Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010808.1 Kokia drynarioides strain JFW-HI SEQ_125775, 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: 274830
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:2190 original size:68 final size:69
Alignment explanation
Indices: 2023--2192 Score: 211
Period size: 68 Copynumber: 2.5 Consensus size: 69
2013 CCCTGCATTG
* * * *
2023 TTGCTGATTTATGTTGTCCAAAGCCA-CTCATATTAATCGTGCTATAACTGTTTCATGCTCTGTT
1 TTGCTGATTTATGTTGTCCAAAGCCAGCACATATTAATCGTGCTATAACTGTTTAATGCCCTGCT
* *
2087 TTGT
66 GTAT
* * **
2091 TTGCTGATTTATGTTGTCCAAAGCCAG-ACATATTAATGGTGTTATTGCTGTTTAATGCCCTGCT
1 TTGCTGATTTATGTTGTCCAAAGCCAGCACATATTAATCGTGCTATAACTGTTTAATGCCCTGCT
2155 GTAT
66 GTAT
* *
2159 TTGCTGATTTATGCTGTCCAAAG-TAGCACATATT
1 TTGCTGATTTATGTTGTCCAAAGCCAGCACATATT
2193 GATTTCGTTT
Statistics
Matches: 88, Mismatches: 12, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
67 2 0.02
68 86 0.98
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.42
Consensus pattern (69 bp):
TTGCTGATTTATGTTGTCCAAAGCCAGCACATATTAATCGTGCTATAACTGTTTAATGCCCTGCT
GTAT
Found at i:7561 original size:27 final size:30
Alignment explanation
Indices: 7501--7566 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
7491 CATTTTTTAT
*
7501 TTTTTAATTAATAAATATGTTATTTTCAAG
1 TTTTTAATTAACAAATATGTTATTTTCAAG
7531 TTTTTAATTAACAAATATG-T-TTTT-AAG
1 TTTTTAATTAACAAATATGTTATTTTCAAG
7558 TTTTTAATT
1 TTTTTAATT
7567 TTATTTTTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
27 12 0.34
28 4 0.11
29 1 0.03
30 18 0.51
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.56
Consensus pattern (30 bp):
TTTTTAATTAACAAATATGTTATTTTCAAG
Found at i:7576 original size:13 final size:14
Alignment explanation
Indices: 7558--7590 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
7548 TGTTTTTAAG
*
7558 TTTTTAATT-TTAT
1 TTTTTAATTAATAT
7571 TTTTTAATTAATAT
1 TTTTTAATTAATAT
7585 TTTTTA
1 TTTTTA
7591 TTTATATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTTTAATTAATAT
Found at i:8003 original size:18 final size:18
Alignment explanation
Indices: 7968--8002 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
7958 TAACATAAAA
7968 AATAAATTAATTATTTTT
1 AATAAATTAATTATTTTT
*
7986 AATAAA-TATTTATTTTT
1 AATAAATTAATTATTTTT
8003 TTCACCTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
AATAAATTAATTATTTTT
Found at i:12426 original size:31 final size:31
Alignment explanation
Indices: 12361--12671 Score: 285
Period size: 31 Copynumber: 10.4 Consensus size: 31
12351 TACTTTTTAG
*
12361 ATATAACCTTTTCA--AGAGTATCCATTT-GA
1 ATATAACCTTTTCATTTGA-TATCCATTTCGA
* **
12390 ATATAACCTTTACATTTGATATTTATTTCGA
1 ATATAACCTTTTCATTTGATATCCATTTCGA
*
12421 ATATAACCTTTTCA--AGAATATCCA-TTC-A
1 ATATAACCTTTTCATTTG-ATATCCATTTCGA
*
12449 GATATAACCTTTTCA--CGAATATCCA-TTC-A
1 -ATATAACCTTTTCATTTG-ATATCCATTTCGA
*
12478 GATATAACCTTTACATTTGATATCCATTTCGA
1 -ATATAACCTTTTCATTTGATATCCATTTCGA
* *
12510 ATATAACCTTTACATTTGATATCCATTTCGG
1 ATATAACCTTTTCATTTGATATCCATTTCGA
* * * *
12541 ATATAACATTTTCA-ATAATATCCATTT-GG
1 ATATAACCTTTTCATTTGATATCCATTTCGA
*
12570 ATATAACCTTTTCATTTGATATCCATTTCGG
1 ATATAACCTTTTCATTTGATATCCATTTCGA
* *
12601 ATATAACCTTTTCA--AGAATATCCA-TTCGG
1 ATATAACCTTTTCATTTG-ATATCCATTTCGA
* * *
12630 ATATAACTTTTTCATTTGACATTCATTTCGA
1 ATATAACCTTTTCATTTGATATCCATTTCGA
12661 ATATAACCTTT
1 ATATAACCTTT
12672 CCATAAATTT
Statistics
Matches: 241, Mismatches: 26, Indels: 28
0.82 0.09 0.09
Matches are distributed among these distances:
28 1 0.00
29 92 0.38
30 53 0.22
31 94 0.39
32 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (31 bp):
ATATAACCTTTTCATTTGATATCCATTTCGA
Found at i:12434 original size:60 final size:60
Alignment explanation
Indices: 12361--12671 Score: 355
Period size: 60 Copynumber: 5.2 Consensus size: 60
12351 TACTTTTTAG
* * **
12361 ATATAACCTTTTCAAGAGTATCCATTTGAATATAACCTTTACATTTGATATTTATTTCGA
1 ATATAACCTTTTCAAGAATATCCATTTGAATATAACCTTTTCATTTGATATCCATTTCGA
* *
12421 ATATAACCTTTTCAAGAATATCCA-TTCAGATATAACCTTTTCA--CGAATATCCA-TTC-A
1 ATATAACCTTTTCAAGAATATCCATTTGA-ATATAACCTTTTCATTTG-ATATCCATTTCGA
* * * *
12478 GATATAACCTTTACATTTG-ATATCCATTTCGAATATAACCTTTACATTTGATATCCATTTCGG
1 -ATATAACCTTTTCA--AGAATATCCATTT-GAATATAACCTTTTCATTTGATATCCATTTCGA
* * * *
12541 ATATAACATTTTCAATAATATCCATTTGGATATAACCTTTTCATTTGATATCCATTTCGG
1 ATATAACCTTTTCAAGAATATCCATTTGAATATAACCTTTTCATTTGATATCCATTTCGA
* * * * *
12601 ATATAACCTTTTCAAGAATATCCATTCGGATATAACTTTTTCATTTGACATTCATTTCGA
1 ATATAACCTTTTCAAGAATATCCATTTGAATATAACCTTTTCATTTGATATCCATTTCGA
12661 ATATAACCTTT
1 ATATAACCTTT
12672 CCATAAATTT
Statistics
Matches: 214, Mismatches: 25, Indels: 24
0.81 0.10 0.09
Matches are distributed among these distances:
57 1 0.00
58 17 0.08
59 15 0.07
60 147 0.69
61 18 0.08
62 16 0.07
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (60 bp):
ATATAACCTTTTCAAGAATATCCATTTGAATATAACCTTTTCATTTGATATCCATTTCGA
Found at i:12441 original size:17 final size:17
Alignment explanation
Indices: 12419--12470 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 17
12409 TATTTATTTC
12419 GAATATAACCTTTTCAA
1 GAATATAACCTTTTCAA
*
12436 GAATAT--CC-ATTC-A
1 GAATATAACCTTTTCAA
*
12449 G-ATATAACCTTTTCAC
1 GAATATAACCTTTTCAA
12465 GAATAT
1 GAATAT
12471 CCATTCAGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 10
0.68 0.08 0.25
Matches are distributed among these distances:
12 4 0.15
13 2 0.07
14 5 0.19
15 5 0.19
16 1 0.04
17 10 0.37
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.35
Consensus pattern (17 bp):
GAATATAACCTTTTCAA
Found at i:12463 original size:29 final size:29
Alignment explanation
Indices: 12360--12643 Score: 243
Period size: 29 Copynumber: 9.5 Consensus size: 29
12350 ATACTTTTTA
* *
12360 GATATAACCTTTTCAAGAGTATCCATTTG
1 GATATAACCTTTTCAAGAATATCCATTCG
* * * **
12389 AATATAACCTTTACATTTG-ATATTTATTTCG
1 GATATAACCTTTTCA--AGAATATCCA-TTCG
* *
12420 AATATAACCTTTTCAAGAATATCCATTCA
1 GATATAACCTTTTCAAGAATATCCATTCG
* *
12449 GATATAACCTTTTCACGAATATCCATTCA
1 GATATAACCTTTTCAAGAATATCCATTCG
* *
12478 GATATAACCTTTACATTTG-ATATCCATTTCG
1 GATATAACCTTTTCA--AGAATATCCA-TTCG
* * *
12509 AATATAACCTTTACATTTG-ATATCCATTTCG
1 GATATAACCTTTTCA--AGAATATCCA-TTCG
* * *
12540 GATATAACATTTTCAATAATATCCATTTG
1 GATATAACCTTTTCAAGAATATCCATTCG
*
12569 GATATAACCTTTTCATTTG-ATATCCATTTCG
1 GATATAACCTTTTCA--AGAATATCCA-TTCG
12600 GATATAACCTTTTCAAGAATATCCATTCG
1 GATATAACCTTTTCAAGAATATCCATTCG
*
12629 GATATAACTTTTTCA
1 GATATAACCTTTTCA
12644 TTTGACATTC
Statistics
Matches: 213, Mismatches: 30, Indels: 24
0.80 0.11 0.09
Matches are distributed among these distances:
29 94 0.44
30 37 0.17
31 82 0.38
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.40
Consensus pattern (29 bp):
GATATAACCTTTTCAAGAATATCCATTCG
Found at i:12524 original size:120 final size:120
Alignment explanation
Indices: 12359--12671 Score: 402
Period size: 120 Copynumber: 2.6 Consensus size: 120
12349 AATACTTTTT
* * *
12359 AGATATAACCTTTTCAAGAGTATCCATTT-GAATATAACCTTTACATTTGATATTTATTTCGAAT
1 AGATATAACCTTTACAAGAATATCCATTTCGAATATAACCTTTACATTTGATATTCATTTCGAAT
