Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008211.1 Hibiscus syriacus cultivar Beakdansim tig00110833_pilon, 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: 2208279
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 10
Found at i:3276 original size:44 final size:43
Alignment explanation
Indices: 3209--3296 Score: 124
Period size: 44 Copynumber: 2.0 Consensus size: 43
3199 ATTCATCTGA
*
3209 CATTTCTGCGAACCAAACAGAATATGAAATTAGATT-TCAATTC
1 CATTTCTGCCAACCAAACAGAATATGAAATTAGATTCT-AATTC
* *
3252 CATTTCCTGCCAACCAAACTGAATATGAAATTGGATTCTAATTC
1 CATTT-CTGCCAACCAAACAGAATATGAAATTAGATTCTAATTC
3296 C
1 C
3297 TGACAGATTC
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
43 5 0.12
44 34 0.85
45 1 0.03
ACGTcount: A:0.36, C:0.22, G:0.11, T:0.31
Consensus pattern (43 bp):
CATTTCTGCCAACCAAACAGAATATGAAATTAGATTCTAATTC
Found at i:3322 original size:18 final size:17
Alignment explanation
Indices: 3285--3331 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
3275 TATGAAATTG
*
3285 GATTCTAATTCCTGACA
1 GATTCTAATTCCTCACA
*
3302 GATTCTAATTCTTTCACA
1 GATTCTAATTC-CTCACA
*
3320 GATTCCAATTCC
1 GATTCTAATTCC
3332 CTCATATACA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.28, C:0.26, G:0.09, T:0.38
Consensus pattern (17 bp):
GATTCTAATTCCTCACA
Found at i:6328 original size:5 final size:5
Alignment explanation
Indices: 6320--6363 Score: 88
Period size: 5 Copynumber: 8.8 Consensus size: 5
6310 CGTCTCGTCT
6320 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
6364 TGGTCGTGGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.00, C:0.41, G:0.39, T:0.20
Consensus pattern (5 bp):
CTCGG
Found at i:6372 original size:6 final size:6
Alignment explanation
Indices: 6361--6400 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
6351 TCGGCTCGGC
6361 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGT
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGT
6401 AATACGTGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.00, C:0.17, G:0.47, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:9275 original size:5 final size:5
Alignment explanation
Indices: 9261--9309 Score: 62
Period size: 5 Copynumber: 9.8 Consensus size: 5
9251 GTCCGTCCGT
* * * *
9261 CTCGT CTCGG CTCGG CACGG CACGG CTCGG CTCGG CTCGG CTTGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
9310 TGGTCGTGGT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.04, C:0.39, G:0.37, T:0.20
Consensus pattern (5 bp):
CTCGG
Found at i:9318 original size:6 final size:6
Alignment explanation
Indices: 9307--9367 Score: 104
Period size: 6 Copynumber: 10.2 Consensus size: 6
9297 TCGGCTTGGC
* *
9307 TCGTGG TCGTGG TCGTGG TCGAGG TCGAGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
9355 TCGTGG TCGTGG T
1 TCGTGG TCGTGG T
9368 AATACGTGTC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.03, C:0.16, G:0.49, T:0.31
Consensus pattern (6 bp):
TCGTGG
Found at i:15210 original size:5 final size:5
Alignment explanation
Indices: 15196--15244 Score: 62
Period size: 5 Copynumber: 9.8 Consensus size: 5
15186 GTCCGTCCGT
* * * *
15196 CTCGT CTCGG CTCGG CACGG CACGG CTCGG CTCGG CTCGG CTTGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
15245 TGGTCGTGGT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.04, C:0.39, G:0.37, T:0.20
Consensus pattern (5 bp):
CTCGG
Found at i:15253 original size:6 final size:6
Alignment explanation
Indices: 15242--15296 Score: 92
Period size: 6 Copynumber: 9.2 Consensus size: 6
15232 TCGGCTTGGC
* *
15242 TCGTGG TCGTGG TCGAGG TCGAGG TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
15290 TCGTGG T
1 TCGTGG T
15297 AATACGTGTC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.04, C:0.16, G:0.49, T:0.31
Consensus pattern (6 bp):
TCGTGG
Found at i:15595 original size:22 final size:22
Alignment explanation
Indices: 15570--15624 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
15560 TCAGGAGTTA
* *
15570 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
15592 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
15614 CGGGAGTTATA
1 CAGGAGTTATA
15625 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:17193 original size:25 final size:22
Alignment explanation
Indices: 17149--17193 Score: 54
Period size: 22 Copynumber: 1.9 Consensus size: 22
17139 TATTAAAATT
*
17149 TTGTTTTTTTAATATTTATATG
1 TTGTTTTTTTAATATATATATG
17171 TTGTTGTTTTTCAATATAATATA
1 TTGTT-TTTTT-AATAT-ATATA
17194 AATTTTTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 5 0.26
23 5 0.26
24 5 0.26
25 4 0.21
ACGTcount: A:0.27, C:0.02, G:0.09, T:0.62
Consensus pattern (22 bp):
TTGTTTTTTTAATATATATATG
Found at i:23246 original size:21 final size:21
Alignment explanation
Indices: 23204--23247 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
23194 AATGAGGATG
* *
23204 CAACCATTTCAGATGGCTCCA
1 CAACCATTTCAGATGCCACCA
*
23225 CAACTATTTCAGATGCCACCA
1 CAACCATTTCAGATGCCACCA
23246 CA
1 CA
23248 GCAACTTCTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.32, C:0.34, G:0.11, T:0.23
Consensus pattern (21 bp):
CAACCATTTCAGATGCCACCA
Found at i:28599 original size:24 final size:24
Alignment explanation
Indices: 28572--28647 Score: 64
Period size: 24 Copynumber: 3.2 Consensus size: 24
28562 TATATCAAAA
28572 ATCAAAACATAAAT-CAGGTCAAGT
1 ATCAAAACA-AAATCCAGGTCAAGT
* * *
28596 ATCATATCAAACTCCAGGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* * * **
28620 ATCAGATCAGAATCCAAATCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
28644 ATCA
1 ATCA
28648 GATCAGAATC
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
23 3 0.07
24 40 0.93
ACGTcount: A:0.45, C:0.21, G:0.12, T:0.22
Consensus pattern (24 bp):
ATCAAAACAAAATCCAGGTCAAGT
Found at i:28648 original size:24 final size:24
Alignment explanation
Indices: 28589--28704 Score: 137
Period size: 24 Copynumber: 4.8 Consensus size: 24
28579 CATAAATCAG
* *
28589 GTCAAGTATCATATCA-AACTCCAG
1 GTCAAGTATCAGATCAGAA-TCCAA
28613 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAA
* * *
28637 ATCAAGTATCAGATCAGAATCTAT
1 GTCAAGTATCAGATCAGAATCCAA
* *
28661 GTC-AGATATCATATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAA
28685 GTCAAGTATCAGATCAGAAT
1 GTCAAGTATCAGATCAGAAT
28705 TCAAATAAAA
Statistics
Matches: 80, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
23 2 0.03
24 74 0.93
25 4 0.05
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.26
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAA
Found at i:28720 original size:48 final size:48
Alignment explanation
Indices: 28620--28722 Score: 118
Period size: 48 Copynumber: 2.1 Consensus size: 48
28610 CAGGTCAAGT
* ** * * *
28620 ATCAGATCAGAATCCAAATCAAGTATCAGATCAGAATCTATGTCAGAT
1 ATCATATCAGAATCCAAATCAAGTATCAGATCAGAATCTAAATAAAAA
**
28668 ATCATATCAGAATCCATGTCAAGTATCAGATCAGAAT-TCAAATAAAAA
1 ATCATATCAGAATCCAAATCAAGTATCAGATCAGAATCT-AAATAAAAA
28716 ATCATAT
1 ATCATAT
28723 AAAATATTCA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
47 1 0.02
48 45 0.98
ACGTcount: A:0.45, C:0.17, G:0.12, T:0.26
Consensus pattern (48 bp):
ATCATATCAGAATCCAAATCAAGTATCAGATCAGAATCTAAATAAAAA
Found at i:29707 original size:26 final size:26
Alignment explanation
Indices: 29678--29730 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
29668 TCAGTTTTAT
*
29678 TCCATTCATTTCAGAGCTCGAGGATA
1 TCCAATCATTTCAGAGCTCGAGGATA
* * *
29704 TCCAATCATTTCTGAGCTTGATGATA
1 TCCAATCATTTCAGAGCTCGAGGATA
29730 T
1 T
29731 TCTTGGGTCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (26 bp):
TCCAATCATTTCAGAGCTCGAGGATA
Found at i:33317 original size:25 final size:23
Alignment explanation
Indices: 33261--33318 Score: 64
Period size: 25 Copynumber: 2.5 Consensus size: 23
33251 TTTATAAAAA
*
33261 AATTAATTA-TTAACTTTTATTG
1 AATTAATTATTTAACTTTAATTG
* *
33283 AATTATTTATTTAACTATTAAATTT
1 AATTAATTATTTAACT-TT-AATTG
33308 AATTAATTATT
1 AATTAATTATT
33319 ATTATTTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 8 0.28
23 6 0.21
24 2 0.07
25 13 0.45
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.55
Consensus pattern (23 bp):
AATTAATTATTTAACTTTAATTG
Found at i:33708 original size:23 final size:23
Alignment explanation
Indices: 33654--33701 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 23
33644 TATGATTTTA
33654 AAAAAAACTAAAAATTTAAATATT
