size:2 final size:2
Alignment explanation
Indices: 26304--26328 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
26294 CTCTAATAAT
26304 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
26329 TATTTTAATA
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:26361 original size:29 final size:28
Alignment explanation
Indices: 26329--26386 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
26319 ATATATATAT
26329 TATTTTAATAATTTTTTAATATTTAAAAA
1 TATTTTAATAATTTTTT-ATATTTAAAAA
** * *
26358 TATTTTTTTTATTTTTTATTTTTAAAAA
1 TATTTTAATAATTTTTTATATTTAAAAA
26386 T
1 T
26387 TAAATAAATG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
28 11 0.44
29 14 0.56
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (28 bp):
TATTTTAATAATTTTTTATATTTAAAAA
Found at i:42578 original size:39 final size:39
Alignment explanation
Indices: 42520--42595 Score: 109
Period size: 39 Copynumber: 1.9 Consensus size: 39
42510 GATTTACAAG
* *
42520 GGGTCCTTGAAGCAGTACTTTCCACCTTATACACTTACT
1 GGGTCCTTGAACCAGTACTTTCAACCTTATACACTTACT
*
42559 GGGTCCTTGAACC-GATACTTTCAACCTTGTACACTTA
1 GGGTCCTTGAACCAG-TACTTTCAACCTTATACACTTA
42596 ATCCATAGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
38 1 0.03
39 32 0.97
ACGTcount: A:0.24, C:0.28, G:0.16, T:0.33
Consensus pattern (39 bp):
GGGTCCTTGAACCAGTACTTTCAACCTTATACACTTACT
Found at i:57097 original size:9 final size:9
Alignment explanation
Indices: 57083--57115 Score: 57
Period size: 9 Copynumber: 3.6 Consensus size: 9
57073 GTAATTTCAT
57083 AAAAAATAAA
1 AAAAAAT-AA
57093 AAAAAATAA
1 AAAAAATAA
57102 AAAAAATAA
1 AAAAAATAA
57111 AAAAA
1 AAAAA
57116 TCCAAATTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 16 0.70
10 7 0.30
ACGTcount: A:0.91, C:0.00, G:0.00, T:0.09
Consensus pattern (9 bp):
AAAAAATAA
Found at i:57098 original size:10 final size:10
Alignment explanation
Indices: 57083--57115 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
57073 GTAATTTCAT
57083 AAAAAATAAA
1 AAAAAATAAA
57093 AAAAAAT-AA
1 AAAAAATAAA
57102 AAAAAATAAA
1 AAAAAATAAA
57112 AAAA
1 AAAA
57116 TCCAAATTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 9 0.41
10 13 0.59
ACGTcount: A:0.91, C:0.00, G:0.00, T:0.09
Consensus pattern (10 bp):
AAAAAATAAA
Found at i:67507 original size:168 final size:169
Alignment explanation
Indices: 67229--67566 Score: 660
Period size: 168 Copynumber: 2.0 Consensus size: 169
67219 TTTCGGCCAC
67229 CATGCATATATATATATATATTCGCTGGTCCAACATTTTTCTTCTTCCCCCCTCTCCACTTTTTT
1 CATGCATATATATATATATATTCGCTGGTCCAACATTTTTCTTCTTCCCCCCTCTCCACTTTTTT
67294 TACTCGACGTATTGCTATTGAAGTTTTGACAATATTCTGCAGCCAT-AAAAAAAAAAAAATGTCA
66 TACTCGACGTATTGCTATTGAAGTTTTGACAATATTCTGCAGCCATAAAAAAAAAAAAAATGTCA
67358 GTTTACGCCAAGATTGGTCTCCCACTTTGGAATTTTGAA
131 GTTTACGCCAAGATTGGTCTCCCACTTTGGAATTTTGAA
67397 CATGCATATATATATATATATTCGCTGGTCCAACATTTTTCTTCTTCCCCCCTCTCCACTTTTTT
1 CATGCATATATATATATATATTCGCTGGTCCAACATTTTTCTTCTTCCCCCCTCTCCACTTTTTT
67462 TACTCGACGTATTGCTATTGAAGTTTTGACAATATTCTGCAGCCATAAAAAAAAAAAAAAATGTC
66 TACTCGACGTATTGCTATTGAAGTTTTGACAATATTCTGCAGCCAT-AAAAAAAAAAAAAATGTC
67527 AGTTTACGCCAAGATTGGTCTCCCACTTTGGAATTTTGAA
130 AGTTTACGCCAAGATTGGTCTCCCACTTTGGAATTTTGAA
67567 AATTTCTAGC
Statistics
Matches: 168, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
168 111 0.66
170 57 0.34
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (169 bp):
CATGCATATATATATATATATTCGCTGGTCCAACATTTTTCTTCTTCCCCCCTCTCCACTTTTTT
TACTCGACGTATTGCTATTGAAGTTTTGACAATATTCTGCAGCCATAAAAAAAAAAAAAATGTCA