12423 ATAACCTTTTCAAGAATATCCATTCAGATATAACCTTTTCA-CGAATATCCA-TTC
66 ATAACCTTTTCAAGAATATCCATTCAGATATAACCTTTTCATCG-ATATCCATTTC
* * *
12477 AGATATAACCTTTACATTTG-ATATCCATTTCGAATATAACCTTTACATTTGATATCCATTTCGG
1 AGATATAACCTTTACA--AGAATATCCATTTCGAATATAACCTTTACATTTGATATTCATTTCGA
* * ** *
12541 ATATAACATTTTCAATAATATCCATTTGGATATAACCTTTTCATTTGATATCCATTTC
64 ATATAACCTTTTCAAGAATATCCATTCAGATATAACCTTTTCA-TCGATATCCATTTC
* * * * * *
12599 GGATATAACCTTTTCAAGAATATCCA-TTCGGATATAACTTTTTCATTTGACATTCATTTCGAAT
1 AGATATAACCTTTACAAGAATATCCATTTCGAATATAACCTTTACATTTGATATTCATTTCGAAT
12663 ATAACCTTT
66 ATAACCTTT
12672 CCATAAATTT
Statistics
Matches: 167, Mismatches: 21, Indels: 12
0.83 0.10 0.06
Matches are distributed among these distances:
118 15 0.09
119 9 0.05
120 111 0.66
121 14 0.08
122 18 0.11
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (120 bp):
AGATATAACCTTTACAAGAATATCCATTTCGAATATAACCTTTACATTTGATATTCATTTCGAAT
ATAACCTTTTCAAGAATATCCATTCAGATATAACCTTTTCATCGATATCCATTTC
Found at i:14178 original size:52 final size:51
Alignment explanation
Indices: 14097--14384 Score: 398
Period size: 52 Copynumber: 5.6 Consensus size: 51
14087 AATGAAAAAT
* * *
14097 GTTCGATGACTATGTCTCATCGTGAGTATATGAATATTTAACAGATTATGAG
1 GTTCGATGACTATGTGTCATCGTGAGTATATGAATCTTT-ACGGATTATGAG
* * *
14149 GTCCGATGACTATGTGACATCATGAGTATATGAATCTTTTACGGATTATGAG
1 GTTCGATGACTATGTGTCATCGTGAGTATATGAATC-TTTACGGATTATGAG
* * *
14201 GTTCGATAAATATGTGTCATCGTGAGTATATGAATCATTTACGGATTATAAG
1 GTTCGATGACTATGTGTCATCGTGAGTATATGAATC-TTTACGGATTATGAG
* * *
14253 GTTCGACGACTATGTGTCATCGTGAGGAT-TGAATCCTTAACGGATTATGAG
1 GTTCGATGACTATGTGTCATCGTGAGTATATGAAT-CTTTACGGATTATGAG
* *
14304 GTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAGAG
1 GTTCGATGACTATGTGTCATCGTGAGTATATGAAT-CTTTACGGATTATGAG
14356 GTTCGATGACTATGTGTCATCGTGAGTAT
1 GTTCGATGACTATGTGTCATCGTGAGTAT
14385 TAAATGAAAT
Statistics
Matches: 208, Mismatches: 25, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
51 44 0.21
52 161 0.77
53 3 0.01
ACGTcount: A:0.28, C:0.13, G:0.24, T:0.35
Consensus pattern (51 bp):
GTTCGATGACTATGTGTCATCGTGAGTATATGAATCTTTACGGATTATGAG
Found at i:14327 original size:103 final size:104
Alignment explanation
Indices: 14100--14381 Score: 399
Period size: 103 Copynumber: 2.7 Consensus size: 104
14090 GAAAAATGTT
* * * *
14100 CGATGACTATGTCTCATCGTGAGTATATGAAT-ATTTAACAGATTATGAGGTCCGATGACTATGT
1 CGATGACTATGTGTCATCGTGAGTATATGAATCATTT-ACGGATTATAAGGTTCGATGACTATGT
* * * * * *
14164 GACATCATGAGTATATGAATCTTTTACGGATTATGAGGTT
65 GTCATCGTGAGGATATGAATCCTTAACGGATTATGAGGTC
* * *
14204 CGATAAATATGTGTCATCGTGAGTATATGAATCATTTACGGATTATAAGGTTCGACGACTATGTG
1 CGATGACTATGTGTCATCGTGAGTATATGAATCATTTACGGATTATAAGGTTCGATGACTATGTG
14269 TCATCGTGAGGAT-TGAATCCTTAACGGATTATGAGGTC
66 TCATCGTGAGGATATGAATCCTTAACGGATTATGAGGTC
*
14307 CGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTA-AGAGGTTCGATGACTATGT
1 CGATGACTATGTGTCATCGTGAGTATATGAATCATTTACGGATTATA-AGGTTCGATGACTATGT
14371 GTCATCGTGAG
65 GTCATCGTGAG
14382 TATTAAATGA
Statistics
Matches: 159, Mismatches: 17, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
102 1 0.01
103 91 0.57
104 63 0.40
105 4 0.03
ACGTcount: A:0.28, C:0.13, G:0.24, T:0.34
Consensus pattern (104 bp):
CGATGACTATGTGTCATCGTGAGTATATGAATCATTTACGGATTATAAGGTTCGATGACTATGTG
TCATCGTGAGGATATGAATCCTTAACGGATTATGAGGTC
Found at i:14380 original size:155 final size:156
Alignment explanation
Indices: 14097--14384 Score: 461
Period size: 155 Copynumber: 1.9 Consensus size: 156
14087 AATGAAAAAT
* * *
14097 GTTCGATGACTATGTCTCATCGTGAGTATATGAATATTTAACAGATTATGAGGTCCGATGACTAT
1 GTTCGACGACTATGTCTCATCGTGAGGATATGAATACTTAACAGATTATGAGGTCCGATGACTAT
* *
14162 GTGACATCATGAGTATATGAATCTTTTACGGATTATGAGGTTCGATAAATATGTGTCATCGTGAG
66 GTGACATCATGAGTATATGAATCCTTTACGGATTAAGAGGTTCGATAAATATGTGTCATCGTGAG
14227 TATATGAATCATTTACGGATTATAAG
131 TATATGAATCATTTACGGATTATAAG
* * *
14253 GTTCGACGACTATGTGTCATCGTGAGGAT-TGAATCCTTAACGGATTATGAGGTCCGATGACTAT
1 GTTCGACGACTATGTCTCATCGTGAGGATATGAATACTTAACAGATTATGAGGTCCGATGACTAT
* * * *
14317 GTGTCATCGTGAGTATATGAATCCTTTACGGATTAAGAGGTTCGATGACTATGTGTCATCGTGAG
66 GTGACATCATGAGTATATGAATCCTTTACGGATTAAGAGGTTCGATAAATATGTGTCATCGTGAG
14382 TAT
131 TAT
14385 TAAATGAAAT
Statistics
Matches: 120, Mismatches: 12, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
155 94 0.78
156 26 0.22
ACGTcount: A:0.28, C:0.13, G:0.24, T:0.35
Consensus pattern (156 bp):
GTTCGACGACTATGTCTCATCGTGAGGATATGAATACTTAACAGATTATGAGGTCCGATGACTAT
GTGACATCATGAGTATATGAATCCTTTACGGATTAAGAGGTTCGATAAATATGTGTCATCGTGAG
TATATGAATCATTTACGGATTATAAG
Found at i:14426 original size:60 final size:60
Alignment explanation
Indices: 14333--14450 Score: 175
Period size: 60 Copynumber: 2.0 Consensus size: 60
14323 TCGTGAGTAT
* * * *
14333 ATGAATCCTTTACGGATTAAGAGGTTCGATGACTATGTGTCATCGTGAGTATTAAATGAA
1 ATGAATCCATTACGGATTAAGAGGTCCAATGACTATGTGTCATCGTGAGTATCAAATGAA
*
14393 ATGAATCCCATTACGGATTAA-AGGTCCAATGACTCTGTGTCATCGTGAGTATCAAATG
1 ATGAAT-CCATTACGGATTAAGAGGTCCAATGACTATGTGTCATCGTGAGTATCAAATG
14451 CGAATTGAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
60 39 0.75
61 13 0.25
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.31
Consensus pattern (60 bp):
ATGAATCCATTACGGATTAAGAGGTCCAATGACTATGTGTCATCGTGAGTATCAAATGAA
Found at i:14870 original size:34 final size:34
Alignment explanation
Indices: 14827--14899 Score: 137
Period size: 34 Copynumber: 2.1 Consensus size: 34
14817 ATGCAAGGTC
*
14827 TTGAAACCATGTACAATGTATTGGTATATTTCAT
1 TTGAAACCATGTACAATGTATCGGTATATTTCAT
14861 TTGAAACCATGTACAATGTATCGGTATATTTCAT
1 TTGAAACCATGTACAATGTATCGGTATATTTCAT
14895 TTGAA
1 TTGAA
14900 GTTATGAAGT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (34 bp):
TTGAAACCATGTACAATGTATCGGTATATTTCAT
Found at i:16262 original size:20 final size:20
Alignment explanation
Indices: 16239--16278 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
16229 AATTTCTTAA
16239 CCAAAATTTAATATGATTAT
1 CCAAAATTTAATATGATTAT
16259 CCAAAATTTAATATGATTAT
1 CCAAAATTTAATATGATTAT
16279 ACTCCTTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (20 bp):
CCAAAATTTAATATGATTAT
Found at i:28617 original size:17 final size:17
Alignment explanation
Indices: 28595--28628 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
28585 TAGTTAAAAA
28595 AATATGAAAAGTTAAAG
1 AATATGAAAAGTTAAAG
* *
28612 AATATGGAAGGTTAAAG
1 AATATGAAAAGTTAAAG
28629 GTAATGAGAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.24, T:0.24
Consensus pattern (17 bp):
AATATGAAAAGTTAAAG
Found at i:29510 original size:11 final size:11
Alignment explanation
Indices: 29489--29538 Score: 59
Period size: 11 Copynumber: 4.7 Consensus size: 11
29479 ATTTTCAATC
*
29489 CTCTCTCAATT
1 CTCTCTTAATT
29500 CTCTCTTAATT
1 CTCTCTTAATT
*
29511 CTCACTTAATT
1 CTCTCTTAATT
29522 CTCTC--AATT
1 CTCTCTTAATT
*
29531 CACTCTTA
1 CTCTCTTA
29539 TTTTTATTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
9 8 0.24
11 25 0.76
ACGTcount: A:0.22, C:0.32, G:0.00, T:0.46
Consensus pattern (11 bp):
CTCTCTTAATT
Found at i:29840 original size:30 final size:30
Alignment explanation