1 AAAAAAA-TAAAAATTTAAATATT
*
33678 AAAAAAATAACAATTTAAATATT
1 AAAAAAATAAAAATTTAAATATT
33701 A
1 A
33702 CTAAAATGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (23 bp):
AAAAAAATAAAAATTTAAATATT
Found at i:34214 original size:31 final size:28
Alignment explanation
Indices: 34158--34220 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 28
34148 TAATCGAATT
*
34158 AACCGAACTTTTTTTTAACCGTTAACCG
1 AACCGAACTTTTTTTTAACCATTAACCG
*
34186 AACCGAACTTTTTTTTCAAACATATTAACCG
1 AACCGAACTTTTTTTT--AAC-CATTAACCG
34217 AACC
1 AACC
34221 AAATTAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 16 0.53
30 3 0.10
31 11 0.37
ACGTcount: A:0.33, C:0.25, G:0.08, T:0.33
Consensus pattern (28 bp):
AACCGAACTTTTTTTTAACCATTAACCG
Found at i:34593 original size:185 final size:185
Alignment explanation
Indices: 34303--34674 Score: 631
Period size: 185 Copynumber: 2.0 Consensus size: 185
34293 AAATTAAATG
* * *
34303 TTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAG
1 TTTTTAATTAAAAAAAAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAC
34368 ATAAATTTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATTGGATCTTAAATTATTAAT
66 ATAAATTTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATTGGATCTTAAATTATTAAT
* * *
34433 TGAGTTTTAAATTGTTTGGGCTTAGCCCAAATGTTATATATAATATATTTAATAT
131 TGAGTTTTAAATGGTTTGGGCTGAGCCCAAATATTATATATAATATATTTAATAT
34488 TTTTTAATTAAAAAAACAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAAATTT-
1 TTTTTAATTAAAAAAA-AGTTTACAATTAATTTAAATAATATATAATTATAAAAT-AAAAATTTC
*
34552 ACAT-AATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTA
64 ACATAAATTTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATTGGATCTTAAATTATTA
* *
34616 ATTGGGTTTTAAATGGTTTGGGCTGAGCCCATATATTATATATAATATATTTAATAT
129 ATTGAGTTTTAAATGGTTTGGGCTGAGCCCAAATATTATATATAATATATTTAATAT
34673 TT
1 TT
34675 AAAATTTAAT
Statistics
Matches: 176, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
185 128 0.73
186 40 0.23
187 8 0.05
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.46
Consensus pattern (185 bp):
TTTTTAATTAAAAAAAAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAC
ATAAATTTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATTGGATCTTAAATTATTAAT
TGAGTTTTAAATGGTTTGGGCTGAGCCCAAATATTATATATAATATATTTAATAT
Found at i:40614 original size:10 final size:11
Alignment explanation
Indices: 40598--40622 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
40588 TTTGACCAAC
40598 TTTTTTTTCGA
1 TTTTTTTTCGA
40609 TTTTTTTTCGA
1 TTTTTTTTCGA
40620 TTT
1 TTT
40623 GCCAAAATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.08, G:0.08, T:0.76
Consensus pattern (11 bp):
TTTTTTTTCGA
Found at i:40811 original size:6 final size:6
Alignment explanation
Indices: 40794--40842 Score: 75
Period size: 6 Copynumber: 8.5 Consensus size: 6
40784 GACACGTATT
*
40794 ACCACG AACACG ACCACG ACCACG ACCACG ACCACG ACC-CG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
40840 ACC
1 ACC
40843 CGAGACGGGA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
5 10 0.24
6 31 0.76
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:41101 original size:19 final size:20
Alignment explanation
Indices: 41076--41166 Score: 105
Period size: 19 Copynumber: 4.4 Consensus size: 20
41066 CTTATTTTGG
41076 ATTTTTCACTATCGCAACAC
1 ATTTTTCACTATCGCAACAC
41096 -TTTTTCACTATCGCAACAAC
1 ATTTTTCACTATCGCAAC-AC
*
41116 ACGTTTTTCAAACTCTCGCAACAC
1 A--TTTTTC--ACTATCGCAACAC
*
41140 A-TTTTAACTATCGCAACAC
1 ATTTTTCACTATCGCAACAC
41159 ATTTTTCA
1 ATTTTTCA
41167 AAATCGCGTT
Statistics
Matches: 60, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
19 30 0.50
20 7 0.12
21 4 0.07
23 6 0.10
24 3 0.05
25 10 0.17
ACGTcount: A:0.31, C:0.29, G:0.05, T:0.35
Consensus pattern (20 bp):
ATTTTTCACTATCGCAACAC
Found at i:41138 original size:44 final size:41
Alignment explanation
Indices: 41087--41168 Score: 119
Period size: 44 Copynumber: 1.9 Consensus size: 41
41077 TTTTTCACTA
* *
41087 TCGCAACACTTTTTCACTATCGCAACAACACGTTTTTCAAACTC
1 TCGCAACACATTTTAACTATCGCAAC-ACA--TTTTTCAAACTC
41131 TCGCAACACATTTTAACTATCGCAACACATTTTTCAAA
1 TCGCAACACATTTTAACTATCGCAACACATTTTTCAAA
41169 ATCGCGTTGC
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
41 9 0.25
43 3 0.08
44 24 0.67
ACGTcount: A:0.33, C:0.29, G:0.06, T:0.32
Consensus pattern (41 bp):
TCGCAACACATTTTAACTATCGCAACACATTTTTCAAACTC
Found at i:41216 original size:21 final size:21
Alignment explanation
Indices: 41170--41249 Score: 117
Period size: 21 Copynumber: 3.9 Consensus size: 21
41160 TTTTTCAAAA
* * *
41170 TCGCGTTGCGAATCT-TACAA
1 TCGCGTTGCGAATCTGGATAT
41190 TCGCGTTGCGAATCTGGATAT
1 TCGCGTTGCGAATCTGGATAT
41211 TCGCGTTGCGAATCTGGATAT
1 TCGCGTTGCGAATCTGGATAT
*
41232 TCGCGTTGCGAATTTGGA
1 TCGCGTTGCGAATCTGGA
41250 AACTGAGTTG
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
20 15 0.27
21 40 0.73
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.33
Consensus pattern (21 bp):
TCGCGTTGCGAATCTGGATAT
Found at i:47391 original size:2 final size:2
Alignment explanation
Indices: 47384--47450 Score: 51
Period size: 2 Copynumber: 37.5 Consensus size: 2
47374 CCGCCCCGAT
* *
47384 TA TA TA TA TA TA TA TA -A TA T- TT TA TA TA T- TT TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
47422 TT TA TA T- TA -A T- TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
47451 TTTATATTTT
Statistics
Matches: 54, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
1 8 0.15
2 46 0.85
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (2 bp):
TA
Found at i:47411 original size:18 final size:18
Alignment explanation
Indices: 47388--47486 Score: 67
Period size: 18 Copynumber: 6.1 Consensus size: 18
47378 CCCGATTATA
47388 TATATATATATAATATTT
1 TATATATATATAATATTT
*
47406 TATATAT-TTTATATATTT
1 TATATATATATA-ATATTT
47424 TATAT-TA-AT--TA---
1 TATATATATATAATATTT
47435 TATATATATATAATATTT
1 TATATATATATAATATTT
* * * *
47453 TATATTTTTATATTA-AT
1 TATATATATATAATATTT
47470 TATATATA-A-AATATTT
1 TATATATATATAATATTT
47486 T
1 T
47487 CGGGTTCGGG
Statistics
Matches: 61, Mismatches: 10, Indels: 22
0.66 0.11 0.24
Matches are distributed among these distances:
11 5 0.08
12 2 0.03
13 2 0.03
14 2 0.03
15 5 0.08
16 3 0.05
17 12 0.20
18 30 0.49
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TATATATATATAATATTT
Found at i:50807 original size:11 final size:11
Alignment explanation
Indices: 50784--50816 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
50774 AATTTTTTAC
*
50784 TTTCTTTTATT
1 TTTCTTTTCTT
50795 TTT-TTTTCTT
1 TTTCTTTTCTT
50805 TTTCTTTTCTT
1 TTTCTTTTCTT
50816 T
1 T
50817 GTTACATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTCTTTTCTT
Found at i:50812 original size:15 final size:15
Alignment explanation
Indices: 50770--50855 Score: 52
Period size: 14 Copynumber: 5.7 Consensus size: 15
50760 GATTTTTAGT
50770 TTTTAATTTTTTACTTTC
1 TTTT-ATTTTTT--TTTC
50788 TTTTATTTTTTTTTC
1 TTTTATTTTTTTTTC
* *
50803 TTTT-TCTTTTCTT-
1 TTTTATTTTTTTTTC
* ** *
50816 TGTTACATTATTTTC
1 TTTTATTTTTTTTTC
* *
50831 TCTTATTTTATTTT-
1 TTTTATTTTTTTTTC
50845 TTTTATTTTTT
1 TTTTATTTTTT
50856 ATTGTAATTT
Statistics
Matches: 54, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
13 3 0.06
14 21 0.39
15 19 0.35
17 7 0.13
18 4 0.07
ACGTcount: A:0.12, C:0.09, G:0.01, T:0.78
Consensus pattern (15 bp):
TTTTATTTTTTTTTC
Found at i:62349 original size:33 final size:31
Alignment explanation
Indices: 62283--62349 Score: 89
Period size: 33 Copynumber: 2.1 Consensus size: 31
62273 CTAAAAATTA
* *
62283 ATATTGAATCATTAAACTATTGTTAAAGGTG
1 ATATTGAATCATTAAACTATTATCAAAGGTG
*
62314 ATATTGATATTCATTAAACTATTATCAAAGTTG
1 ATATTGA-A-TCATTAAACTATTATCAAAGGTG
62347 ATA
1 ATA
62350 GCTACCTAGG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
31 7 0.23
32 1 0.03
33 23 0.74
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.40
Consensus pattern (31 bp):
ATATTGAATCATTAAACTATTATCAAAGGTG
Found at i:62638 original size:22 final size:22
Alignment explanation
Indices: 62610--62663 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
62600 CGGGTTAAAA
* * *
62610 TTCGGTTTCGGTTCGAGTTATT
1 TTCGGTTTCGATTCGAGATACT
62632 TTCGGTTTCGATTCGAGATACT
1 TTCGGTTTCGATTCGAGATACT
*
62654 TTCAGTTTCG
1 TTCGGTTTCG