GTTTACGCCAAGATTGGTCTCCCACTTTGGAATTTTGAA
Found at i:72016 original size:20 final size:21
Alignment explanation
Indices: 71984--72023 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
71974 TTAATAGATG
71984 TGATTTTTAAAATAAATTTAA
1 TGATTTTTAAAATAAATTTAA
72005 TGATTTTT-AAATAAATTTA
1 TGATTTTTAAAATAAATTTA
72024 GTATTTGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (21 bp):
TGATTTTTAAAATAAATTTAA
Found at i:72048 original size:15 final size:15
Alignment explanation
Indices: 72028--72058 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
72018 AATTTAGTAT
*
72028 TTGTATTCAGTTAAA
1 TTGTATTCAATTAAA
72043 TTGTATTCAATTAAA
1 TTGTATTCAATTAAA
72058 T
1 T
72059 CCTCAGTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.48
Consensus pattern (15 bp):
TTGTATTCAATTAAA
Found at i:74204 original size:18 final size:17
Alignment explanation
Indices: 74174--74286 Score: 63
Period size: 18 Copynumber: 6.4 Consensus size: 17
74164 ATATGTCTTA
*
74174 TTTAATTTAATTTATTGT
1 TTTAAATTAATTTATT-T
*
74192 TTTAAATTGATTTATTATT
1 TTTAAATTAATTTA-T-TT
*
74211 CTTTAAA-T-ATGTA-TT
1 -TTTAAATTAATTTATTT
74226 TTT-AATTAAATTATATTT
1 TTTAAATT-AATT-TATTT
* *
74244 TTAAAATTTAATTTATTGC
1 TTTAAA-TTAATTTATT-T
* *
74263 TTTAAATTGATTTATTC
1 TTTAAATTAATTTATTT
74280 TTTAAAT
1 TTTAAAT
74287 ATTTCTCTTT
Statistics
Matches: 76, Mismatches: 8, Indels: 23
0.71 0.07 0.21
Matches are distributed among these distances:
13 2 0.03
14 4 0.05
15 2 0.03
16 2 0.03
17 10 0.13
18 33 0.43
19 14 0.18
20 9 0.12
ACGTcount: A:0.34, C:0.03, G:0.04, T:0.59
Consensus pattern (17 bp):
TTTAAATTAATTTATTT
Found at i:74205 original size:53 final size:52
Alignment explanation
Indices: 74125--74260 Score: 184
Period size: 53 Copynumber: 2.6 Consensus size: 52
74115 TTTAAAAAAG
* *
74125 TTAAATTTATTGCTTTTAAAATAATTTATTATTCTTTAAATATGTCTTATTTAA
1 TTAAATTTATTG-TTTTAAATTAATTTATTATTCTTTAAATATGTATT-TTTAA
* *
74179 TTTAATTTATTGTTTTAAATTGATTTATTATTCTTTAAATATGTATTTTTAA
1 TTAAATTTATTGTTTTAAATTAATTTATTATTCTTTAAATATGTATTTTTAA
*
74231 TTAAATTATATT-TTTAAAATTTAATTTATT
1 TTAAATT-TATTGTTTTAAA-TTAATTTATT
74261 GCTTTAAATT
Statistics
Matches: 73, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
52 17 0.23
53 45 0.62
54 11 0.15
ACGTcount: A:0.35, C:0.03, G:0.04, T:0.59
Consensus pattern (52 bp):
TTAAATTTATTGTTTTAAATTAATTTATTATTCTTTAAATATGTATTTTTAA
Found at i:74254 original size:71 final size:70
Alignment explanation
Indices: 74177--74324 Score: 210
Period size: 71 Copynumber: 2.1 Consensus size: 70
74167 TGTCTTATTT
* *
74177 AATTTAATTTATTGTTTTAAATTGATTTATTATTCTTTAAATATGTATTTTTAA-TTAAATT-AT
1 AATTTAATTTATTGCTTTAAATTGA--T-TTATTCTTTAAATATGTATCTTTAATTTAAATTAAT
74240 ATTTTTAA
63 ATTTTTAA
* *
74248 AATTTAATTTATTGCTTTAAATTGATTTATTCTTTAAATATTTCTCTTTAATTTAAATTAATATT
1 AATTTAATTTATTGCTTTAAATTGATTTATTCTTTAAATATGTATCTTTAATTTAAATTAATATT
74313 TTTAA
66 TTTAA
*
74318 ATTTTAA
1 AATTTAA
74325 GTATCTGATA
Statistics
Matches: 70, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
68 22 0.31
69 8 0.11
70 16 0.23
71 24 0.34
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.58
Consensus pattern (70 bp):
AATTTAATTTATTGCTTTAAATTGATTTATTCTTTAAATATGTATCTTTAATTTAAATTAATATT
TTTAA
Found at i:80901 original size:21 final size:20
Alignment explanation
Indices: 80847--80901 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
80837 TCCCACATCA
* *
80847 ATTTAATATTAAAGAATAGT
1 ATTTAATATAAAAGAATAAT
**
80867 ATTTTCTATCAAAAGAATAAT
1 ATTTAATAT-AAAAGAATAAT
80888 ATTTAAATATAAAA
1 ATTT-AATATAAAA