Indices: 29804--29865 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
29794 TTTGCAATCT
29804 ATTCACTCCTCCATCGCCTTTAATCGAACC
1 ATTCACTCCTCCATCGCCTTTAATCGAACC
*
29834 ATTCACTCCTCCATCGCCTTTAATCTAACC
1 ATTCACTCCTCCATCGCCTTTAATCGAACC
29864 AT
1 AT
29866 ACTTGAGAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.24, C:0.39, G:0.05, T:0.32
Consensus pattern (30 bp):
ATTCACTCCTCCATCGCCTTTAATCGAACC
Found at i:32351 original size:21 final size:23
Alignment explanation
Indices: 32327--32381 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 23
32317 CCTACAACTT
*
32327 CTACCGATACAAGTATGC-A-AA
1 CTACCGATACAACTATGCAATAA
*
32348 CTACCGATACATCTATGCATATAA
1 CTACCGATACAACTATGCA-ATAA
32372 CTACCGATAC
1 CTACCGATAC
32382 TCACAATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 16 0.55
23 1 0.03
24 12 0.41
ACGTcount: A:0.38, C:0.27, G:0.11, T:0.24
Consensus pattern (23 bp):
CTACCGATACAACTATGCAATAA
Found at i:33096 original size:52 final size:52
Alignment explanation
Indices: 32989--33172 Score: 316
Period size: 52 Copynumber: 3.6 Consensus size: 52
32979 TTACGTTTAA
* * *
32989 TACTCACGATGACACTTAGTCATCGAACC-TATAATCCGTGAAAGATTCATG
1 TACTCACGATGACACTTAGTCATCGGACCTTATAATCCATGAAGGATTCATG
33040 TACTCACGATGACACTTAGTCATCGGACCTTATAATCCATGAAGGATTCATG
1 TACTCACGATGACACTTAGTCATCGGACCTTATAATCCATGAAGGATTCATG
*
33092 TACTCACGATGACACTTAGTCATCAGACCTTATAATCCATGAAGGATTCATG
1 TACTCACGATGACACTTAGTCATCGGACCTTATAATCCATGAAGGATTCATG
*
33144 TACTCACGATAACACTTAGTCATCGGACC
1 TACTCACGATGACACTTAGTCATCGGACC
33173 CTTTTTCATT
Statistics
Matches: 126, Mismatches: 6, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
51 28 0.22
52 98 0.78
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (52 bp):
TACTCACGATGACACTTAGTCATCGGACCTTATAATCCATGAAGGATTCATG
Found at i:40773 original size:24 final size:24
Alignment explanation
Indices: 40687--40761 Score: 105
Period size: 24 Copynumber: 3.1 Consensus size: 24
40677 AGAAATAATC
*
40687 TTTAAGTTAAACTCTATTTATTTGT
1 TTTAA-TTAAACTCTGTTTATTTGT
* **
40712 TTTAATTAAACTATGTTTGGTTGT
1 TTTAATTAAACTCTGTTTATTTGT
40736 TTTAATTAAACTCTGTTTATTTGT
1 TTTAATTAAACTCTGTTTATTTGT
40760 TT
1 TT
40762 GAGTCAAACT
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
24 38 0.88
25 5 0.12
ACGTcount: A:0.25, C:0.07, G:0.11, T:0.57
Consensus pattern (24 bp):
TTTAATTAAACTCTGTTTATTTGT
Found at i:42736 original size:24 final size:24
Alignment explanation
Indices: 42651--42726 Score: 116
Period size: 24 Copynumber: 3.1 Consensus size: 24
42641 AGAAATAATC
* *
42651 TTTCAGTTAAACTCTTATTTATTTG
1 TTTCAATTAAACTC-TGTTTATTTG
*
42676 TTTCAATTAAACTCTGTTTAGTTG
1 TTTCAATTAAACTCTGTTTATTTG
42700 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
42724 TTT
1 TTT
42727 GAGTCAAACT
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
24 34 0.72
25 13 0.28
ACGTcount: A:0.24, C:0.12, G:0.09, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:42736 original size:48 final size:49
Alignment explanation
Indices: 42651--42745 Score: 120
Period size: 48 Copynumber: 2.0 Consensus size: 49
42641 AGAAATAATC
* *
42651 TTTCAGTTAAACTCTTATTTATTTGTTTCAATTAAACTCTGTTTAGTTG
1 TTTCAATTAAACTCTTATTTATTTGTTTCAATCAAACTCTGTTTAGTTG
* * * * *
42700 TTTCAATTAAACTC-TGTTTATTTGTTTGAGTCAAACTTTTTTTAGT
1 TTTCAATTAAACTCTTATTTATTTGTTTCAATCAAACTCTGTTTAGT
42746 CTAAATTATT
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
48 26 0.67
49 13 0.33
ACGTcount: A:0.24, C:0.12, G:0.11, T:0.54
Consensus pattern (49 bp):
TTTCAATTAAACTCTTATTTATTTGTTTCAATCAAACTCTGTTTAGTTG
Found at i:46017 original size:19 final size:20
Alignment explanation
Indices: 45982--46019 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
45972 AAGGTAGAAT
45982 ATGATTACTTTGGTCTGCAC
1 ATGATTACTTTGGTCTGCAC
*
46002 ATGATT-CTTTGTTCTGCA
1 ATGATTACTTTGGTCTGCA
46020 GACTGAAGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.45
Consensus pattern (20 bp):
ATGATTACTTTGGTCTGCAC
Found at i:51085 original size:19 final size:19
Alignment explanation
Indices: 51061--51098 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
51051 TGCTATAGCA
*
51061 AAATTCGATCTTTGGAAAC
1 AAATTCAATCTTTGGAAAC
51080 AAATTCAATCTTTGGAAAC
1 AAATTCAATCTTTGGAAAC
51099 CCGGAAGCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.32
Consensus pattern (19 bp):
AAATTCAATCTTTGGAAAC
Found at i:60063 original size:19 final size:20
Alignment explanation
Indices: 60028--60079 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 20
60018 TAATATTAAA
60028 AGAAATTTAGTAAATCTGTA-
1 AGAAATTTAGTAAATCT-TAT
*
60048 ATAAATTTAG-AAATCTTAT
1 AGAAATTTAGTAAATCTTAT
60067 AGAAATTTAGTAA
1 AGAAATTTAGTAA
60080 TTCTATAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 2 0.07
19 15 0.54
20 11 0.39
ACGTcount: A:0.48, C:0.04, G:0.12, T:0.37
Consensus pattern (20 bp):
AGAAATTTAGTAAATCTTAT
Found at i:60086 original size:19 final size:19
Alignment explanation
Indices: 60028--60086 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
60018 TAATATTAAA
*
60028 AGAAATTTAGTAAATCTGT
1 AGAAATTTAGTAAATCTAT
*
60047 AATAAATTTAG-AAATCTTAT
1 -AGAAATTTAGTAAATC-TAT
*
60067 AGAAATTTAGTAATTCTAT
1 AGAAATTTAGTAAATCTAT
60086 A
1 A
60087 ATATATTAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.46, C:0.05, G:0.10, T:0.39
Consensus pattern (19 bp):
AGAAATTTAGTAAATCTAT
Found at i:61011 original size:20 final size:20
Alignment explanation
Indices: 60986--61059 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
60976 CCAACAAAAC
60986 TTAATAATTTTGTAAGAAAT
1 TTAATAATTTTGTAAGAAAT
*
61006 TTAATAATTTTATAACG-AAT
1 TTAATAATTTTGTAA-GAAAT
* *
61026 CTAATTATTTT-TAAGAAA-
1 TTAATAATTTTGTAAGAAAT
*
61044 TTAGGTAATTTTGTAA
1 TTA-ATAATTTTGTAA
61060 AATAAATAGT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
18 3 0.07
19 11 0.25
20 29 0.66
21 1 0.02
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.46
Consensus pattern (20 bp):
TTAATAATTTTGTAAGAAAT
Found at i:65880 original size:18 final size:17
Alignment explanation
Indices: 65853--65886 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
65843 AACTTAGGTA
*
65853 TCAAATAGTATATTAAC
1 TCAAATAGTAAATTAAC
65870 TCAACATAGTAAATTAA
1 TCAA-ATAGTAAATTAA
65887 ACATTGTCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.50, C:0.12, G:0.06, T:0.32
Consensus pattern (17 bp):
TCAAATAGTAAATTAAC
Found at i:69872 original size:25 final size:27
Alignment explanation
Indices: 69830--69882 Score: 76
Period size: 25 Copynumber: 2.0 Consensus size: 27
69820 AATTATTGAT
69830 TAAATAAAATATGCATTAT-AA-AAAA
1 TAAATAAAATATGCATTATCAATAAAA
69855 TAAATAAAATATTG-ATTATCAATAAAA
1 TAAATAAAATA-TGCATTATCAATAAAA
69882 T
1 T
69883 TACATTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 16 0.64
26 4 0.16
27 5 0.20
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.32
Consensus pattern (27 bp):
TAAATAAAATATGCATTATCAATAAAA
Found at i:72065 original size:15 final size:18
Alignment explanation
Indices: 72028--72068 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
72018 TGTTTAACTT
72028 TTAATTAATCATAATTAAC
1 TTAATTAATCAT-ATTAAC
72047 TTAATTAATC-T-TTAA-
1 TTAATTAATCATATTAAC