62664 CTAAATTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.13, C:0.17, G:0.24, T:0.46
Consensus pattern (22 bp):
TTCGGTTTCGATTCGAGATACT
Found at i:64567 original size:22 final size:22
Alignment explanation
Indices: 64535--64579 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
64525 AAGTCAAAGA
*
64535 AAAATGGTAAAATTTTACCATT
1 AAAATGATAAAATTTTACCATT
64557 AAAATGATAAAATTTTACCATT
1 AAAATGATAAAATTTTACCATT
64579 A
1 A
64580 GTCCTTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.49, C:0.09, G:0.07, T:0.36
Consensus pattern (22 bp):
AAAATGATAAAATTTTACCATT
Found at i:64744 original size:24 final size:24
Alignment explanation
Indices: 64694--64747 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
64684 TTGAGAACTG
*
64694 AATAAACGAGCTCATAAACAAGTC
1 AATAAACGAGCTCATAAACAAGCC
* * **
64718 AATAAAGGAGCTTATAAATGAGCC
1 AATAAACGAGCTCATAAACAAGCC
64742 AATAAA
1 AATAAA
64748 TGAGTTTGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.52, C:0.15, G:0.15, T:0.19
Consensus pattern (24 bp):
AATAAACGAGCTCATAAACAAGCC
Found at i:66240 original size:37 final size:37
Alignment explanation
Indices: 66199--66272 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
66189 CATGTTCGTG
66199 GTACGAACTCGTATTTCTTAATTCAAACTTTCAGTGT
1 GTACGAACTCGTATTTCTTAATTCAAACTTTCAGTGT
*
66236 GTACGAACTCGTATTTCTTAATTCGAACTTTCAGTGT
1 GTACGAACTCGTATTTCTTAATTCAAACTTTCAGTGT
66273 TTTTCAAGTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.41
Consensus pattern (37 bp):
GTACGAACTCGTATTTCTTAATTCAAACTTTCAGTGT
Found at i:67875 original size:31 final size:31
Alignment explanation
Indices: 67801--67876 Score: 80
Period size: 31 Copynumber: 2.5 Consensus size: 31
67791 TTCAAATTTC
* *
67801 ATAAGATATGTTCACTTATATTTTTATTTAA
1 ATAAGATATGGTCACTTACATTTTTATTTAA
* * * *
67832 ACAATATTTGGTCACTTACGTTTTTATTTAA
1 ATAAGATATGGTCACTTACATTTTTATTTAA
* *
67863 TTAAGATGTGGTCA
1 ATAAGATATGGTCA
67877 TCCCGAGTTA
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.32, C:0.09, G:0.12, T:0.47
Consensus pattern (31 bp):
ATAAGATATGGTCACTTACATTTTTATTTAA
Found at i:69031 original size:27 final size:25
Alignment explanation
Indices: 68973--69043 Score: 74
Period size: 24 Copynumber: 2.8 Consensus size: 25
68963 ATATATATAT
68973 TAATTTAAAATATTTTTATATCAAC
1 TAATTTAAAATATTTTTATATCAAC
* *
68998 TTA-TT-AAATATATTTTATTATTAACC
1 TAATTTAAAATAT-TTTTA-TATCAA-C
69024 TAATTTAAAAATATTTTTAT
1 TAATTT-AAAATATTTTTAT
69044 TTTTATTTTC
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
23 6 0.16
24 7 0.19
25 7 0.19
26 3 0.08
27 3 0.08
28 5 0.14
29 6 0.16
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (25 bp):
TAATTTAAAATATTTTTATATCAAC
Found at i:69057 original size:28 final size:29
Alignment explanation
Indices: 69026--69082 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 29
69016 TATTAACCTA
69026 ATTTAAAAATAT-T-TTTATTTTTATTTTC
1 ATTTAAAAATATATATTTA-TTTTATTTTC
69054 ATTTAAAAATATATAATTTATTTTATTTT
1 ATTTAAAAATATAT-ATTTATTTTATTTT
69083 ATTGAAAGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
28 12 0.46
29 1 0.04
30 9 0.35
31 4 0.15
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (29 bp):
ATTTAAAAATATATATTTATTTTATTTTC
Found at i:70318 original size:20 final size:20
Alignment explanation
Indices: 70293--70331 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
70283 TCGTAGAGTG
70293 AAATTATATTAGAGTTGACT
1 AAATTATATTAGAGTTGACT
70313 AAATTATATTAGAGTTGAC
1 AAATTATATTAGAGTTGAC
70332 AGAGATCACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.05, G:0.15, T:0.38
Consensus pattern (20 bp):
AAATTATATTAGAGTTGACT
Found at i:74789 original size:19 final size:19
Alignment explanation
Indices: 74762--74806 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
74752 TAAATGTCCT
* *
74762 TGATTTTTATAGTAAATTG
1 TGATATTTATAGTAAACTG
74781 TGATATTTATAGTAAACTG
1 TGATATTTATAGTAAACTG
74800 TGATATT
1 TGATATT
74807 AACTACTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (19 bp):
TGATATTTATAGTAAACTG
Found at i:75658 original size:54 final size:54
Alignment explanation
Indices: 75594--75697 Score: 199
Period size: 54 Copynumber: 1.9 Consensus size: 54
75584 TCAGCTTAGG
75594 TGTGGAATTATATTATTTCAGAGTGCAAAAGTAGATCATCAATTCAGGGTACGA
1 TGTGGAATTATATTATTTCAGAGTGCAAAAGTAGATCATCAATTCAGGGTACGA
*
75648 TGTGGAATTATATTATTTCAGAGTGCGAAAGTAGATCATCAATTCAGGGT
1 TGTGGAATTATATTATTTCAGAGTGCAAAAGTAGATCATCAATTCAGGGT
75698 GCGAAATTAT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.33
Consensus pattern (54 bp):
TGTGGAATTATATTATTTCAGAGTGCAAAAGTAGATCATCAATTCAGGGTACGA
Found at i:75694 original size:26 final size:26
Alignment explanation
Indices: 75610--75703 Score: 75
Period size: 26 Copynumber: 3.5 Consensus size: 26
75600 ATTATATTAT
*
75610 TTCAGAGTGCAAAAGTAGATCATCAA
1 TTCAGAGTGCGAAAGTAGATCATCAA
* * * * *
75636 TTCAGGGTACG-ATGTGGAATTAT-ATTA
1 TTCAGAGTGCGAAAGTAG-ATCATCA--A
75663 TTTCAGAGTGCGAAAGTAGATCATCAA
1 -TTCAGAGTGCGAAAGTAGATCATCAA
*
75690 TTCAGGGTGCGAAA
1 TTCAGAGTGCGAAA
75704 TTATACGAGA
Statistics
Matches: 50, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
25 5 0.10
26 25 0.50
27 2 0.04
28 13 0.26
29 5 0.10
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (26 bp):
TTCAGAGTGCGAAAGTAGATCATCAA
Found at i:81201 original size:20 final size:20
Alignment explanation
Indices: 81176--81213 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
81166 TTGGAGCGTG
81176 GGGGGAATCGGTACCCTATA
1 GGGGGAATCGGTACCCTATA
* *
81196 GGGGGAATTGGTTCCCTA
1 GGGGGAATCGGTACCCTA
81214 AGTGTAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.18, G:0.37, T:0.24
Consensus pattern (20 bp):
GGGGGAATCGGTACCCTATA
Found at i:82348 original size:12 final size:12
Alignment explanation
Indices: 82331--82371 Score: 73
Period size: 12 Copynumber: 3.4 Consensus size: 12
82321 TTATTGTGCT
82331 TGCTCCTCGGGC
1 TGCTCCTCGGGC
82343 TGCTCCTCGGGC
1 TGCTCCTCGGGC
82355 TGCTCCTCGGGC
1 TGCTCCTCGGGC
*
82367 AGCTC
1 TGCTC
82372 AGGCTCATCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.02, C:0.41, G:0.32, T:0.24
Consensus pattern (12 bp):
TGCTCCTCGGGC
Found at i:84012 original size:21 final size:20
Alignment explanation
Indices: 83987--84067 Score: 63
Period size: 20 Copynumber: 3.9 Consensus size: 20
83977 CAGAACCCCA
* *
83987 GGGGGTATCGATTCCCTTGT
1 GGGGGAATCGATTCCCTTAT
* *
84007 GGGGGGAATCGGTTCCCCTTCAAA
1 -GGGGGAATCGATT-CCCTT--AT
* *
84031 GGGGGAATCGGTTCCCTCAT
1 GGGGGAATCGATTCCCTTAT
*
84051 GGGGGTATCGATTCCCT
1 GGGGGAATCGATTCCCT
84068 CTGCACCAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
20 16 0.33
21 11 0.22
22 9 0.18
23 13 0.27
ACGTcount: A:0.15, C:0.23, G:0.35, T:0.27
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTTAT
Found at i:89001 original size:24 final size:24
Alignment explanation
Indices: 88957--89006 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
88947 ATAATGAACC
*
88957 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
88981 AAAATAAAGTTCAAACA-ACCATTA
1 AAAATAAACTT-AAACATACCATTA
89005 AA
1 AA
89007 TCAAACACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.60, C:0.14, G:0.02, T:0.24
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:98969 original size:2 final size:2
Alignment explanation
Indices: 98962--98992 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
98952 ACTCACATAC
98962 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
98993 ATTATGTAAA
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:99283 original size:29 final size:29
Alignment explanation
Indices: 99241--99297 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
99231 AGTATTTGCC
99241 GTAGGTCGCCATGC-CTTCCGGGCGACCTT
1 GTAGGTCGCCATGCAC-TCCGGGCGACCTT
* *
99270 GTAGGTCGTCATGCACTCCGGGTGACCT
1 GTAGGTCGCCATGCACTCCGGGCGACCT
99298 ACCCTTGCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 24 0.96
30 1 0.04
ACGTcount: A:0.12, C:0.32, G:0.32, T:0.25
Consensus pattern (29 bp):
GTAGGTCGCCATGCACTCCGGGCGACCTT
Found at i:99389 original size:29 final size:29
Alignment explanation
Indices: 99356--99411 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
99346 TTCCAACACA
*
99356 TAGGTCGCCATGCCCTCCGGGCGACCTTT
1 TAGGTCGCCATGCACTCCGGGCGACCTTT
99385 TAGGTCGCCATGCACTCCGGGCGACCT
1 TAGGTCGCCATGCACTCCGGGCGACCT
99412 ACCCTCGCTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.12, C:0.38, G:0.29, T:0.21