80902 TAGTTAAATA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
20 7 0.26
21 17 0.63
22 3 0.11
ACGTcount: A:0.53, C:0.04, G:0.05, T:0.38
Consensus pattern (20 bp):
ATTTAATATAAAAGAATAAT
Found at i:80951 original size:28 final size:27
Alignment explanation
Indices: 80912--81000 Score: 121
Period size: 25 Copynumber: 3.3 Consensus size: 27
80902 TAGTTAAATA
80912 ATATTTTATATTAAATTATATTAAAAG
1 ATATTTTATATTAAATTATATTAAAAG
* *
80939 ACTTTTTTATATTAACTTATATT-AAA-
1 A-TATTTTATATTAAATTATATTAAAAG
80965 ATATTTTATATTAAATTATATTAAAAG
1 ATATTTTATATTAAATTATATTAAAAG
80992 A-ATTATTAT
1 ATATT-TTAT
81001 TTTTTTTATT
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
25 19 0.35
26 7 0.13
27 9 0.17
28 19 0.35
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (27 bp):
ATATTTTATATTAAATTATATTAAAAG
Found at i:84204 original size:21 final size:21
Alignment explanation
Indices: 84153--84204 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 21
84143 ATAAACAAAA
*
84153 TTAACAGAAAGTACCAAAGTAC
1 TTAACAG-AAGTACCAAAATAC
84175 TT-ACTAGAAGTACCAAAATAC
1 TTAAC-AGAAGTACCAAAATAC
84196 TTAACAGAA
1 TTAACAGAA
84205 TTACATAACT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 21 0.78
22 6 0.22
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (21 bp):
TTAACAGAAGTACCAAAATAC
Found at i:84279 original size:22 final size:22
Alignment explanation
Indices: 84224--84307 Score: 132
Period size: 22 Copynumber: 3.8 Consensus size: 22
84214 TGCCGGGGAC
84224 ACAGAAGCACACACAGTGTTGA
1 ACAGAAGCACACACAGTGTTGA
84246 ACAGTAAGCACACACAGTGTTGA
1 ACAG-AAGCACACACAGTGTTGA
* *
84269 ACAGAAGCACACATAGTGCTGA
1 ACAGAAGCACACACAGTGTTGA
*
84291 ACAGCAGCACACACAGT
1 ACAGAAGCACACACAGT
84308 TCTAATTCGT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
22 35 0.61
23 22 0.39
ACGTcount: A:0.40, C:0.25, G:0.21, T:0.13
Consensus pattern (22 bp):
ACAGAAGCACACACAGTGTTGA
Found at i:86145 original size:18 final size:16
Alignment explanation
Indices: 86115--86155 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 16
86105 AAGATGAGAA
86115 TAAATTTTTAATTAAT
1 TAAATTTTTAATTAAT
86131 TAAATATTTTAAATTAAT
1 TAAAT-TTTT-AATTAAT
86149 TACAATT
1 TA-AATT
86156 AAAAAGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 5 0.23
17 4 0.18
18 10 0.45
19 3 0.14
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (16 bp):
TAAATTTTTAATTAAT
Found at i:94447 original size:20 final size:19
Alignment explanation
Indices: 94374--94447 Score: 60
Period size: 19 Copynumber: 3.8 Consensus size: 19
94364 TTTAAATTTC
* *
94374 AAAATAATATATAAAATTTG
1 AAAATATTATATAAAA-TTA
* **
94394 AAAATATTAT-CAAAAGAA
1 AAAATATTATATAAAATTA
* *
94412 AAAATATTTTAAAAAATTA
1 AAAATATTATATAAAATTA
94431 AAAATATATATATAAAA
1 AAAATAT-TATATAAAA
94448 ATTGAAGTTT
Statistics
Matches: 41, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
18 9 0.22
19 16 0.39
20 16 0.39
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (19 bp):
AAAATATTATATAAAATTA
Found at i:103164 original size:19 final size:19
Alignment explanation
Indices: 103142--103178 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
103132 TTTTATCGTT
103142 CTTTAAAAACTCAAAATTC
1 CTTTAAAAACTCAAAATTC
**
103161 CTTTAAAATGTCAAAATT
1 CTTTAAAAACTCAAAATT
103179 TTCATAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.46, C:0.16, G:0.03, T:0.35
Consensus pattern (19 bp):
CTTTAAAAACTCAAAATTC
Found at i:103368 original size:18 final size:18
Alignment explanation
Indices: 103341--103375 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