72062 TTAATTA
1 TTAATTA
72069 GTTTTTTTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 7 0.32
16 4 0.18
18 1 0.05
19 10 0.45
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (18 bp):
TTAATTAATCATATTAAC
Found at i:78897 original size:14 final size:14
Alignment explanation
Indices: 78878--78915 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
78868 CCAGTGTCTT
78878 ATTGTTCATCTATC
1 ATTGTTCATCTATC
* *
78892 ATTGTTCATCTTTT
1 ATTGTTCATCTATC
78906 ATT-TTCATCT
1 ATTGTTCATCT
78916 CATTCAATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 7 0.32
14 15 0.68
ACGTcount: A:0.18, C:0.18, G:0.05, T:0.58
Consensus pattern (14 bp):
ATTGTTCATCTATC
Found at i:79145 original size:21 final size:21
Alignment explanation
Indices: 79121--79171 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
79111 GAGATAATAT
*
79121 TACCGATACAAGT-GTGACTTC
1 TACCGATACAAGTCATG-CTTC
* *
79142 TACCGAAACATGTCATGCTTC
1 TACCGATACAAGTCATGCTTC
79163 TACCGATAC
1 TACCGATAC
79172 TAAAAACTCT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 23 0.92
22 2 0.08
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.27
Consensus pattern (21 bp):
TACCGATACAAGTCATGCTTC
Found at i:80161 original size:52 final size:52
Alignment explanation
Indices: 80064--80450 Score: 513
Period size: 52 Copynumber: 7.6 Consensus size: 52
80054 TTCCCATTTA
* * * * * *
80064 ATACTCATGATGACACAAAGTCATCGGACCTTA-AATCTGAAAAAGGATCCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCG-TAAAGGATTCAT
* * *
80116 ATGCTCACGATGACACATAGTCATTGGACCTTATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
80168 ATACTCACAATGACACATAGTCATTGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
80220 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* * * *
80272 ATACTCACAATGACACATAGTCATCGAATCTCATAATCCGTAAAAGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
80324 ATACTCATGATGACACATAGTCATCGAACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
80376 ATACTCACGATG--AC--A-T--T-GAACCTCATAATCCGTAAATGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
80420 ATACTCACGATGACACATATTCATCGAACCT
1 ATACTCACGATGACACATAGTCATCGGACCT
80451 TTTCCCTTTA
Statistics
Matches: 304, Mismatches: 22, Indels: 18
0.88 0.06 0.05
Matches are distributed among these distances:
44 38 0.12
45 1 0.00
46 2 0.01
47 1 0.00
48 2 0.01
49 1 0.00
50 2 0.01
51 1 0.00
52 251 0.83
53 5 0.02
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
Found at i:80417 original size:44 final size:44
Alignment explanation
Indices: 80349--80434 Score: 163
Period size: 44 Copynumber: 2.0 Consensus size: 44
80339 CATAGTCATC
80349 GAACCTCATAATCCGTAAAGGATTCATATACTCACGATGACATT
1 GAACCTCATAATCCGTAAAGGATTCATATACTCACGATGACATT
*
80393 GAACCTCATAATCCGTAAATGATTCATATACTCACGATGACA
1 GAACCTCATAATCCGTAAAGGATTCATATACTCACGATGACA
80435 CATATTCATC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (44 bp):
GAACCTCATAATCCGTAAAGGATTCATATACTCACGATGACATT
Found at i:85583 original size:52 final size:52
Alignment explanation
Indices: 85497--85787 Score: 460
Period size: 52 Copynumber: 5.6 Consensus size: 52
85487 AAAATGATCT
* *
85497 ATATGCTCACGATGACAC--AGTCATCGGACCTCATAATCCGTAAAGTATTC
1 ATATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTC
* *
85547 ATATACTCATGATGACACATAGTCATCGGATCTCATAATCCGTAAAGGATTC
1 ATATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTC
* * * *
85599 ATATACTTACGATGACACATAATCATCGGACCTTATAATCCATAAAGGATTC
1 ATATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTC
* *
85651 ATATACTCACGATGACACATAGTCATCGGACCTCATAATTCGTAAAGGATCC
1 ATATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTC
*
85703 ATATACTCACGATGACACATAGTCATTGGACCTCATAATCCGTAAAGGATTC
1 ATATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTC
*
85755 ATATACTCATGATGACACATAGTCATCGGACCT
1 ATATACTCACGATGACACATAGTCATCGGACCT
85788 TTTTCGTTTA
Statistics
Matches: 218, Mismatches: 21, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
50 16 0.07
52 202 0.93
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (52 bp):
ATATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTC
Found at i:85659 original size:104 final size:104
Alignment explanation
Indices: 85447--85787 Score: 474
Period size: 104 Copynumber: 3.3 Consensus size: 104
85437 TCCCAATTTA
* * * * * * * *
85447 ATACTCATGATGACACAAAATCATCGGA-CT-TTGAATCTGAAAAATGATCTATATGCTCACGAT
1 ATACTCATGATGACACATAGTCATCGGACCTCAT-AATCCG-TAAAGGATCCATATACTCACGAT
*
85510 GACAC--AGTCATCGGACCTCATAATCCGTAAAGTATTCAT
64 GACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* * *
85549 ATACTCATGATGACACATAGTCATCGGATCTCATAATCCGTAAAGGATTCATATACTTACGATGA
1 ATACTCATGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATCCATATACTCACGATGA
* * *
85614 CACATAATCATCGGACCTTATAATCCATAAAGGATTCAT
66 CACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
85653 ATACTCACGATGACACATAGTCATCGGACCTCATAATTCGTAAAGGATCCATATACTCACGATGA
1 ATACTCATGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATCCATATACTCACGATGA
*
85718 CACATAGTCATTGGACCTCATAATCCGTAAAGGATTCAT
66 CACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
85757 ATACTCATGATGACACATAGTCATCGGACCT
1 ATACTCATGATGACACATAGTCATCGGACCT
85788 TTTTCGTTTA
Statistics
Matches: 211, Mismatches: 24, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
102 48 0.23
103 7 0.03
104 156 0.74
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (104 bp):
ATACTCATGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATCCATATACTCACGATGA
CACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
Found at i:85738 original size:156 final size:155
Alignment explanation
Indices: 85447--85789 Score: 487
Period size: 156 Copynumber: 2.2 Consensus size: 155
85437 TCCCAATTTA
* * * * *
85447 ATACTCATGATGACACAAAATCATCGGA-CTTTGAATCTGAAAAATGATCTATATGCTCACGATG
1 ATACTCACGATGACACATAATCATCGGACCTTTGAATCTCAAAAAGGATCTATATACTCACGATG
* * *
85511 ACACAGTCATCGGACCTCATAATCCGTAAAGTATTCATATACTCATGATGACACATAGTCATCGG
66 ACACAGTCATCGGACCTCATAATCCGTAAAGGATCCATATACTCACGATGACACATAGTCATCGG
*
85576 ATCTCATAATCCGTAAAGGATTCAT
131 ACCTCATAATCCGTAAAGGATTCAT
* *
85601 ATACTTACGATGACACATAATCATCGGACCTTAT-AATC-CATAAAGGAT-TCATATACTCACGA
1 ATACTCACGATGACACATAATCATCGGACCTT-TGAATCTCAAAAAGGATCT-ATATACTCACGA
*
85663 TGACACATAGTCATCGGACCTCATAATTCGTAAAGGATCCATATACTCACGATGACACATAGTCA
64 TGACAC--AGTCATCGGACCTCATAATCCGTAAAGGATCCATATACTCACGATGACACATAGTCA
*
85728 TTGGACCTCATAATCCGTAAAGGATTCAT
127 TCGGACCTCATAATCCGTAAAGGATTCAT
* *
85757 ATACTCATGATGACACATAGTCATCGGACCTTT
1 ATACTCACGATGACACATAATCATCGGACCTTT
85790 TTCGTTTACG
Statistics
Matches: 168, Mismatches: 16, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
153 1 0.01
154 49 0.29
155 8 0.05
156 110 0.65
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (155 bp):
ATACTCACGATGACACATAATCATCGGACCTTTGAATCTCAAAAAGGATCTATATACTCACGATG
ACACAGTCATCGGACCTCATAATCCGTAAAGGATCCATATACTCACGATGACACATAGTCATCGG
ACCTCATAATCCGTAAAGGATTCAT
Found at i:90371 original size:38 final size:39
Alignment explanation
Indices: 90329--90410 Score: 112
Period size: 39 Copynumber: 2.1 Consensus size: 39