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCGGGCGACCTTT
Found at i:100399 original size:17 final size:17
Alignment explanation
Indices: 100374--100406 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
100364 TTGGTCGTTA
100374 AAATATAAATATTTTTT
1 AAATATAAATATTTTTT
*
100391 AAATTTAAATATTTTT
1 AAATATAAATATTTTT
100407 ATTTTAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
AAATATAAATATTTTTT
Found at i:101307 original size:15 final size:15
Alignment explanation
Indices: 101287--101338 Score: 95
Period size: 15 Copynumber: 3.5 Consensus size: 15
101277 TGAGACATTA
101287 CCCGCCCCGCATCCG
1 CCCGCCCCGCATCCG
101302 CCCGCCCCGCATCCG
1 CCCGCCCCGCATCCG
*
101317 CCCGCCCCACATCCG
1 CCCGCCCCGCATCCG
101332 CCCGCCC
1 CCCGCCC
101339 AGCTAAATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.08, C:0.69, G:0.17, T:0.06
Consensus pattern (15 bp):
CCCGCCCCGCATCCG
Found at i:106885 original size:13 final size:13
Alignment explanation
Indices: 106836--106875 Score: 80
Period size: 13 Copynumber: 3.1 Consensus size: 13
106826 CATTTAAATG
106836 ATAAACGAACATA
1 ATAAACGAACATA
106849 ATAAACGAACATA
1 ATAAACGAACATA
106862 ATAAACGAACATA
1 ATAAACGAACATA
106875 A
1 A
106876 ACGAACAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.62, C:0.15, G:0.07, T:0.15
Consensus pattern (13 bp):
ATAAACGAACATA
Found at i:107937 original size:6 final size:6
Alignment explanation
Indices: 107922--107954 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
107912 TTCATGTGGG
*
107922 AAAAGA AAAAGC AAAAGC AAAAGC AAAAGC AAA
1 AAAAGC AAAAGC AAAAGC AAAAGC AAAAGC AAA
107955 CCCACGCCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.73, C:0.12, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAGC
Found at i:109433 original size:15 final size:15
Alignment explanation
Indices: 109395--109436 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
109385 AATCATTTAA
*
109395 TAATTTATTATTTTAT
1 TAATTT-TTATTGTAT
109411 T-ATATTTTATTGTAT
1 TAAT-TTTTATTGTAT
109426 TAATTTTTATT
1 TAATTTTTATT
109437 ACTTTTTGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
15 18 0.78
16 5 0.22
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (15 bp):
TAATTTTTATTGTAT
Found at i:111568 original size:45 final size:45
Alignment explanation
Indices: 111506--111683 Score: 220
Period size: 48 Copynumber: 3.9 Consensus size: 45
111496 CAATAAACTT
*
111506 ATTTTTATTTATCTTGTTTCTTAATG-TTT-TTATTTAATTATGG
1 ATTTTTATTTATTTTGTTTCTTAATGTTTTATTATTTAATTATGG
111549 ATTTTTTTATTTATTTTGTTTCTTAATGTTTTTATTATTTAATTATGG
1 A--TTTTTATTTATTTTGTTTCTTAATG-TTTTATTATTTAATTATGG
* *
111597 ATTTTTATTTA-TTT-ATTCTTAATGTTTTATTATTTAATTATGAA
1 ATTTTTATTTATTTTGTTTCTTAATGTTTTATTATTTAATTATG-G
* * *
111641 ACTTTTATTTATTTTGTTTTTTAAATTTTTTTATTATTTAATT
1 ATTTTTATTTATTTTGTTTCTT-AA-TGTTTTATTATTTAATT
111684 GTTTGAATTG
Statistics
Matches: 118, Mismatches: 7, Indels: 15
0.84 0.05 0.11
Matches are distributed among these distances:
43 19 0.16
44 19 0.16
45 30 0.25
46 14 0.12
47 5 0.04
48 31 0.26
ACGTcount: A:0.24, C:0.03, G:0.06, T:0.67
Consensus pattern (45 bp):
ATTTTTATTTATTTTGTTTCTTAATGTTTTATTATTTAATTATGG
Found at i:111608 original size:22 final size:21
Alignment explanation
Indices: 111577--111654 Score: 77
Period size: 22 Copynumber: 3.6 Consensus size: 21
111567 TTTCTTAATG
*
111577 TTTTTATTATTTAATTATGGA
1 TTTTTATTATTTAATTATGAA
* *
111598 TTTTTATTTATTT-ATTCTTAA
1 TTTTTA-TTATTTAATTATGAA
111619 TGTTTTATTATTTAATTATGAAA
1 T-TTTTATTATTTAATTATG-AA
*
111642 CTTTTATTTATTT
1 TTTTTA-TTATTT
111655 TGTTTTTTAA
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
21 18 0.39
22 20 0.43
23 8 0.17
ACGTcount: A:0.27, C:0.03, G:0.05, T:0.65
Consensus pattern (21 bp):
TTTTTATTATTTAATTATGAA
Found at i:111647 original size:44 final size:45
Alignment explanation
Indices: 111506--111683 Score: 202
Period size: 45 Copynumber: 3.9 Consensus size: 45
111496 CAATAAACTT
*
111506 ATTTTTATTTATCTTGTTTCTTAATG-TTT-TTATTTAATTATGGAT
1 ATTTTTATTTAT-TTGTTTCTTAATGTTTTATTATTTAATTAT-GAA
* *
111551 TTTTTTATTTATTTTGTTTCTTAATGTTTTTATTATTTAATTATG-G
1 ATTTTTATTTA-TTTGTTTCTTAATG-TTTTATTATTTAATTATGAA
*
111597 ATTTTTATTTATTT-ATTCTTAATGTTTTATTATTTAATTATGAA
1 ATTTTTATTTATTTGTTTCTTAATGTTTTATTATTTAATTATGAA
* * *
111641 ACTTTTATTTATTTTGTTTTTTAAATTTTTTTATTATTTAATT
1 ATTTTTATTTA-TTTGTTTCTT-AA-TGTTTTATTATTTAATT
111684 GTTTGAATTG
Statistics
Matches: 115, Mismatches: 9, Indels: 15
0.83 0.06 0.11
Matches are distributed among these distances:
43 18 0.16
44 19 0.17
45 29 0.25
46 15 0.13
47 6 0.05
48 28 0.24
ACGTcount: A:0.24, C:0.03, G:0.06, T:0.67
Consensus pattern (45 bp):
ATTTTTATTTATTTGTTTCTTAATGTTTTATTATTTAATTATGAA
Found at i:111672 original size:91 final size:91
Alignment explanation
Indices: 111506--111683 Score: 254
Period size: 91 Copynumber: 2.0 Consensus size: 91
111496 CAATAAACTT
* ***
111506 ATTTTTATTTATCTTGTTTCTTAATGTTTTTATTTAATTATGGATTTTTTTATTTATTTTGTTTC
1 ATTTTTATTTATCTTGATTCTTAATGTTTTTATTTAATTATGGAAACTTTTATTTATTTTGTTTC
111571 TTAATGTTTTTATTATTTAATTATGG
66 TTAATGTTTTTATTATTTAATTATGG
111597 ATTTTTATTTAT-TT-ATTCTTAATGTTTTATTATTTAATTAT-GAAACTTTTATTTATTTTGTT
1 ATTTTTATTTATCTTGATTCTTAATG-TTT-TTATTTAATTATGGAAACTTTTATTTATTTTGTT
* *
111659 TTTTAAATTTTTTTATTATTTAATT
64 TCTT-AATGTTTTTATTATTTAATT
111684 GTTTGAATTG
Statistics
Matches: 78, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
89 9 0.12
90 26 0.33
91 43 0.55
ACGTcount: A:0.24, C:0.03, G:0.06, T:0.67
Consensus pattern (91 bp):
ATTTTTATTTATCTTGATTCTTAATGTTTTTATTTAATTATGGAAACTTTTATTTATTTTGTTTC
TTAATGTTTTTATTATTTAATTATGG
Found at i:111703 original size:91 final size:89
Alignment explanation
Indices: 111523--111723 Score: 221
Period size: 91 Copynumber: 2.2 Consensus size: 89
111513 TTTATCTTGT
***
111523 TTCTTAATGTTTTTATTTAATTATGGATTTTTTTATTTATTTTGTTTCTTAATGTTTTTATTATT
1 TTCTTAATGTTTTTATTTAATTATGGAAACTTTTATTTATTTTGTTTCTTAATGTTTTTATTATT
* * *
111588 TAATTATGGATTTTTATTTATTTA
66 TAATTATGGAATTGTATATATTTA
* *
111612 TTCTTAATGTTTTATTATTTAATTAT-GAAACTTTTATTTATTTTGTTTTTTAAATTTTTTTATT
1 TTCTTAATG-TTT-TTATTTAATTATGGAAACTTTTATTTATTTTGTTTCTT-AATGTTTTTATT
* * *
111676 ATTTAATTGTTTGAATTGTA-ATGTTTA
63 ATTTAATT-ATGGAATTGTATATATTTA
*
111703 TAT-TTAA-GTTTCTATTTAATT
1 T-TCTTAATGTTTTTATTTAATT
111724 GTTTTTTTTT
Statistics
Matches: 95, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
88 9 0.09
89 12 0.13
90 25 0.26
91 41 0.43
92 8 0.08
ACGTcount: A:0.25, C:0.02, G:0.07, T:0.65
Consensus pattern (89 bp):
TTCTTAATGTTTTTATTTAATTATGGAAACTTTTATTTATTTTGTTTCTTAATGTTTTTATTATT
TAATTATGGAATTGTATATATTTA
Found at i:111748 original size:20 final size:21
Alignment explanation
Indices: 111717--111759 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
111707 TAAGTTTCTA
* *
111717 TTTAATTGTTTTTTTTTAGTT
1 TTTAATTGTTTTTATTTAATT
111738 TTTAA-TGTTTTTATTTAATT
1 TTTAATTGTTTTTATTTAATT
111758 TT
1 TT
111760 CACTTTAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.19, C:0.00, G:0.07, T:0.74
Consensus pattern (21 bp):
TTTAATTGTTTTTATTTAATT
Found at i:112382 original size:17 final size:17
Alignment explanation
Indices: 112358--112403 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 17
112348 ATAATTATTA
112358 TATATATATATATAATAT
1 TATATATATATATAAT-T
112376 T-TATATAT-T-TAATT
1 TATATATATATATAATT
*
112390 TAAATATATATATA
1 TATATATATATATA
112404 CATGGCCCGA
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
14 2 0.08
15 10 0.42
16 2 0.08
17 9 0.38
18 1 0.04
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TATATATATATATAATT
Found at i:113329 original size:23 final size:23
Alignment explanation
Indices: 113299--113347 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
113289 TGGTGGTTGG
*
113299 TTTAATGG-ATGTTTAGACTTTAT
1 TTTAATGGTATATTTA-ACTTTAT
*
113322 TTTAATGGTATATTTAAGTTTAT
1 TTTAATGGTATATTTAACTTTAT
113345 TTT
1 TTT
113348 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.27, C:0.02, G:0.14, T:0.57
Consensus pattern (23 bp):
TTTAATGGTATATTTAACTTTAT
Found at i:117025 original size:21 final size:20
Alignment explanation
Indices: 116999--117039 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
116989 ATATTTGGTC
116999 AAATAAT-TAAATATAAAATAA
1 AAATAATAT-AATA-AAAATAA
117020 AAATAATATAATAAAAATAA