103331 CAAAAATAAA
*
103341 TTATAGTTTTTTAAGTTT
1 TTATAATTTTTTAAGTTT
103359 TTATAATTTTTTAAGTT
1 TTATAATTTTTTAAGTT
103376 AATATTTTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.66
Consensus pattern (18 bp):
TTATAATTTTTTAAGTTT
Found at i:113899 original size:23 final size:23
Alignment explanation
Indices: 113826--113999 Score: 149
Period size: 23 Copynumber: 7.5 Consensus size: 23
113816 TATACGGAAC
* *
113826 AAACAGAGAGTAC-CAAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
*
113848 -AACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
113869 GGGCAACAGAGAGCACACACAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
* *
113895 AAACAGAGAGTACACAAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
* *
113918 AATCAGAGAGCATACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
113941 AATCAGAGAGCACACAGAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
113964 AATAACAGAGAGCACGA-GATGTGCT
1 -A-AACAGAGAGCAC-ACAAAGTGCT
113989 AAACAGAGAGC
1 AAACAGAGAGC
114000 GCGCTAGTGT
Statistics
Matches: 124, Mismatches: 19, Indels: 17
0.77 0.12 0.11
Matches are distributed among these distances:
21 17 0.14
23 69 0.56
24 2 0.02
25 29 0.23
26 7 0.06
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.13
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:113948 original size:69 final size:67
Alignment explanation
Indices: 113826--113975 Score: 189
Period size: 69 Copynumber: 2.1 Consensus size: 67
113816 TATACGGAAC
113826 AAACAGAGAGTACCAAAGTACTAACAGAGAGCACATAAGTGCTGGGCAACAGAGAGCACACACAG
1 AAACAGAGAGTACCAAAGTACTAACAGAGAGCACATAAGTGCT--G-AACAGAGAGCACACACAG
113891 TGCT-
63 TGCTA
*
113895 AAACAGAGAGTACACAAAGTACTAATCAGAGAGCATACA-AAGTGCT-AATCAGAGAGCACACAG
1 AAACAGAGAGTAC-CAAAGTACTAA-CAGAGAGC--ACATAAGTGCTGAA-CAGAGAGCACACAC
113958 AGTGCTA
61 AGTGCTA
113965 ATAACAGAGAG
1 A-AACAGAGAG
113976 CACGAGATGT
Statistics
Matches: 73, Mismatches: 1, Indels: 12
0.85 0.01 0.14
Matches are distributed among these distances:
68 2 0.03
69 32 0.44
70 12 0.16
71 17 0.23
72 7 0.10
73 3 0.04
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.13
Consensus pattern (67 bp):
AAACAGAGAGTACCAAAGTACTAACAGAGAGCACATAAGTGCTGAACAGAGAGCACACACAGTGC
TA
Found at i:115926 original size:24 final size:24
Alignment explanation
Indices: 115899--115945 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
115889 TCACGAACAA
*
115899 GCTCATTTAAAAGCTCGTTTATTG
1 GCTCATTTAAAAGCTCATTTATTG
* **
115923 GCTCGTTTTTAAGCTCATTTATT
1 GCTCATTTAAAAGCTCATTTATT
115946 TATTAATGAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.21, C:0.17, G:0.15, T:0.47
Consensus pattern (24 bp):
GCTCATTTAAAAGCTCATTTATTG
Found at i:116086 original size:23 final size:23
Alignment explanation
Indices: 116027--116114 Score: 79
Period size: 23 Copynumber: 3.8 Consensus size: 23
116017 TCATTAACAT
* * * *
116027 TGTTCTTGAACGTGTTCAATTGTA
1 TGTTCATGAACATGTTCGATT-AA
*
116051 TGTTCATGCACATGTTCGATTAA
1 TGTTCATGAACATGTTCGATTAA
*
116074 TGTTCGTGAACATGTTCGATTAA
1 TGTTCATGAACATGTTCGATTAA
* *
116097 -GTTAAATGAACATATTCG
1 TGTT-CATGAACATGTTCG
116115 TGAACATTAA
Statistics
Matches: 53, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
22 3 0.06
23 33 0.62
24 17 0.32
ACGTcount: A:0.27, C:0.14, G:0.19, T:0.40
Consensus pattern (23 bp):
TGTTCATGAACATGTTCGATTAA
Found at i:118059 original size:24 final size:23
Alignment explanation
Indices: 118015--118082 Score: 61
Period size: 22 Copynumber: 2.9 Consensus size: 23
118005 TTGATCGATA
118015 AAAAAAATCATTAAAATTTTATTTTT