90319 CGACGAGATA
* * *
90329 AAGATTAAATGACGAGATA-AAGATGTGTGTTTGATTTG
1 AAGATTAAACGACGAGAAACAAGATATGTGTTTGATTTG
* *
90367 AAGATTAAGCGACGGGAAACAAGATATGTGTTTGATTTG
1 AAGATTAAACGACGAGAAACAAGATATGTGTTTGATTTG
90406 AAGAT
1 AAGAT
90411 AGTTTAAGCG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
38 15 0.39
39 23 0.61
ACGTcount: A:0.38, C:0.05, G:0.27, T:0.30
Consensus pattern (39 bp):
AAGATTAAACGACGAGAAACAAGATATGTGTTTGATTTG
Found at i:94384 original size:7 final size:7
Alignment explanation
Indices: 94360--94392 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
94350 ACTAACTTTT
94360 AATTCAA
1 AATTCAA
94367 TAATT-AA
1 -AATTCAA
94374 AATTCAA
1 AATTCAA
94381 AATTCAA
1 AATTCAA
94388 AATTC
1 AATTC
94393 CACATAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 4 0.17
7 16 0.67
8 4 0.17
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (7 bp):
AATTCAA
Found at i:97312 original size:137 final size:137
Alignment explanation
Indices: 97066--97333 Score: 455
Period size: 137 Copynumber: 2.0 Consensus size: 137
97056 TAGTACAACG
*
97066 ACAACACGTCAACAATAGACTGTCGCCACAAGAAGAGCAAATTCAAAACAGGACAATTAGAGATT
1 ACAACACGTCAACAATAGACTGCCGCCACAAGAAGAGCAAATTCAAAACAGGACAATTAGAGATT
* *
97131 TTATTGTTCTTGTGCTCGATAATCTACAACCAGGGGTTGTTAGACCAATAATACAAGCTGGGAAT
66 TTATTGTTCCTGTGCTCGATAATCTACAACCAGGGGTTGTTAGACCAACAATACAAGCTGGGAAT
97196 TATAACC
131 TATAACC
*
97203 ACAACACGTCAACAATAGACTGCCGCCACAAGAAGAGCAAATTCAAAACAGGACAATTTGAGATT
1 ACAACACGTCAACAATAGACTGCCGCCACAAGAAGAGCAAATTCAAAACAGGACAATTAGAGATT
* * * * *
97268 TTATTGTTCCTGTGCTCGATGATTTACAACCAGGGGTTTTTAGACTAACAATACAAGTTGGGAAT
66 TTATTGTTCCTGTGCTCGATAATCTACAACCAGGGGTTGTTAGACCAACAATACAAGCTGGGAAT
97333 T
131 T
97334 TTGAATTAAA
Statistics
Matches: 122, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
137 122 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (137 bp):
ACAACACGTCAACAATAGACTGCCGCCACAAGAAGAGCAAATTCAAAACAGGACAATTAGAGATT
TTATTGTTCCTGTGCTCGATAATCTACAACCAGGGGTTGTTAGACCAACAATACAAGCTGGGAAT
TATAACC
Found at i:98334 original size:18 final size:18
Alignment explanation
Indices: 98311--98353 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
98301 CAGCTTGATA
*
98311 AGATGCAATCACATAATC
1 AGATGCAACCACATAATC
98329 AGATGCAACCACATAATC
1 AGATGCAACCACATAATC
*
98347 GGATGCA
1 AGATGCA
98354 GCCATAGCAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.42, C:0.23, G:0.16, T:0.19
Consensus pattern (18 bp):
AGATGCAACCACATAATC
Found at i:102683 original size:16 final size:17
Alignment explanation
Indices: 102649--102686 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
102639 CTGAATTCGT
102649 AAAATAATATTAAATTA
1 AAAATAATATTAAATTA
102666 AAAATAATATTAAA-TA
1 AAAATAATATTAAATTA
102682 AAAAT
1 AAAAT
102687 TATTCATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AAAATAATATTAAATTA
Found at i:108698 original size:145 final size:147
Alignment explanation
Indices: 108427--108711 Score: 391
Period size: 145 Copynumber: 2.0 Consensus size: 147
108417 TCCACCATTG
* * *
108427 ATAAAGTTAATTATATGTTTAGGGCTTAAAGTTACGTATTATTAATATAAAATGTACATTATAAT
1 ATAAAGTTAATTATATGTTTAGGGCTTAAAGTTACATATCATTAATATAAAATATACATTATAAT
* * *
108492 ATAATAATTATATATAACGCTACATATCATTAATAATCTACCTTAATTATATAATGCTAATTATA
66 ATAATAATTATATATAACGATACACATCATCAATAATCTACCTTAATTATATAATGCTAATTATA
108557 TATAT-TATAACCTACT
131 TATATATATAACCTACT
* *
108573 ATAAAGTTACTTATATGTTTA-GGCTT-AAGCTTACATATCATTAATATAAAAATATGCATTATA
1 ATAAAGTTAATTATATGTTTAGGGCTTAAAG-TTACATATCATTAATAT-AAAATATACATTATA
* * * *
108636 ATA-ACATAGTTATATAT-AGGATACACATCATCAATAATCTACCTTAATTATATTATGTTAATT
64 ATATA-ATAATTATATATAACGATACACATCATCAATAATCTACCTTAATTATATAATGCTAATT
*
108699 GTATATATATATA
128 ATATATATATATA
108712 CACTATAATC
Statistics
Matches: 122, Mismatches: 13, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
144 3 0.02
145 68 0.56
146 51 0.42
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (147 bp):
ATAAAGTTAATTATATGTTTAGGGCTTAAAGTTACATATCATTAATATAAAATATACATTATAAT
ATAATAATTATATATAACGATACACATCATCAATAATCTACCTTAATTATATAATGCTAATTATA
TATATATATAACCTACT
Found at i:108769 original size:153 final size:146
Alignment explanation
Indices: 108427--108796 Score: 351
Period size: 145 Copynumber: 2.5 Consensus size: 146
108417 TCCACCATTG
* * * * * *
108427 ATAAAGTTAATTATATGTTTAGGGCTTAA-AGTTACGTATTATTAATAT-AAAATGTACATTATA
1 ATAAAATTAATTACATGTTTA-GGCTTAAGA-TTACATATCATTAATATAAAAATATGCATTATA
* * *
108490 ATATA-ATAATTATATATAACGCTACATATCATTAATAATCTACCTTAATTATATAATGCTAATT
64 ATA-ACATAATTATATATAACGATACACATCATCAATAATCTACCTTAATTATATAATGCTAATT
*
108554 ATATATATTATAACCTACT
128 ATATATATTATAACCTACC
* * * *
108573 ATAAAGTTACTTATATGTTTAGGCTTAAGCTTACATATCATTAATATAAAAATATGCATTATAAT
1 ATAAAATTAATTACATGTTTAGGCTTAAGATTACATATCATTAATATAAAAATATGCATTATAAT
* * * *
108638 AACATAGTTATATAT-AGGATACACATCATCAATAATCTACCTTAATTATATTATGTTAATTGTA
66 AACATAATTATATATAACGATACACATCATCAATAATCTACCTTAATTATATAATGCTAA---T-
*
108702 TATATATATACACTATAATCTACC
127 TATATATAT----TATAACCTACC
* *
108726 ATAAAATTAATTACATGTTTAAGG-TTTAGATTGA-ATATCATTAATA-AAATA-ATGCACATTA
1 ATAAAATTAATTACATGTTT-AGGCTTAAGATT-ACATATCATTAATATAAAAATATG--CATTA
*
108787 TAATATCATA
62 TAATAACATA
108797 TTTGTATAAT
Statistics
Matches: 187, Mismatches: 22, Indels: 23
0.81 0.09 0.10
Matches are distributed among these distances:
145 61 0.33
146 47 0.25
148 1 0.01
149 9 0.05
151 3 0.02
152 4 0.02
153 58 0.31
154 4 0.02
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (146 bp):
ATAAAATTAATTACATGTTTAGGCTTAAGATTACATATCATTAATATAAAAATATGCATTATAAT
AACATAATTATATATAACGATACACATCATCAATAATCTACCTTAATTATATAATGCTAATTATA
TATATTATAACCTACC
Found at i:110843 original size:3 final size:3
Alignment explanation
Indices: 110837--110868 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
110827 AATGTAAGTT
110837 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
110869 TTTAATTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:112612 original size:43 final size:43
Alignment explanation
Indices: 112551--112650 Score: 166
Period size: 43 Copynumber: 2.3 Consensus size: 43
112541 CGTTATTCCT
*
112551 TGACATGTTATTAAATTATATTACTTG-TCCTATGTTAATATCG
1 TGACATGTTATTAAATTATATTACTTGACCCT-TGTTAATATCG
*
112594 TGACATATTATTAAATTATATTACTTGACCCTTGTTAATATCG
1 TGACATGTTATTAAATTATATTACTTGACCCTTGTTAATATCG
112637 TGACATGTTATTAA
1 TGACATGTTATTAA
112651 TTGTGCAATT
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
43 50 0.94
44 3 0.06
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.45
Consensus pattern (43 bp):
TGACATGTTATTAAATTATATTACTTGACCCTTGTTAATATCG
Found at i:113118 original size:6 final size:6
Alignment explanation
Indices: 113103--113136 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
113093 CTCATGCACT
* *
113103 AGAGCA AGAGCC AGAGCC AGAGCC AGAGCA AGAG
1 AGAGCC AGAGCC AGAGCC AGAGCC AGAGCC AGAG
113137 GAAGAGGTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.41, C:0.24, G:0.35, T:0.00
Consensus pattern (6 bp):
AGAGCC
Found at i:113142 original size:12 final size:12
Alignment explanation