1 AAATAATATAATAAAAATAA
117040 TTTTACCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.37
21 11 0.58
22 1 0.05
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (20 bp):
AAATAATATAATAAAAATAA
Found at i:118846 original size:24 final size:24
Alignment explanation
Indices: 118805--118877 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
118795 AGGAAAATGA
** *
118805 TAATCGAGTAAATGAGCTTATAAAC
1 TAATCG-GTAAACAAGCTAATAAAC
118830 TAATCGGTAAACAAGCTAATAAAC
1 TAATCGGTAAACAAGCTAATAAAC
* *
118854 TAGTTGGTAAACAAGCTAATAAAC
1 TAATCGGTAAACAAGCTAATAAAC
118878 AAGTTGGAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
24 37 0.86
25 6 0.14
ACGTcount: A:0.47, C:0.14, G:0.15, T:0.25
Consensus pattern (24 bp):
TAATCGGTAAACAAGCTAATAAAC
Found at i:118852 original size:12 final size:12
Alignment explanation
Indices: 118837--118880 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
118827 AACTAATCGG
118837 TAAACAAGCTAA
1 TAAACAAGCTAA
* * **
118849 TAAACTAGTTGG
1 TAAACAAGCTAA
118861 TAAACAAGCTAA
1 TAAACAAGCTAA
118873 TAAACAAG
1 TAAACAAG
118881 TTGGAAAGGA
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.52, C:0.14, G:0.14, T:0.20
Consensus pattern (12 bp):
TAAACAAGCTAA
Found at i:118882 original size:24 final size:24
Alignment explanation
Indices: 118835--118884 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
118825 TAAACTAATC
*
118835 GGTAAACAAGCTAATAAACTAGTT
1 GGTAAACAAGCTAATAAACAAGTT
118859 GGTAAACAAGCTAATAAACAAGTT
1 GGTAAACAAGCTAATAAACAAGTT
118883 GG
1 GG
118885 AAAGGATGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.46, C:0.12, G:0.20, T:0.22
Consensus pattern (24 bp):
GGTAAACAAGCTAATAAACAAGTT
Found at i:131659 original size:16 final size:16
Alignment explanation
Indices: 131638--131683 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
131628 CTAAAGTTTA
131638 AATTTTCTTTAATTAT
1 AATTTTCTTTAATTAT
*
131654 AATTTTTTTTAATTAT
1 AATTTTCTTTAATTAT
*
131670 -ATTTGTCTTAAATT
1 AATTT-TCTTTAATT
131684 TTATATTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 4 0.15
16 22 0.85
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.63
Consensus pattern (16 bp):
AATTTTCTTTAATTAT
Found at i:132735 original size:27 final size:26
Alignment explanation
Indices: 132705--132759 Score: 83
Period size: 27 Copynumber: 2.1 Consensus size: 26
132695 CTATATTTTA
*
132705 TTTTTAATATAATCATTAAATTAACTT
1 TTTTTAATATAATCAATAAATTAA-TT
*
132732 TTTTTAATATAATTAATAAATTAATT
1 TTTTTAATATAATCAATAAATTAATT
132758 TT
1 TT
132760 ATGATTATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 4 0.15
27 22 0.85
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.55
Consensus pattern (26 bp):
TTTTTAATATAATCAATAAATTAATT
Found at i:142456 original size:28 final size:28
Alignment explanation
Indices: 142416--142472 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
142406 AAATTAAAAG
142416 AATGTGTTGTGTCACCACCGGATTGGAT
1 AATGTGTTGTGTCACCACCGGATTGGAT
142444 AATGTGTTGTGTCACCACCGGATTGGAT
1 AATGTGTTGTGTCACCACCGGATTGGAT
142472 A
1 A
142473 CAAAATAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.32
Consensus pattern (28 bp):
AATGTGTTGTGTCACCACCGGATTGGAT
Found at i:142489 original size:9 final size:9
Alignment explanation
Indices: 142475--142511 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
142465 ATTGGATACA
142475 AAATAAAAT
1 AAATAAAAT
142484 AAATAAAAT
1 AAATAAAAT
*
142493 AATTAAAAT
1 AAATAAAAT
*
142502 GAATAAAAT
1 AAATAAAAT
142511 A
1 A
142512 GCCTCCAATC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (9 bp):
AAATAAAAT
Found at i:142578 original size:183 final size:183
Alignment explanation
Indices: 142270--142601 Score: 547
Period size: 183 Copynumber: 1.8 Consensus size: 183
142260 GTGTTACACA
* * * * *
142270 TGTCACCACTGGATTGTATACAAAATAAAATAAATTAAATAATTAAAATGAATAAAATATCCTTC
1 TGTCACCACCGGATTGGATACAAAATAAAATAAATAAAATAATTAAAATGAATAAAATAGCCTCC
** *
142335 AATATGGTAGTGACACATGTTGCCACCTAATTGGAAAATCAAATTTATTAAATTGAATTAAAACT
66 AATATGGTAGTGACACATGTCACAACCTAATTGGAAAATCAAATTTATTAAATTGAATTAAAACT
*
142400 ATGACTAAATTAAAAGAATGTGTTGTGTCACCACCGGATTGGATAATGTGTTG
131 ATGACCAAATTAAAAGAATGTGTTGTGTCACCACCGGATTGGATAATGTGTTG
142453 TGTCACCACCGGATTGGATACAAAATAAAATAAATAAAATAATTAAAATGAATAAAATAGCCTCC
1 TGTCACCACCGGATTGGATACAAAATAAAATAAATAAAATAATTAAAATGAATAAAATAGCCTCC
* * *
142518 AATCTGGTAGTGACACATGTCACAATCTAATTTGAAAATCAAATTTATTAAATTGAATTAAAACT
66 AATATGGTAGTGACACATGTCACAACCTAATTGGAAAATCAAATTTATTAAATTGAATTAAAACT
*
142583 ATGACCAAATTGAAAGAAT
131 ATGACCAAATTAAAAGAAT
142602 ATACAAATAT
Statistics
Matches: 136, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
183 136 1.00
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.30
Consensus pattern (183 bp):
TGTCACCACCGGATTGGATACAAAATAAAATAAATAAAATAATTAAAATGAATAAAATAGCCTCC
AATATGGTAGTGACACATGTCACAACCTAATTGGAAAATCAAATTTATTAAATTGAATTAAAACT
ATGACCAAATTAAAAGAATGTGTTGTGTCACCACCGGATTGGATAATGTGTTG
Found at i:143398 original size:18 final size:18
Alignment explanation
Indices: 143375--143420 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
143365 TTATCTCATA
143375 ATCTCAAATAACTATTAT
1 ATCTCAAATAACTATTAT
*
143393 ATCTCAAATGACTATTAT
1 ATCTCAAATAACTATTAT
143411 ATCTCAAATA
1 ATCTCAAATA
143421 GTATATTAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.43, C:0.17, G:0.02, T:0.37
Consensus pattern (18 bp):
ATCTCAAATAACTATTAT
Found at i:150547 original size:2 final size:2
Alignment explanation
Indices: 150542--150568 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
150532 AGTGAATCGA
150542 AG 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 AG A
150569 TGAGTTTGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:154288 original size:34 final size:34
Alignment explanation
Indices: 154243--154320 Score: 129
Period size: 34 Copynumber: 2.3 Consensus size: 34
154233 AAAAAATACT
*
154243 ATAACACCATTAAATCTCAATAAGTCTAAAATAA
1 ATAACACCATTAAATCTCAATAAATCTAAAATAA
* *
154277 ATAACATCATTAAGTCTCAATAAATCTAAAATAA
1 ATAACACCATTAAATCTCAATAAATCTAAAATAA
154311 ATAACACCAT
1 ATAACACCAT
154321 AACAGTAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.53, C:0.18, G:0.03, T:0.27
Consensus pattern (34 bp):
ATAACACCATTAAATCTCAATAAATCTAAAATAA
Found at i:165878 original size:18 final size:18
Alignment explanation
Indices: 165855--165892 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
165845 AATAGTGTGT
165855 TTGACATTATTAGCAAAA
1 TTGACATTATTAGCAAAA
165873 TTGACATTATTAGCAAAA
1 TTGACATTATTAGCAAAA
165891 TT
1 TT
165893 ATTTAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (18 bp):
TTGACATTATTAGCAAAA
Found at i:166707 original size:21 final size:22
Alignment explanation
Indices: 166667--166710 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 22
166657 TAAATACTTC
166667 ACAAAAAATAATTATAATATAA
1 ACAAAAAATAATTATAATATAA
166689 ACAAAATAATAATT-T-ATATAA
1 ACAAAA-AATAATTATAATATAA
166710 A
1 A
166711 TTTACAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.33
22 7 0.33
23 7 0.33
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.30
Consensus pattern (22 bp):
ACAAAAAATAATTATAATATAA
Found at i:167995 original size:21 final size:21
Alignment explanation
Indices: 167947--167996 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
167937 ATGACTATCG
*
167947 CAATGCGATTTTCCAATTTCG
1 CAATGCGATTTTCCAATTTCA
**
167968 CGTTGCGATTTTCCCAA-TTCA
1 CAATGCGATTTT-CCAATTTCA
167989 CAATGCGA
1 CAATGCGA
167997 ATTTGGAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (21 bp):
CAATGCGATTTTCCAATTTCA
Found at i:168053 original size:20 final size:20
Alignment explanation
Indices: 168028--168093 Score: 89
Period size: 20 Copynumber: 3.3 Consensus size: 20
168018 TAATACAAAA
168028 TCGCAATGCGATACTGACTT
1 TCGCAATGCGATACTGACTT
* *
168048 TCGCAACGCGATACTTACTT
1 TCGCAATGCGATACTGACTT
*
168068 TCGCAACT-AGATACTGACTT
1 TCGCAA-TGCGATACTGACTT
168088 TCGCAA
1 TCGCAA
168094 CGAGATAATA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (20 bp):
TCGCAATGCGATACTGACTT
Found at i:168094 original size:20 final size:20
Alignment explanation
Indices: 168037--168100 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
168027 ATCGCAATGC
*
168037 GATACTGACTTTCGCAACGC
1 GATACTGACTTTCGCAACGA
* *
168057 GATACTTACTTTCGCAACTA
1 GATACTGACTTTCGCAACGA
168077 GATACTGACTTTCGCAACGA