1 AAAAAAAT--TTAAAA-TTTATTTTT
*
118041 AAAAAAATTGTAAAATTTA--GTT
1 AAAAAAATT-TAAAATTTATTTTT
*
118063 AAAAAAGTTT-AAATTTATTT
1 AAAAAAATTTAAAATTTATTT
118083 AAAGAATATA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
20 7 0.19
21 1 0.03
22 10 0.28
24 5 0.14
25 5 0.14
26 8 0.22
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.43
Consensus pattern (23 bp):
AAAAAAATTTAAAATTTATTTTT
Found at i:118076 original size:20 final size:22
Alignment explanation
Indices: 118039--118085 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
118029 AATTTTATTT
118039 TTAAAAAAATTGTAAAATTTAG
1 TTAAAAAAATTGTAAAATTTAG
* *
118061 TTAAAAAAGTT-T-AAATTTAT
1 TTAAAAAAATTGTAAAATTTAG
118081 TTAAA
1 TTAAA
118086 GAATATAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 12 0.52
21 1 0.04
22 10 0.43
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.40
Consensus pattern (22 bp):
TTAAAAAAATTGTAAAATTTAG
Found at i:126287 original size:2 final size:2
Alignment explanation
Indices: 126282--126310 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
126272 TACAATATTT
126282 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 T
126311 GTTATAGGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:131462 original size:3 final size:3
Alignment explanation
Indices: 131454--131488 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
131444 GTACTCTCTA
131454 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
131489 ACTATATATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:139497 original size:19 final size:21
Alignment explanation
Indices: 139465--139513 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
139455 ATAAGTCCAA
139465 TAAAAATTAAAT-AAA-TAAT
1 TAAAAATTAAATAAAATTAAT
** *
139484 TAAAAATTTTATAAAATTATT
1 TAAAAATTAAATAAAATTAAT
139505 TAAAAATTA
1 TAAAAATTA
139514 TAAATTGGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 10 0.42
20 3 0.12
21 11 0.46
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
TAAAAATTAAATAAAATTAAT
Found at i:148264 original size:11 final size:11
Alignment explanation
Indices: 148248--148277 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
148238 AATTTTGAGA
148248 GAGGAGGGAGG
1 GAGGAGGGAGG
148259 GAGGAGGGAGG
1 GAGGAGGGAGG
*
148270 GGGGAGGG
1 GAGGAGGG
148278 GCGGTGACTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.77, T:0.00
Consensus pattern (11 bp):
GAGGAGGGAGG
Found at i:157152 original size:41 final size:41
Alignment explanation
Indices: 157095--157214 Score: 231
Period size: 41 Copynumber: 2.9 Consensus size: 41
157085 TTTTTGTCGT
157095 ACTTGTACCCTTTAAATCATGAGTTTTATACCAATTGTGAG
1 ACTTGTACCCTTTAAATCATGAGTTTTATACCAATTGTGAG
*
157136 ACTTGTACCCTTTAAATCATTAGTTTTATACCAATTGTGAG
1 ACTTGTACCCTTTAAATCATGAGTTTTATACCAATTGTGAG
157177 ACTTGTACCCTTTAAATCATGAGTTTTATACCAATTGT
1 ACTTGTACCCTTTAAATCATGAGTTTTATACCAATTGT
157215 TTTGTTCCAA
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 77 1.00
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.41
Consensus pattern (41 bp):
ACTTGTACCCTTTAAATCATGAGTTTTATACCAATTGTGAG
Found at i:159952 original size:25 final size:26
Alignment explanation
Indices: 159905--159956 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 26
159895 TAAGTAAAAA
*
159905 TTTGAAAGTTTAAATTTTCATATATTT
1 TTTGAAAGTTTAAATTTTAATAT-TTT
159932 TTTGAAA-TTT-AATTTTAATATTTT
1 TTTGAAAGTTTAAATTTTAATATTTT
159956 T
1 T
159957 AATTTTAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 4 0.17
25 10 0.42
26 3 0.12
27 7 0.29
ACGTcount: A:0.33, C:0.02, G:0.06, T:0.60