Indices: 113103--113136 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
113093 CTCATGCACT
113103 AGAGCAAGAGCC
1 AGAGCAAGAGCC
*
113115 AGAGCCAGAGCC
1 AGAGCAAGAGCC
113127 AGAGCAAGAG
1 AGAGCAAGAG
113137 GAAGAGGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.41, C:0.24, G:0.35, T:0.00
Consensus pattern (12 bp):
AGAGCAAGAGCC
Found at i:113594 original size:14 final size:14
Alignment explanation
Indices: 113569--113627 Score: 57
Period size: 14 Copynumber: 4.2 Consensus size: 14
113559 ACATTTTAGG
*
113569 GGTTTAGGGTTTAA
1 GGTTTAGAGTTTAA
*
113583 GTTTTAGAGTTTAA
1 GGTTTAGAGTTTAA
*
113597 GGTTTA-ATGTTTAT
1 GGTTTAGA-GTTTAA
* *
113611 GGTTTAGGGTTTTA
1 GGTTTAGAGTTTAA
113625 GGT
1 GGT
113628 ATAAAAACAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
13 1 0.03
14 35 0.97
ACGTcount: A:0.20, C:0.00, G:0.31, T:0.49
Consensus pattern (14 bp):
GGTTTAGAGTTTAA
Found at i:113609 original size:21 final size:21
Alignment explanation
Indices: 113569--113622 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
113559 ACATTTTAGG
113569 GGTTTAGGGTTTAAGTTTTA-
1 GGTTTAGGGTTTAAGTTTTAT
*
113589 GAGTTTAAGGTTTAA-TGTTTAT
1 G-GTTTAGGGTTTAAGT-TTTAT
113611 GGTTTAGGGTTT
1 GGTTTAGGGTTT
113623 TAGGTATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 2 0.07
21 26 0.90
22 1 0.03
ACGTcount: A:0.20, C:0.00, G:0.30, T:0.50
Consensus pattern (21 bp):
GGTTTAGGGTTTAAGTTTTAT
Found at i:116773 original size:27 final size:27
Alignment explanation
Indices: 116743--116799 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
116733 TTAAAAAGGG
* *
116743 CACTTTCAGTGCCGCCTATTAAATTGT
1 CACTTTCAGTGCCGCCCATTAAACTGT
* *
116770 CACTTTCAGTGCTGCCCATTAGACTGT
1 CACTTTCAGTGCCGCCCATTAAACTGT
116797 CAC
1 CAC
116800 AACCCTAGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.21, C:0.30, G:0.16, T:0.33
Consensus pattern (27 bp):
CACTTTCAGTGCCGCCCATTAAACTGT
Found at i:119297 original size:29 final size:29
Alignment explanation
Indices: 119242--119352 Score: 89
Period size: 31 Copynumber: 3.7 Consensus size: 29
119232 ATCTCAAAAT
* *
119242 TATACATGAACTTTGATTTAATGTGCAATTG
1 TATACATGAACTTTAATTT--GGTGCAATTG
* *
119273 TATACATGAACTTTAATTTGGTGCATTTA
1 TATACATGAACTTTAATTTGGTGCAATTG
* * *
119302 TATACATAAAACTCTAATTGTGGTTC-ATATG
1 TATACAT-GAACTTTAATT-TGGTGCAAT-TG
*
119333 TATACTTGAAACTTTAATTT
1 TATACATG-AACTTTAATTT
119353 AAATTTAATC
Statistics
Matches: 64, Mismatches: 12, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
29 14 0.22
30 11 0.17
31 39 0.61
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.43
Consensus pattern (29 bp):
TATACATGAACTTTAATTTGGTGCAATTG
Found at i:120260 original size:22 final size:22
Alignment explanation
Indices: 120219--120261 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
120209 TATCTAAATA
**
120219 ATAATAATAAAATATTAACAAT
1 ATAATAATAAAATAACAACAAT
*
120241 ATAATAGTAAAATAACAACAA
1 ATAATAATAAAATAACAACAA
120262 ACAACCAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.65, C:0.07, G:0.02, T:0.26
Consensus pattern (22 bp):
ATAATAATAAAATAACAACAAT
Found at i:121282 original size:46 final size:45
Alignment explanation
Indices: 121188--121291 Score: 145
Period size: 46 Copynumber: 2.3 Consensus size: 45
121178 GTTTGCAAAT
* *
121188 TAAAATTGCTAATACGGTGTGGTTAAACCACTCAAACAGTGCAGA
1 TAAAATTGCTAATACGGTGTGGATAAACCACTCAAACAGTGAAGA
** *
121233 TAAAACTTGCTAATACGGTGTGGATAAACCACTCAAATGGTGAATA
1 TAAAA-TTGCTAATACGGTGTGGATAAACCACTCAAACAGTGAAGA
121279 TAAAAGTTGCTAA
1 TAAAA-TTGCTAA
121292 AATGGTACAA
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
45 5 0.10
46 47 0.90
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.26
Consensus pattern (45 bp):
TAAAATTGCTAATACGGTGTGGATAAACCACTCAAACAGTGAAGA
Found at i:122535 original size:14 final size:14
Alignment explanation
Indices: 122513--122547 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
122503 AAATTTGAAA
122513 CTCAAACCCTAAAT
1 CTCAAACCCTAAAT
*
122527 CTTAAACCCTAAAT
1 CTCAAACCCTAAAT
122541 CTCAAAC
1 CTCAAAC
122548 TCAAACCATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.43, C:0.34, G:0.00, T:0.23
Consensus pattern (14 bp):
CTCAAACCCTAAAT
Found at i:122571 original size:40 final size:41
Alignment explanation
Indices: 122513--122620 Score: 125
Period size: 40 Copynumber: 2.7 Consensus size: 41
122503 AAATTTGAAA
* * *
122513 CTCAAACCCTAAATCTTAAACC-CTAAATCTCAAACT-CAAAC
1 CTCAAACTCTAAACCTTAAACCTC-AAATCACAAA-TGCAAAC
122554 CAT-AAA-TCTAAACCTTAAACCTCAAATCACAAATGCAAAC
1 C-TCAAACTCTAAACCTTAAACCTCAAATCACAAATGCAAAC
*
122594 CTCAAACTCTAAACCTTAAATCTCAAA
1 CTCAAACTCTAAACCTTAAACCTCAAA
122621 ATTTAAACTT
Statistics
Matches: 58, Mismatches: 4, Indels: 10
0.81 0.06 0.14
Matches are distributed among these distances:
39 2 0.03
40 31 0.53
41 24 0.41
42 1 0.02
ACGTcount: A:0.46, C:0.31, G:0.01, T:0.22
Consensus pattern (41 bp):
CTCAAACTCTAAACCTTAAACCTCAAATCACAAATGCAAAC
Found at i:122580 original size:20 final size:20
Alignment explanation
Indices: 122484--122620 Score: 70
Period size: 20 Copynumber: 6.7 Consensus size: 20
122474 TTTTTTTTTG
*
122484 CCTTAAACCTCAAACCATAAA
1 CCTTAAACCTCAAATC-TAAA
** *
122505 ATTTGAAA-CTCAAACCCTAAA
1 CCTT-AAACCTCAAA-TCTAAA
*
122526 TCTTAAACC-CTAAATCTCAAA
1 CCTTAAACCTC-AAATCT-AAA
*
122547 -CTCAAACCAT-AAATCTAAA
1 CCTTAAACC-TCAAATCTAAA
122566 CCTTAAACCTCAAATC-ACAA
1 CCTTAAACCTCAAATCTA-AA
* *
122586 -ATGCAAACCTCAAACTCTAAA
1 CCT-TAAACCTCAAA-TCTAAA
*
122607 CCTTAAATCTCAAA
1 CCTTAAACCTCAAA
122621 ATTTAAACTT
Statistics
Matches: 90, Mismatches: 12, Indels: 28
0.69 0.09 0.22
Matches are distributed among these distances:
19 6 0.07
20 43 0.48
21 34 0.38
22 7 0.08
ACGTcount: A:0.47, C:0.29, G:0.01, T:0.23
Consensus pattern (20 bp):
CCTTAAACCTCAAATCTAAA
Found at i:122609 original size:14 final size:14
Alignment explanation
Indices: 122513--122609 Score: 53
Period size: 14 Copynumber: 7.1 Consensus size: 14
122503 AAATTTGAAA
* *
122513 CTCAAACCCTAAAT
1 CTCAAACTCTAAAC
* * *
122527 CTTAAACCCTAAAT
1 CTCAAACTCTAAAC
122541 CTCAAACTC-AAAC
1 CTCAAACTCTAAAC
122554 CAT-AAA-TCTAAAC
1 C-TCAAACTCTAAAC
* *
122567 CTTAAAC-CTCAAAT
1 CTCAAACTCT-AAAC
*
122581 CACAAA-TGC-AAAC
1 CTCAAACT-CTAAAC
122594 CTCAAACTCTAAAC
1 CTCAAACTCTAAAC
122608 CT
1 CT
122610 TAAATCTCAA
Statistics
Matches: 65, Mismatches: 9, Indels: 18
0.71 0.10 0.20
Matches are distributed among these distances:
12 3 0.05
13 26 0.40
14 35 0.54
15 1 0.02
ACGTcount: A:0.45, C:0.32, G:0.01, T:0.22
Consensus pattern (14 bp):
CTCAAACTCTAAAC
Found at i:122642 original size:35 final size:35
Alignment explanation
Indices: 122563--122670 Score: 121
Period size: 35 Copynumber: 3.1 Consensus size: 35
122553 CCATAAATCT
* * **
122563 AAACCTTAAACCTCAAATCAC-AAATGCAAACCTC
1 AAACCTTAAACCTTAAATCTCAAAATTAAAACCTC
* *
122597 AAA-CTCTAAACCTTAAATCTCAAAATTTAAACTTC
1 AAACCT-TAAACCTTAAATCTCAAAATTAAAACCTC
* *
122632 AAACCTTAAACCCTAAATCTCAAAATTAAAACCCC
1 AAACCTTAAACCTTAAATCTCAAAATTAAAACCTC
122667 AAAC
1 AAAC
122671 TCAAATCATG
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
33 2 0.03
34 16 0.26
35 42 0.68
36 2 0.03
ACGTcount: A:0.48, C:0.29, G:0.01, T:0.22