1 GATACTGACTTTCGCAACGA
168097 GATA
1 GATA
168101 ATACATAATC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (20 bp):
GATACTGACTTTCGCAACGA
Found at i:168343 original size:20 final size:21
Alignment explanation
Indices: 168298--168345 Score: 71
Period size: 22 Copynumber: 2.3 Consensus size: 21
168288 TCTCTCACCC
168298 ATCTCCGACGAAATCCGTCCCT
1 ATCTCCGACGAAATCCGT-CCT
*
168320 ATCTCCGGCGAAATCCGT-CT
1 ATCTCCGACGAAATCCGTCCT
168340 ATCTCC
1 ATCTCC
168346 ATCTCTTAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 8 0.32
22 17 0.68
ACGTcount: A:0.21, C:0.40, G:0.15, T:0.25
Consensus pattern (21 bp):
ATCTCCGACGAAATCCGTCCT
Found at i:168650 original size:20 final size:20
Alignment explanation
Indices: 168601--168659 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
168591 TTTATTCTCT
* **
168601 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTGTCATTTTCG
168621 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATTGTCATTTTCG
* *
168641 TGTTGCGATTTTCATTTTC
1 CGTTGCGATTGTCATTTTC
168660 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.15, C:0.19, G:0.22, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTGTCATTTTCG
Found at i:168850 original size:25 final size:24
Alignment explanation
Indices: 168796--168850 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
168786 TGTTTATTAT
* *
168796 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
168820 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
168846 TGTTT
1 TGTTT
168851 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:170000 original size:18 final size:18
Alignment explanation
Indices: 169979--170026 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
169969 TTCACTTCGG
*
169979 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACACA
* *
169997 GAGCTATCACCTCACATA
1 GAGCCATCACCTCACACA
170015 GAGCCATCACCT
1 GAGCCATCACCT
170027 GATCGACCCG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.29, C:0.42, G:0.12, T:0.17
Consensus pattern (18 bp):
GAGCCATCACCTCACACA
Found at i:170586 original size:20 final size:20
Alignment explanation
Indices: 170561--170606 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
170551 TAGTTTACTT
170561 TCGCAACACGAAAATAACTA
1 TCGCAACACGAAAATAACTA
* * **
170581 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATAACTA
170601 TCGCAA
1 TCGCAA
170607 TGCGAAATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.39, C:0.26, G:0.20, T:0.15
Consensus pattern (20 bp):
TCGCAACACGAAAATAACTA
Found at i:170615 original size:19 final size:20
Alignment explanation
Indices: 170578--170615 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
170568 ACGAAAATAA
170578 CTATCGCAACGCGGAAATGG
1 CTATCGCAACGCGGAAATGG
*
170598 CTATCGCAATGC-GAAATG
1 CTATCGCAACGCGGAAATG
170616 AAAACCGCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.32, C:0.24, G:0.26, T:0.18
Consensus pattern (20 bp):
CTATCGCAACGCGGAAATGG
Found at i:170624 original size:19 final size:19
Alignment explanation
Indices: 170600--170682 Score: 104
Period size: 19 Copynumber: 4.6 Consensus size: 19
170590 GGAAATGGCT
170600 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
170619 ACCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
170633 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
170652 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
170671 ATCGCAATGCGA
1 ATCGCAATGCGA
170683 TTTGTGTTTC
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
14 9 0.17
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 38 0.72
ACGTcount: A:0.46, C:0.22, G:0.20, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:170754 original size:20 final size:20
Alignment explanation
Indices: 170708--170794 Score: 122
Period size: 20 Copynumber: 4.4 Consensus size: 20
170698 GCGATTTTGT
**
170708 CGTTGCGATTTTCATTT-CG
1 CGTTGCGATAGTCATTTCCG
* *
170727 CATTGCGATAGCCATTTCCG
1 CGTTGCGATAGTCATTTCCG
170747 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
170767 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTCCG
170787 CGTTGCGA
1 CGTTGCGA
170795 AAGTATGTTT
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
19 13 0.22
20 47 0.78
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:170805 original size:20 final size:20
Alignment explanation
Indices: 170722--170818 Score: 106
Period size: 20 Copynumber: 4.8 Consensus size: 20
170712 GCGATTTTCA
* * *
170722 TTTCGCATTGCGATAGCCAT
1 TTTCGCGTTGCGAAAGTCAT
* *
170742 TTCCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGAAAGTCAT
* *
170762 TTCCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGAAAGTCAT
170782 TTTCGCGTTGCGAAAGT-AT
1 TTTCGCGTTGCGAAAGTCAT
*
170801 GTTTCGTGTTGCGAAAGT
1 -TTTCGCGTTGCGAAAGT
170819 AAACTATTCT
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
19 2 0.03
20 68 0.97
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.36
Consensus pattern (20 bp):
TTTCGCGTTGCGAAAGTCAT
Found at i:171195 original size:21 final size:20
Alignment explanation
Indices: 171169--171237 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 20
171159 CTGTCATCCC
171169 TCAAGAGTCCCCTCCAATCGT
1 TCAAGAGTCCCCTCC-ATCGT
* * **
171190 TCAAGAGGCCCCTATCATCCC
1 TCAAGAGTCCCCT-CCATCGT
* *
171211 TCAAGAGTCCCCCCCACCGT
1 TCAAGAGTCCCCTCCATCGT
171231 TCAAGAG
1 TCAAGAG
171238 GCCACTGTCA
Statistics
Matches: 37, Mismatches: 10, Indels: 3
0.74 0.20 0.06
Matches are distributed among these distances:
20 10 0.27
21 26 0.70
22 1 0.03
ACGTcount: A:0.25, C:0.41, G:0.16, T:0.19
Consensus pattern (20 bp):
TCAAGAGTCCCCTCCATCGT
Found at i:171249 original size:41 final size:42
Alignment explanation
Indices: 171159--171249 Score: 139
Period size: 41 Copynumber: 2.2 Consensus size: 42
171149 CCCGACTCAC
* *
171159 CTGTCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCC
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
* *
171201 CTATCATCCCTCAAGAGTCCCC-CCCACCGTTCAAGAGGCCA
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
171242 CTGTCATC
1 CTGTCATC
171250 GTTGAAGAGG
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 23 0.52
42 21 0.48
ACGTcount: A:0.22, C:0.42, G:0.15, T:0.21
Consensus pattern (42 bp):
CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
Found at i:172694 original size:14 final size:14
Alignment explanation
Indices: 172660--172698 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
172650 TTGATTGTTT
172660 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
172674 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
172688 TGTTGATTTGT
1 AATTGATTTGT
172699 TTAATTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:172915 original size:20 final size:20
Alignment explanation
Indices: 172890--172943 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
172880 GCGATTTTCA
172890 TTTCGCGTTGCGATAGCCAT
1 TTTCGCGTTGCGATAGCCAT
*
172910 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGCCAT
172930 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
172944 TTCCCCGTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.13, C:0.22, G:0.26, T:0.39
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGCCAT
Found at i:173516 original size:20 final size:20
Alignment explanation
Indices: 173495--173582 Score: 149
Period size: 20 Copynumber: 4.4 Consensus size: 20
173485 TGTATTATCT
* *
173495 CGTTGCGATAGTCAGAATCT
1 CGTTGCGAAAGTCAGAATCG
173515 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
173535 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
*
173555 CGTTGCGAAAGTCAGTATCG
1 CGTTGCGAAAGTCAGAATCG
173575 CGTTGCGA
1 CGTTGCGA
173583 TTTTGTATTA
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 65 1.00
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGAATCG
Found at i:173616 original size:20 final size:20
Alignment explanation
Indices: 173490--173624 Score: 146
Period size: 20 Copynumber: 6.7 Consensus size: 20
173480 GATTCTGTAT
*
173490 TATCTCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
173510 AATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
173530 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
173550 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
173570 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--TAGTCAG
173591 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