Consensus pattern (26 bp):
TTTGAAAGTTTAAATTTTAATATTTT
Found at i:163934 original size:14 final size:15
Alignment explanation
Indices: 163903--163937 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
163893 ATATGTCCAA
*
163903 TTTTTATTATTTTAC
1 TTTTCATTATTTTAC
163918 TTTTCATTATTTT-C
1 TTTTCATTATTTTAC
163932 TTTTCA
1 TTTTCA
163938 ACAACTTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.17, C:0.11, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTCATTATTTTAC
Found at i:165810 original size:31 final size:31
Alignment explanation
Indices: 165769--165835 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
165759 TTCTGCATAC
165769 GCAAAAGAAGCTTGACCAGTTAAATTATTTG
1 GCAAAAGAAGCTTGACCAGTTAAATTATTTG
* *
165800 GCAAATGAAGCTTGACCATTTAAATTATTTG
1 GCAAAAGAAGCTTGACCAGTTAAATTATTTG
165831 GCAAA
1 GCAAA
165836 CGTAAAATCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (31 bp):
GCAAAAGAAGCTTGACCAGTTAAATTATTTG
Found at i:171802 original size:9 final size:9
Alignment explanation
Indices: 171789--171831 Score: 54
Period size: 9 Copynumber: 5.0 Consensus size: 9
171779 AATTATTATT
171789 TTAATTAAA
1 TTAATTAAA
*
171798 GTAATTAAA
1 TTAATTAAA
171807 TTAA-TAAA
1 TTAATTAAA
*
171815 -AAATTAAA
1 TTAATTAAA
171823 TTAATTAAA
1 TTAATTAAA
171832 ATAGCAATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
7 2 0.07
8 8 0.29
9 18 0.64
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (9 bp):
TTAATTAAA
Found at i:171821 original size:16 final size:17
Alignment explanation
Indices: 171789--171832 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
171779 AATTATTATT
*
171789 TTAATTAAAGTAATTAAA
1 TTAATTAAA-AAATTAAA
171807 TTAA-TAAAAAATTAAA
1 TTAATTAAAAAATTAAA
171823 TTAATTAAAA
1 TTAATTAAAA
171833 TAGCAATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 11 0.46
17 9 0.38
18 4 0.17
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (17 bp):
TTAATTAAAAAATTAAA
Found at i:177238 original size:2 final size:2
Alignment explanation
Indices: 177233--177257 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
177223 ATATAATATT
177233 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
177258 AGGGCATGCA
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:183048 original size:14 final size:13
Alignment explanation
Indices: 183025--183060 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
183015 CCAAAATACT
183025 TCTTTAATTATTA
1 TCTTTAATTATTA
183038 TCTTATAATTATTA
1 TCTT-TAATTATTA
*
183052 TATTTAATT
1 TCTTTAATT
183061 GATAATCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (13 bp):
TCTTTAATTATTA
Found at i:183967 original size:16 final size:16
Alignment explanation
Indices: 183946--183991 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
183936 AAAATATATC
*
183946 AATATTATTATAAATT
1 AATATTATTTTAAATT
183962 AATATTATTTTAATATT
1 AATATTATTTTAA-ATT
183979 -ATATTATTTTAAA
1 AATATTATTTTAAA
183992 AAGGAATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 1 0.04
16 24 0.86
17 3 0.11
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
AATATTATTTTAAATT
Found at i:185723 original size:3 final size:3
Alignment explanation
Indices: 185715--185744 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
185705 TACCTCCATG
185715 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
185745 GTGCAATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:189402 original size:40 final size:38
Alignment explanation
Indices: 189334--189468 Score: 96