Consensus pattern (35 bp):
AAACCTTAAACCTTAAATCTCAAAATTAAAACCTC
Found at i:138579 original size:28 final size:28
Alignment explanation
Indices: 138566--138627 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
138556 TAATTAAACT
138566 TAAATTTTAAAATATAAAAAATAAAGAC
1 TAAATTTTAAAATATAAAAAATAAAGAC
* * *
138594 TAAATTTCTAAAATACAAATAA-AATGAC
1 TAAATTT-TAAAATATAAAAAATAAAGAC
138622 TAAATT
1 TAAATT
138628 CTTACTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 18 0.60
29 12 0.40
ACGTcount: A:0.60, C:0.06, G:0.03, T:0.31
Consensus pattern (28 bp):
TAAATTTTAAAATATAAAAAATAAAGAC
Found at i:143062 original size:27 final size:27
Alignment explanation
Indices: 143024--143077 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
143014 GAAGCAACTT
* * *
143024 TCTCGCTGTTGTTGGCTTCGTGTTGAA
1 TCTCACTGTTGTTCGCTTCATGTTGAA
143051 TCTCACTGTTGTTCGCTTCATGTTGAA
1 TCTCACTGTTGTTCGCTTCATGTTGAA
143078 GTTTGAGATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.11, C:0.20, G:0.24, T:0.44
Consensus pattern (27 bp):
TCTCACTGTTGTTCGCTTCATGTTGAA
Found at i:155012 original size:30 final size:31
Alignment explanation
Indices: 154959--155022 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 31
154949 TAATAATGGT
* *
154959 AAAATTTTATTTTGACCTCTTAAAAATAATA
1 AAAATTTGATTTTAACCTCTTAAAAATAATA
* *
154990 AAAATTTGA-TTTAACCTTTTAAAAATTATA
1 AAAATTTGATTTTAACCTCTTAAAAATAATA
155020 AAA
1 AAA
155023 TATAAACTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 21 0.72
31 8 0.28
ACGTcount: A:0.48, C:0.08, G:0.03, T:0.41
Consensus pattern (31 bp):
AAAATTTGATTTTAACCTCTTAAAAATAATA
Found at i:157462 original size:16 final size:17
Alignment explanation
Indices: 157425--157459 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
157415 ATACAAATTT
*
157425 AATAATTAAAAAATAAA
1 AATAAATAAAAAATAAA
*
157442 AATAAATAAAAACTAAA
1 AATAAATAAAAAATAAA
157459 A
1 A
157460 TAATCTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (17 bp):
AATAAATAAAAAATAAA
Found at i:163436 original size:62 final size:62
Alignment explanation
Indices: 163360--163552 Score: 307
Period size: 62 Copynumber: 3.1 Consensus size: 62
163350 TAAAAATCTT
* * *
163360 CGATATCTTTGTGATATCGTGAGTATTACATGAGAAATGAATCCTATTACAGATTAAAGGTT
1 CGATGTCTTTGTGATATCGTGAGTATTACATGAGAAATGAATCCTATTACGGATTAAAGGTC
* * *
163422 CGATGTATTTGTGATATCATGAGTATTACATGAGAAATGGATCCTATTACGGATTAAAGG-C
1 CGATGTCTTTGTGATATCGTGAGTATTACATGAGAAATGAATCCTATTACGGATTAAAGGTC
*
163483 CTGATGTCTTTGTGATATCGTGAGTATTACGTGAGAAATGAATCCTATTACGGATTAAAGGTC
1 C-GATGTCTTTGTGATATCGTGAGTATTACATGAGAAATGAATCCTATTACGGATTAAAGGTC
163546 CGATGTC
1 CGATGTC
163553 AAAAATCTTG
Statistics
Matches: 119, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
61 1 0.01
62 116 0.97
63 2 0.02
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.34
Consensus pattern (62 bp):
CGATGTCTTTGTGATATCGTGAGTATTACATGAGAAATGAATCCTATTACGGATTAAAGGTC
Found at i:165563 original size:39 final size:39
Alignment explanation
Indices: 165519--165628 Score: 132
Period size: 39 Copynumber: 2.8 Consensus size: 39
165509 TACTAAATTG
* *
165519 GCAGTGACACTATAAACACTGCAATGTTATACT-AAACCA
1 GCAGTGACACTGTAAACACTGCAATGTTATA-TGAAAACA
* * * *
165558 GCAGTGACATTGTAAACACTACAATATTATATGAAAATA
1 GCAGTGACACTGTAAACACTGCAATGTTATATGAAAACA
* *
165597 GCAGTGACACTGTAAACATTGCGATGTTATAT
1 GCAGTGACACTGTAAACACTGCAATGTTATAT
165629 TGAACTGGCG
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
38 1 0.02
39 58 0.98
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.27
Consensus pattern (39 bp):
GCAGTGACACTGTAAACACTGCAATGTTATATGAAAACA
Found at i:169166 original size:23 final size:24
Alignment explanation
Indices: 169140--169192 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
169130 AAAACATAAA
*
169140 AATAACATCTAAACA-ACCAAAAT
1 AATAACATCAAAACACACCAAAAT
*
169163 AAT-A-ATCAAAACAGCAGCAAAAT
1 AATAACATCAAAACA-CACCAAAAT
169186 AATAACA
1 AATAACA
169193 AAACAATAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
21 8 0.33
22 1 0.04
23 13 0.54
24 1 0.04
25 1 0.04
ACGTcount: A:0.62, C:0.19, G:0.04, T:0.15
Consensus pattern (24 bp):
AATAACATCAAAACACACCAAAAT
Found at i:169207 original size:23 final size:23
Alignment explanation
Indices: 169151--169242 Score: 78
Period size: 23 Copynumber: 4.0 Consensus size: 23
169141 ATAACATCTA
*
169151 AACAACCAAAATAATAATCAAAAC
1 AACAACAAAAATAATAA-CAAAAC
* *
169175 AGCAGC-AAAATAATAACAAAAC
1 AACAACAAAAATAATAACAAAAC
* ** *
169197 AATAACAAAAATAGCAACAAAAAT
1 AACAACAAAAATAATAAC-AAAAC
* *
169221 AACAGCAAAAATAATAGCAAAA
1 AACAACAAAAATAATAACAAAA
169243 ATAACAATAA
Statistics
Matches: 53, Mismatches: 13, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
22 9 0.17
23 23 0.43
24 21 0.40
ACGTcount: A:0.67, C:0.16, G:0.05, T:0.11
Consensus pattern (23 bp):
AACAACAAAAATAATAACAAAAC
Found at i:169215 original size:12 final size:12
Alignment explanation
Indices: 169181--169279 Score: 74
Period size: 12 Copynumber: 8.3 Consensus size: 12
169171 AAACAGCAGC
*
169181 AAAATAATAAC-
1 AAAATAACAACA
* *
169192 AAAACAATAACA
1 AAAATAACAACA
*
169204 AAAATAGCAACA
1 AAAATAACAACA
*
169216 AAAATAACAGCA
1 AAAATAACAACA
* *
169228 AAAATAATAGCA
1 AAAATAACAACA
*
169240 AAAATAACAATA
1 AAAATAACAACA
* * *
169252 AAAGTAGCAATA
1 AAAATAACAACA
* *
169264 AAAACAACAATA
1 AAAATAACAACA
169276 AAAA
1 AAAA
169280 CAATAAAAAA
Statistics
Matches: 72, Mismatches: 15, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
11 10 0.14
12 62 0.86
ACGTcount: A:0.71, C:0.12, G:0.05, T:0.12
Consensus pattern (12 bp):
AAAATAACAACA
Found at i:169283 original size:21 final size:23
Alignment explanation
Indices: 169239--169288 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
169229 AAATAATAGC
*
169239 AAAAATAACAATAAAAGTAGCAAT
1 AAAAACAACAATAAAAG-AGCAAT
169263 AAAAACAACAATAAAA-A-CAAT
1 AAAAACAACAATAAAAGAGCAAT
169284 AAAAA
1 AAAAA
169289 AAAAGCACCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 9 0.36
22 1 0.04
24 15 0.60
ACGTcount: A:0.74, C:0.10, G:0.04, T:0.12
Consensus pattern (23 bp):
AAAAACAACAATAAAAGAGCAAT
Found at i:169301 original size:22 final size:22
Alignment explanation
Indices: 169276--169350 Score: 89
Period size: 22 Copynumber: 3.4 Consensus size: 22
169266 AACAACAATA
169276 AAAACAATAAAAAAAAAGCACC
1 AAAACAATAAAAAAAAAGCACC
* *
169298 AAAACAA-CAAAAAACAGCAACC
1 AAAACAATAAAAAAAAAGC-ACC
* * *
169320 AAAACAGTAAAAAAATAGTACC
1 AAAACAATAAAAAAAAAGCACC
169342 AAAACAATA
1 AAAACAATA
169351 GTATAATTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
21 9 0.20
22 27 0.61
23 8 0.18
ACGTcount: A:0.69, C:0.19, G:0.05, T:0.07
Consensus pattern (22 bp):
AAAACAATAAAAAAAAAGCACC
Found at i:171759 original size:18 final size:19
Alignment explanation
Indices: 171725--171762 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
171715 AAGTTACAAA
171725 AAAAATTCAAAATATTTAT
1 AAAAATTCAAAATATTTAT
*
171744 AAAAATTCCAAA-ATTTAT
1 AAAAATTCAAAATATTTAT
171762 A
1 A
171763 TTTTAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAAATTCAAAATATTTAT
Found at i:175528 original size:12 final size:11
Alignment explanation