173611 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
173625 TTTCCAAATT
Statistics
Matches: 102, Mismatches: 10, Indels: 6
0.86 0.08 0.05
Matches are distributed among these distances:
19 3 0.03
20 83 0.81
21 14 0.14
22 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:173643 original size:41 final size:41
Alignment explanation
Indices: 173515--173645 Score: 122
Period size: 41 Copynumber: 3.2 Consensus size: 41
173505 GTCAGAATCT
* * * *** *
173515 CGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGA-ATCG
1 CGTTGCGATAGTCAGTATCGCATTGCGATTTTCAAATATCG
* * ** *
173555 CGTTGCGAAAGTCAGTATCGCGTTGCGATTTTGTATTATCG
1 CGTTGCGATAGTCAGTATCGCATTGCGATTTTCAAATATCG
173596 CGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAAT-TCG
1 CGTTGCGATAGTCAGTATCGCATTGCGATTTT-CAAATATCG
*
173637 CATTGCGAT
1 CGTTGCGAT
173646 TTACTTATTC
Statistics
Matches: 75, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
40 28 0.37
41 45 0.60
42 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.31
Consensus pattern (41 bp):
CGTTGCGATAGTCAGTATCGCATTGCGATTTTCAAATATCG
Found at i:173657 original size:20 final size:21
Alignment explanation
Indices: 173613--173664 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
173603 ATAGTCAGTA
*
173613 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
173634 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
*
173654 TCGCGTTGCGA
1 TCGCATTGCGA
173665 ATTGGGAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:173684 original size:21 final size:20
Alignment explanation
Indices: 173660--173706 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 20
173650 TTATTCGCGT
173660 TGCGAATTGGGAAAATCGCAA
1 TGCGAATT-GGAAAATCGCAA
*
173681 TGCGAAATTGGAAAATCGCAT
1 TGCG-AATTGGAAAATCGCAA
173702 TGCGA
1 TGCGA
173707 TAGTCATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 1 0.04
21 19 0.79
22 4 0.17
ACGTcount: A:0.36, C:0.15, G:0.28, T:0.21
Consensus pattern (20 bp):
TGCGAATTGGAAAATCGCAA
Found at i:174342 original size:19 final size:19
Alignment explanation
Indices: 174318--174354 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
174308 AATGACCAAC
*
174318 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
174337 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
174355 CAGTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:175071 original size:39 final size:40
Alignment explanation
Indices: 174991--175082 Score: 107
Period size: 39 Copynumber: 2.3 Consensus size: 40
174981 GATAGTCAAA
** * * *
174991 TTCGCGTTGCGATAGTCATTTTCGTGTTGTGATTTTCATT
1 TTCGCGTTGCGATAGTCAAATTCGCGTTGCGATGTTCATT
175031 TT-GCGTTGCGATAGTCAAATTCGCGTTGCGATAGTT-ATT
1 TTCGCGTTGCGATAGTCAAATTCGCGTTGCGAT-GTTCATT
*
175070 TTCGTGTTGCGAT
1 TTCGCGTTGCGAT
175083 TTTAAGTTTC
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
39 31 0.70
40 13 0.30
ACGTcount: A:0.15, C:0.15, G:0.25, T:0.45
Consensus pattern (40 bp):
TTCGCGTTGCGATAGTCAAATTCGCGTTGCGATGTTCATT
Found at i:175073 original size:20 final size:20
Alignment explanation
Indices: 174980--175082 Score: 109
Period size: 20 Copynumber: 5.2 Consensus size: 20
174970 AAAATCGCAA
**
174980 CGATAGTCAAATTCGCGTTG
1 CGATAGTCATTTTCGCGTTG
*
175000 CGATAGTCATTTTCGTGTTG
1 CGATAGTCATTTTCGCGTTG
* **
175020 TGATTTTCATTTT-GCGTTG
1 CGATAGTCATTTTCGCGTTG
**
175039 CGATAGTCAAATTCGCGTTG
1 CGATAGTCATTTTCGCGTTG
* *
175059 CGATAGTTATTTTCGTGTTG
1 CGATAGTCATTTTCGCGTTG
175079 CGAT
1 CGAT
175083 TTTAAGTTTC
Statistics
Matches: 66, Mismatches: 16, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
19 13 0.20
20 53 0.80
ACGTcount: A:0.18, C:0.16, G:0.24, T:0.42
Consensus pattern (20 bp):
CGATAGTCATTTTCGCGTTG
Found at i:176453 original size:28 final size:27
Alignment explanation
Indices: 176400--176453 Score: 63
Period size: 28 Copynumber: 2.0 Consensus size: 27
176390 GTACACTTTT
****
176400 TTTGATTGTTTAATTGATTCTTAAAAG
1 TTTGATTGTTTAATTGATGAGGAAAAG
176427 TTTGATTTGTTTAATTGATGAGGAAAA
1 TTTGA-TTGTTTAATTGATGAGGAAAA
176454 TAAGAATTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
27 5 0.23
28 17 0.77
ACGTcount: A:0.31, C:0.02, G:0.19, T:0.48
Consensus pattern (27 bp):
TTTGATTGTTTAATTGATGAGGAAAAG
Found at i:176669 original size:20 final size:20
Alignment explanation
Indices: 176644--176682 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
176634 ACGCTAAACT
* *
176644 CAAAATCGCAATGCGAAAGC
1 CAAAATCACAACGCGAAAGC
176664 CAAAATCACAACGCGAAAG
1 CAAAATCACAACGCGAAAG
176683 TCACAACTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.49, C:0.26, G:0.18, T:0.08
Consensus pattern (20 bp):
CAAAATCACAACGCGAAAGC
Found at i:176742 original size:20 final size:20
Alignment explanation
Indices: 176713--176864 Score: 137
Period size: 20 Copynumber: 8.2 Consensus size: 20
176703 TGATTTGTTT
* *
176713 AATTCACGTTACGATAGTCA
1 AATTCGCGTTGCGATAGTCA
*
176733 AATTCGCGTTGCAATAGTCA
1 AATTCGCGTTGCGATAGTCA
176753 AATTCGCGTTGCGAT--T--
1 AATTCGCGTTGCGATAGTCA
*
176769 --TTTGCGTTGCGATAGTCA
1 AATTCGCGTTGCGATAGTCA
*
176787 TATTCGCGTTGCGAT--T--
1 AATTCGCGTTGCGATAGTCA
* * * *
176803 -TTTTGAGTTGCGATAATCA
1 AATTCGCGTTGCGATAGTCA
176822 AATTCGCGTTGCGATAGTCA
1 AATTCGCGTTGCGATAGTCA
*
176842 AATTCGCGTTGCGATATTCA
1 AATTCGCGTTGCGATAGTCA
176862 AAT
1 AAT
176865 GAATGTGTAA
Statistics
Matches: 107, Mismatches: 14, Indels: 22
0.75 0.10 0.15
Matches are distributed among these distances:
14 12 0.11
15 11 0.10
16 1 0.01
17 1 0.01
18 2 0.02
20 80 0.75
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.36
Consensus pattern (20 bp):
AATTCGCGTTGCGATAGTCA
Found at i:176784 original size:34 final size:34
Alignment explanation
Indices: 176738--176836 Score: 153
Period size: 35 Copynumber: 2.9 Consensus size: 34
176728 AGTCAAATTC
*
176738 GCGTTGCAATAGTCAAATTCGCGTTGCGATTTTT
1 GCGTTGCGATAGTCAAATTCGCGTTGCGATTTTT
*
176772 GCGTTGCGATAGTCATATTCGCGTTGCGATTTTTT
1 GCGTTGCGATAGTCAAATTCGCGTTGCGA-TTTTT
* *
176807 GAGTTGCGATAATCAAATTCGCGTTGCGAT
1 GCGTTGCGATAGTCAAATTCGCGTTGCGAT
176837 AGTCAAATTC
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
34 28 0.47
35 31 0.53
ACGTcount: A:0.20, C:0.17, G:0.25, T:0.37
Consensus pattern (34 bp):
GCGTTGCGATAGTCAAATTCGCGTTGCGATTTTT
Found at i:178969 original size:15 final size:14
Alignment explanation
Indices: 178933--178969 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
178923 TCCCGTGACA
178933 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
*
178947 TTTTCTTCGGGGAT
1 TTTTCTTCGGGGAC
178961 TTATTCTTC
1 TT-TTCTTC
178970 TCCTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.08, C:0.19, G:0.22, T:0.51
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:179193 original size:24 final size:24
Alignment explanation
Indices: 179159--179212 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
179149 CTGAAACATC
179159 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* * * *
179183 ATCAAAGTCCGGGTATTGACGAAT
1 ATCAAAATCCGAGTATTGACCAAG
179207 ATCAAA
1 ATCAAA
179213 TTTCAAATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:180248 original size:20 final size:20
Alignment explanation
Indices: 180223--180330 Score: 76
Period size: 20 Copynumber: 5.3 Consensus size: 20
180213 GAAATTCAGT
*
180223 GTTGCGACAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
** *
180243 GTTGCGATTATGT-ATTATCGT
1 GTTGCGA-TA-GTCAGAATCGC
*
180264 GTTGCGATAGTCAGAATCAC
1 GTTGCGATAGTCAGAATCGC
* * *
180284 GTTGCGAT-TTACATATTCGC
1 GTTGCGATAGT-CAGAATCGC
* * *
180304 ATTGCGATAGTCAAAATTGC
1 GTTGCGATAGTCAGAATCGC
180324 GTTGCGA
1 GTTGCGA
180331 ATCTGGAAAT
Statistics
Matches: 65, Mismatches: 18, Indels: 10
0.70 0.19 0.11
Matches are distributed among these distances:
19 3 0.05
20 46 0.71
21 14 0.22
22 2 0.03
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:183406 original size:13 final size:14
Alignment explanation
Indices: 183375--183414 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
183365 TAACTCAACA
183375 AACATAAACGAACC
1 AACATAAACGAACC
* *
183389 GACATAAA-GAACT
1 AACATAAACGAACC
183402 AACATAAACGAAC
1 AACATAAACGAAC
183415 GCATTATCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.57, C:0.23, G:0.10, T:0.10
Consensus pattern (14 bp):
AACATAAACGAACC
Found at i:190532 original size:8 final size:8
Alignment explanation