Period size: 40 Copynumber: 3.4 Consensus size: 38
189324 ACCAGAATGG
* *
189334 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAAAGTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAG-AATAAAGTGA
* *
189374 CACCCAGTGTCTCATCGGCCTAGCCGAAG--TAAAGTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGAATAAAGTGA
* * * * *
189411 TACCCAGTACCTCATCGAATCTATCCGAAGTAA-AATAATGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAG-AATAA-AGTGA
*
189452 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
189469 ACTCAAGGTC
Statistics
Matches: 74, Mismatches: 14, Indels: 13
0.73 0.14 0.13
Matches are distributed among these distances:
37 21 0.28
38 9 0.12
40 24 0.32
41 20 0.27
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.21
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGAATAAAGTGA
Found at i:189466 original size:41 final size:38
Alignment explanation
Indices: 189366--189469 Score: 93
Period size: 37 Copynumber: 2.7 Consensus size: 38
189356 TTCGAAGCAA
* *
189366 TAAAGTGACACCCAGTGTCTCATCG-GCCTAGCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
* ** ** * *
189403 TAAAGTGGTACCCAGTACCTCATCGAATCTATCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
189441 TAAAATAATGACACCCAGTGTCTCATCGA
1 T--AA-AATGACACCCAGTGTCTCATCGA
189470 CTCAAGGTCG
Statistics
Matches: 51, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
37 21 0.41
38 10 0.20
40 2 0.04
41 18 0.35
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (38 bp):
TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
Found at i:203459 original size:15 final size:14
Alignment explanation
Indices: 203441--203486 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
203431 TTTTAGTTGG
203441 AATAATTTTTTGAAA
1 AATAATTTTTT-AAA
*
203456 AATAATTTTATAAA
1 AATAATTTTTTAAA
*
203470 AAAATATTTTTTAAA
1 AATA-ATTTTTTAAA
203485 AA
1 AA
203487 ATAAATAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
14 6 0.22
15 21 0.78
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (14 bp):
AATAATTTTTTAAA
Found at i:205170 original size:15 final size:15
Alignment explanation
Indices: 205150--205211 Score: 70
Period size: 15 Copynumber: 4.1 Consensus size: 15
205140 TTGAATTTAG
205150 TACTTAAATTTTCAA
1 TACTTAAATTTTCAA
205165 TACTTAAATTTTCAA
1 TACTTAAATTTTCAA
* ** *
205180 CACTTACTTTTTCCA
1 TACTTAAATTTTCAA
*
205195 TACTTAATTTTTTCAA
1 TACTTAA-ATTTTCAA
205211 T
1 T
205212 TTATGAAACA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
15 31 0.79
16 8 0.21
ACGTcount: A:0.32, C:0.18, G:0.00, T:0.50
Consensus pattern (15 bp):
TACTTAAATTTTCAA
Found at i:206967 original size:7 final size:7
Alignment explanation
Indices: 206955--206985 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
206945 CAATTAAGAA
206955 ATTCTCC
1 ATTCTCC
206962 ATTCTCC
1 ATTCTCC
*
206969 ATTCTCT
1 ATTCTCC
206976 ATTCTCC
1 ATTCTCC
206983 ATT
1 ATT
206986 TCTTCTTGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.16, C:0.35, G:0.00, T:0.48
Consensus pattern (7 bp):
ATTCTCC
Found at i:210660 original size:2 final size:2
Alignment explanation
Indices: 210653--210697 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
210643 TGTTTTAATC
210653 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
210695 TA T
1 TA T
210698 TAGATGCAAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:222795 original size:16 final size:17
Alignment explanation
Indices: 222774--222812 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
222764 TTTCTATCAT
222774 AAAATT-ATATCAAATC
1 AAAATTCATATCAAATC
*