Indices: 190519--190559 Score: 66
Period size: 8 Copynumber: 5.2 Consensus size: 8
190509 CTCATTTTCA
190519 GAGAATTT
1 GAGAATTT
190527 GAGAATTT
1 GAGAATTT
*
190535 -AGAGTTT
1 GAGAATTT
190542 GAGAATTT
1 GAGAATTT
190550 GAGAATTT
1 GAGAATTT
190558 GA
1 GA
190560 AAGCTTGTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
7 6 0.20
8 24 0.80
ACGTcount: A:0.37, C:0.00, G:0.27, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:190544 original size:15 final size:16
Alignment explanation
Indices: 190519--190559 Score: 66
Period size: 15 Copynumber: 2.6 Consensus size: 16
190509 CTCATTTTCA
190519 GAGAATTTGAGAATTT
1 GAGAATTTGAGAATTT
*
190535 -AGAGTTTGAGAATTT
1 GAGAATTTGAGAATTT
190550 GAGAATTTGA
1 GAGAATTTGA
190560 AAGCTTGTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.37, C:0.00, G:0.27, T:0.37
Consensus pattern (16 bp):
GAGAATTTGAGAATTT
Found at i:190837 original size:128 final size:128
Alignment explanation
Indices: 190630--191383 Score: 1216
Period size: 128 Copynumber: 5.9 Consensus size: 128
190620 TAATTGGAGT
** * *
190630 ACTATTCACATGAAGGCATGTTCCCGGGGGCGCGCCTTCTATTA--TT-TCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTTAT
190692 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *
190755 ACTATTCACATGAAGGCGCGTTCTCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTTAT
190820 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
190883 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTTAT
*
190948 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATTAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
191011 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTTAT
* *
191076 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACATTA-TTCATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGAT-ATATCAGTACCTATTATTTC
* *** * *
191139 TC-AGGGGACTTGAAGGCGCGTTCCCGAGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTTA
1 ACTA-TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTTA
* *
191203 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACATTA-TTCATATCAGTACCTATTATTTC
65 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGAT-ATATCAGTACCTATTATTTC
* *** * *
191267 TC-AGGGGACTTGAAGGCGCGTTCCCGGGGGCGCGCCTTCTATTATTTTGTCATAGAATATGTTA
1 ACTA-TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTTA
191331 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
65 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
191384 AATCAGGTAA
Statistics
Matches: 603, Mismatches: 20, Indels: 9
0.95 0.03 0.01
Matches are distributed among these distances:
125 40 0.07
127 4 0.01
128 558 0.93
129 1 0.00
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (128 bp):
ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTTAT
CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
Found at i:191821 original size:34 final size:34
Alignment explanation
Indices: 191783--191883 Score: 139
Period size: 34 Copynumber: 3.0 Consensus size: 34
191773 AAATTTAATG
* *
191783 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTTGAATAATATAATTTATATTTTAAAT
* * * *
191817 TTAAATTTTGAATAATATTATTTTTATTTTTATT
1 TTAAATTTTGAATAATATAATTTATATTTTAAAT
*
191851 TTAAATTTTGAATAATATAATTTGTATTTTAAA
1 TTAAATTTTGAATAATATAATTTATATTTTAAA
191884 AACATTTATC
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 57 1.00
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (34 bp):
TTAAATTTTGAATAATATAATTTATATTTTAAAT
Found at i:192429 original size:21 final size:21
Alignment explanation
Indices: 192403--192454 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
192393 TATGGTATAA
192403 AACCCTGCGGGCTAGGAATGT
1 AACCCTGCGGGCTAGGAATGT
*
192424 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
192445 AACCCTGCGG
1 AACCCTGCGG
192455 AGATGGCATA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.21, C:0.29, G:0.33, T:0.17
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:194274 original size:31 final size:33
Alignment explanation
Indices: 194232--194306 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 33
194222 ATAATTCTAA
* * *
194232 ATAAATAATAATTATATAAAT-ATTATTTTAAT
1 ATAAAAAATAATTATATAAATAAATATATTAAT
* *
194264 A-AAAAAATAA-TATTTACATAAATATATTAAT
1 ATAAAAAATAATTATATAAATAAATATATTAAT
194295 ATAAAAAATAAT
1 ATAAAAAATAAT
194307 AACTATTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
30 7 0.20
31 18 0.51
32 10 0.29
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (33 bp):
ATAAAAAATAATTATATAAATAAATATATTAAT
Found at i:194285 original size:34 final size:31
Alignment explanation
Indices: 194229--194308 Score: 97
Period size: 34 Copynumber: 2.5 Consensus size: 31
194219 TTAATAATTC
* *
194229 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAAAAAATAATAATTACATAAATA-TA--TTAA
*
194263 TAAAAAAATAATATTTACATAAATATATTAA
1 TAAAAAAATAATAATTACATAAATATATTAA
194294 TATAAAAAATAATAA
1 TA-AAAAAATAATAA
194309 CTATTTAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
31 6 0.15
32 11 0.27
33 2 0.05
34 22 0.54
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (31 bp):
TAAAAAAATAATAATTACATAAATATATTAA
Found at i:199782 original size:15 final size:16
Alignment explanation
Indices: 199755--199785 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
199745 GATGACAATT
199755 AATACACATTCATATA
1 AATACACATTCATATA
199771 AATACA-ATTCATATA
1 AATACACATTCATATA
199786 CAAACGAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (16 bp):
AATACACATTCATATA
Found at i:207018 original size:28 final size:30
Alignment explanation
Indices: 206958--207018 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 30
206948 TTGCAAGTTT
* * *
206958 AAAATTTATAAACTTGATTTGAACTCATAA
1 AAAAATTATAAACTTGACTCGAACTCATAA
*
206988 AAAAATTA-AAACTTGACTCGAGCTCA-AA
1 AAAAATTATAAACTTGACTCGAACTCATAA
207016 AAA
1 AAA
207019 CTTGAATTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 5 0.19
29 15 0.56
30 7 0.26
ACGTcount: A:0.51, C:0.13, G:0.08, T:0.28
Consensus pattern (30 bp):
AAAAATTATAAACTTGACTCGAACTCATAA
Found at i:212334 original size:14 final size:14
Alignment explanation
Indices: 212312--212344 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
212302 AAATCTTATA
212312 TTATATTTAAAAAT
1 TTATATTTAAAAAT
*
212326 TTATTTTTAAAAAT
1 TTATATTTAAAAAT
212340 TTATA
1 TTATA
212345 ATTATCAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TTATATTTAAAAAT
Found at i:217070 original size:19 final size:19
Alignment explanation
Indices: 217019--217064 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
217009 TGTCGCAAGA
*
217019 AGCACTTGACAACCTATGG
1 AGCACTTGACGACCTATGG
*
217038 AGTACTTGACGACCTATGG
1 AGCACTTGACGACCTATGG
217057 AGCACTTG
1 AGCACTTG
217065 GTGACCAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (19 bp):
AGCACTTGACGACCTATGG
Found at i:222221 original size:22 final size:21
Alignment explanation
Indices: 222192--222249 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 21
222182 TTTATTAATT
*
222192 TTTTTAAATATTTATGAAA-AA
1 TTTTTAAA-ATTTATCAAATAA
222213 TATTTTAAAATTTTATCAAATAA
1 T-TTTTAAAA-TTTATCAAATAA
222236 TTTTTAAAATTTAT
1 TTTTTAAAATTTAT
222250 ATAATGAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
21 7 0.21
22 23 0.70
23 3 0.09
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (21 bp):
TTTTTAAAATTTATCAAATAA
Found at i:222668 original size:2 final size:2
Alignment explanation
Indices: 222656--222684 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
222646 ATGTGATCCA
222656 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
222685 TTTTAGAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:224129 original size:39 final size:39
Alignment explanation
Indices: 224086--224194 Score: 116
Period size: 39 Copynumber: 2.8 Consensus size: 39
224076 TTTTAAAAAT
224086 AATTTAGAACGTTA-ATGTGAAATAATTTAAGAAATTAAG
1 AATTTAGAACGTTATA-GTGAAATAATTTAAGAAATTAAG
* * * *
224125 AATTTAAAACGTTATGGTGTCAA-AATTTAAGAAATTAGG
1 AATTTAGAACGTTATAGTG-AAATAATTTAAGAAATTAAG
* *
224164 ATTTTAGAATGTTATAGT-AAATTAATTTAAG
1 AATTTAGAACGTTATAGTGAAA-TAATTTAAG
224195 GATTATAAAT
Statistics
Matches: 57, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
37 2 0.04
39 53 0.93
40 2 0.04
ACGTcount: A:0.45, C:0.03, G:0.16, T:0.37
Consensus pattern (39 bp):
AATTTAGAACGTTATAGTGAAATAATTTAAGAAATTAAG
Done.