222790 AAAATTCATATTAAATC
1 AAAATTCATATCAAATC
222807 AAAATT
1 AAAATT
222813 TACATGTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAATTCATATCAAATC
Found at i:226383 original size:23 final size:23
Alignment explanation
Indices: 226353--226398 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
226343 ACGCTAGCGC
226353 GCTTACTGTTTCGCACTTCGTGT
1 GCTTACTGTTTCGCACTTCGTGT
*
226376 GCTTACTGTTTCGCACTTTGTGT
1 GCTTACTGTTTCGCACTTCGTGT
226399 TTATGTGCGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.09, C:0.24, G:0.22, T:0.46
Consensus pattern (23 bp):
GCTTACTGTTTCGCACTTCGTGT
Found at i:226435 original size:22 final size:23
Alignment explanation
Indices: 226407--226453 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
226397 GTTTATGTGC
226407 GCCTATT-GATTGCACTGTATGT
1 GCCTATTGGATTGCACTGTATGT
* *
226429 GCCTATTGGATTGCATTGTGTGT
1 GCCTATTGGATTGCACTGTATGT
226452 GC
1 GC
226454 TTACTGTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.15, C:0.17, G:0.28, T:0.40
Consensus pattern (23 bp):
GCCTATTGGATTGCACTGTATGT
Found at i:231476 original size:79 final size:79
Alignment explanation
Indices: 231379--231537 Score: 309
Period size: 79 Copynumber: 2.0 Consensus size: 79
231369 CTGATACATG
231379 CTTATGCTGCCAGCAAAACAAGTTTCTGTGTAACCAAATGCACCGCAACATGACAATGGCCCTCT
1 CTTATGCTGCCAGCAAAACAAGTTTCTGTGTAACCAAATGCACCGCAACATGACAATGGCCCTCT
231444 CCCTTGTTACAACA
66 CCCTTGTTACAACA
*
231458 CTTATGCTGCCAGCAAAACAAGTTTCTGTGTAACCAAATGCGCCGCAACATGACAATGGCCCTCT
1 CTTATGCTGCCAGCAAAACAAGTTTCTGTGTAACCAAATGCACCGCAACATGACAATGGCCCTCT
231523 CCCTTGTTACAACA
66 CCCTTGTTACAACA
231537 C
1 C
231538 CCTGCAAGCT
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 79 1.00
ACGTcount: A:0.30, C:0.31, G:0.16, T:0.24
Consensus pattern (79 bp):
CTTATGCTGCCAGCAAAACAAGTTTCTGTGTAACCAAATGCACCGCAACATGACAATGGCCCTCT
CCCTTGTTACAACA
Found at i:234159 original size:6 final size:6
Alignment explanation
Indices: 234150--234190 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
234140 AAACAAAAGA
* *
234150 GTGTGA GTGTGT GTGTGC GTGTGC GTGTGC GTGTGC GTGTG
1 GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTGC GTGTG
234191 TATGTATATG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.02, C:0.10, G:0.51, T:0.37
Consensus pattern (6 bp):
GTGTGC
Found at i:237206 original size:12 final size:12
Alignment explanation
Indices: 237189--237215 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
237179 AACTTATTGA
237189 AGAACAAGTTTG
1 AGAACAAGTTTG
237201 AGAACAAGTTTG
1 AGAACAAGTTTG
237213 AGA
1 AGA
237216 GTAGGAACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.07, G:0.26, T:0.22
Consensus pattern (12 bp):
AGAACAAGTTTG
Found at i:246436 original size:8 final size:8
Alignment explanation
Indices: 246425--246451 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
246415 GCAAAAAAAA
246425 AAAAAACT
1 AAAAAACT
246433 AAAAAACT
1 AAAAAACT
246441 AAAAAACT
1 AAAAAACT
246449 AAA
1 AAA
246452 TGACGTTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.78, C:0.11, G:0.00, T:0.11
Consensus pattern (8 bp):
AAAAAACT
Found at i:246438 original size:16 final size:16
Alignment explanation
Indices: 246417--246451 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
246407 TTTGTGTTGC
246417 AAAAAAAAAAAAAACT
1 AAAAAAAAAAAAAACT
**
246433 AAAAAACTAAAAAACT
1 AAAAAAAAAAAAAACT
246449 AAA
1 AAA
246452 TGACGTTGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.83, C:0.09, G:0.00, T:0.09
Consensus pattern (16 bp):
AAAAAAAAAAAAAACT
Done.