Indices: 175511--175556 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
175501 TTCAAAACTT
175511 AAAAATCATTAA
1 AAAAATCA-TAA
175523 AAAAAT-A-AA
1 AAAAATCATAA
175532 AAAAATCATAA
1 AAAAATCATAA
* *
175543 AAAAGTTATAA
1 AAAAATCATAA
175554 AAA
1 AAA
175557 TTTTAACTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
9 8 0.27
10 1 0.03
11 15 0.50
12 6 0.20
ACGTcount: A:0.74, C:0.04, G:0.02, T:0.20
Consensus pattern (11 bp):
AAAAATCATAA
Found at i:180652 original size:102 final size:102
Alignment explanation
Indices: 180476--180682 Score: 414
Period size: 102 Copynumber: 2.0 Consensus size: 102
180466 CTATAAAAAG
180476 CATCTTGAGCTTGAACACAAACCATGTTACACTGCCTAATTTAAACATAAGTATCAAGTTAAAGT
1 CATCTTGAGCTTGAACACAAACCATGTTACACTGCCTAATTTAAACATAAGTATCAAGTTAAAGT
180541 GGTAGAGTCTCTGCAGATTCATAGAAGCATCAACAAA
66 GGTAGAGTCTCTGCAGATTCATAGAAGCATCAACAAA
180578 CATCTTGAGCTTGAACACAAACCATGTTACACTGCCTAATTTAAACATAAGTATCAAGTTAAAGT
1 CATCTTGAGCTTGAACACAAACCATGTTACACTGCCTAATTTAAACATAAGTATCAAGTTAAAGT
180643 GGTAGAGTCTCTGCAGATTCATAGAAGCATCAACAAA
66 GGTAGAGTCTCTGCAGATTCATAGAAGCATCAACAAA
180680 CAT
1 CAT
180683 ACAACAAAAC
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
102 105 1.00
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (102 bp):
CATCTTGAGCTTGAACACAAACCATGTTACACTGCCTAATTTAAACATAAGTATCAAGTTAAAGT
GGTAGAGTCTCTGCAGATTCATAGAAGCATCAACAAA
Found at i:181464 original size:3 final size:3
Alignment explanation
Indices: 181451--181484 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
181441 GGGTAATAAA
181451 TTC TCTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC T-TC TTC TTC TTC TTC TTC TTC TTC TTC TTC
181485 AAGAGTTACA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TTC
Found at i:182086 original size:7 final size:8
Alignment explanation
Indices: 182065--182094 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
182055 TTATTCTAGA
182065 AATTTTTT
1 AATTTTTT
182073 AATTTTTT
1 AATTTTTT
182081 AATTTTTT
1 AATTTTTT
182089 AATTTT
1 AATTTT
182095 CTTTATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (8 bp):
AATTTTTT
Found at i:182203 original size:20 final size:21
Alignment explanation
Indices: 182178--182222 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 21
182168 ATATTTCGAA
182178 TTTTAAAAATTATGTTG-AAT
1 TTTTAAAAATTATGTTGTAAT
*
182198 TTTTAAAAATTATTTTGTAAT
1 TTTTAAAAATTATGTTGTAAT
182219 TTTT
1 TTTT
182223 GTTGAAAGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.58
Consensus pattern (21 bp):
TTTTAAAAATTATGTTGTAAT
Found at i:183033 original size:20 final size:21
Alignment explanation
Indices: 182992--183038 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
182982 TTTTTAAATG
*
182992 ATTATAAAAATATTATAGAAA
1 ATTATTAAAATATTATAGAAA
183013 ATTATTAAAAT-TTAT-GAAAA
1 ATTATTAAAATATTATAG-AAA
183033 ATTATT
1 ATTATT
183039 TTTTTGAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 1 0.04
20 13 0.54
21 10 0.42
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.40
Consensus pattern (21 bp):
ATTATTAAAATATTATAGAAA
Found at i:184821 original size:26 final size:26
Alignment explanation
Indices: 184792--184896 Score: 106
Period size: 26 Copynumber: 4.0 Consensus size: 26
184782 TAAGAGCGTT
*
184792 ACTCTACCTGGGCTCG-AATAAGCTAA
1 ACTCTATCTGGGCTCGTAA-AAGCTAA
* * *
184818 ACTCTGTTTGGGCTCGTAAGAGCTAA
1 ACTCTATCTGGGCTCGTAAAAGCTAA
* *
184844 ACTCTATTTGGGCTCGTAAGAGCTAA
1 ACTCTATCTGGGCTCGTAAAAGCTAA
* *
184870 AC-CTTGTCTGGGCTCGTATAAGCTAA
1 ACTC-TATCTGGGCTCGTAAAAGCTAA
184896 A
1 A
184897 TTCTGGAATG
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
25 1 0.01
26 65 0.96
27 2 0.03
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.29
Consensus pattern (26 bp):
ACTCTATCTGGGCTCGTAAAAGCTAA
Found at i:184848 original size:52 final size:52
Alignment explanation
Indices: 184775--184896 Score: 126
Period size: 52 Copynumber: 2.3 Consensus size: 52
184765 TCTAAACTCT
* *
184775 GGCTCGTTAAGAGCGT-TACTCTACCTGGGCTCG-AATAAGCTAAA-CTCTGTTTG
1 GGCTCG-TAAGAGC-TAAACTCTACCTGGGCTCGTAA-AAGCTAAACCT-TGTCTG
** *
184828 GGCTCGTAAGAGCTAAACTCTATTTGGGCTCGTAAGAGCTAAACCTTGTCTG
1 GGCTCGTAAGAGCTAAACTCTACCTGGGCTCGTAAAAGCTAAACCTTGTCTG
184880 GGCTCGTATA-AGCTAAA
1 GGCTCGTA-AGAGCTAAA
184897 TTCTGGAATG
Statistics
Matches: 60, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
51 1 0.02
52 48 0.80
53 11 0.18
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (52 bp):
GGCTCGTAAGAGCTAAACTCTACCTGGGCTCGTAAAAGCTAAACCTTGTCTG
Found at i:193447 original size:22 final size:20
Alignment explanation
Indices: 193412--193451 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
193402 GTAAACCTTT
193412 TTAAATAAAAATAAATTGAG
1 TTAAATAAAAATAAATTGAG
193432 TTAATATAATAAATAAATTG
1 TTAA-ATAA-AAATAAATTG
193452 GAAGTTGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 4 0.22
22 10 0.56
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.35
Consensus pattern (20 bp):
TTAAATAAAAATAAATTGAG
Found at i:197341 original size:134 final size:134
Alignment explanation
Indices: 197101--197370 Score: 531
Period size: 134 Copynumber: 2.0 Consensus size: 134
197091 TACAGGAACG
197101 TGTCTTGTTTGTCTTTCTAATGTGAATATCATTTCATATTTCACGCCTGAACACAGACTAAAAAC
1 TGTCTTGTTTGTCTTTCTAATGTGAATATCATTTCATATTTCACGCCTGAACACAGACTAAAAAC
197166 TTTTAAATCGAAGGAAAGTTTTTATTTTCGACTTTCAGAAAATGATATTTGGAAAATAATTTATT
66 TTTTAAATCGAAGGAAAGTTTTTATTTTCGACTTTCAGAAAATGATATTTGGAAAATAATTTATT
197231 TTTT
131 TTTT
*
197235 TGTCTTGTTTGTCTTTCTAATGTGAATATCATTTCATGTTTCACGCCTGAACACAGACTAAAAAC
1 TGTCTTGTTTGTCTTTCTAATGTGAATATCATTTCATATTTCACGCCTGAACACAGACTAAAAAC
197300 TTTTAAATCGAAGGAAAGTTTTTATTTTCGACTTTCAGAAAATGATATTTGGAAAATAATTTATT
66 TTTTAAATCGAAGGAAAGTTTTTATTTTCGACTTTCAGAAAATGATATTTGGAAAATAATTTATT
197365 TTTT
131 TTTT
197369 TG
1 TG
197371 AAAAAAATTA
Statistics
Matches: 135, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
134 135 1.00
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.43
Consensus pattern (134 bp):
TGTCTTGTTTGTCTTTCTAATGTGAATATCATTTCATATTTCACGCCTGAACACAGACTAAAAAC
TTTTAAATCGAAGGAAAGTTTTTATTTTCGACTTTCAGAAAATGATATTTGGAAAATAATTTATT
TTTT
Found at i:197379 original size:19 final size:20
Alignment explanation
Indices: 197351--197389 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
197341 ATGATATTTG
*
197351 GAAAATAATT-TATTTTTTT
1 GAAAAAAATTATATTTTTTT
197370 GAAAAAAATTAATATTTTTT
1 GAAAAAAATT-ATATTTTTT
197390 AGGATTTGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
21 8 0.47
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (20 bp):
GAAAAAAATTATATTTTTTT
Found at i:204683 original size:24 final size:24
Alignment explanation
Indices: 204647--204821 Score: 185
Period size: 24 Copynumber: 7.4 Consensus size: 24
204637 AGTAAATGAA
*
204647 GTAAATGT-ATCATGCTGACGAGC
1 GTAAACGTAATCATGCTGACGAGC
* *
204670 GTAAACATAATCATGCTGACAAGC
1 GTAAACGTAATCATGCTGACGAGC
* * *
204694 ATAAACGT-ATCATGCTAACGAGT
1 GTAAACGTAATCATGCTGACGAGC
* *
204717 GTAAATGTAATCATGCTAACGAGC
1 GTAAACGTAATCATGCTGACGAGC
* * ** * *
204741 ATAAACGTATTCATTTTTACGAGT
1 GTAAACGTAATCATGCTGACGAGC
*
204765 GTGAACGT-ATCATGCTGACGAGC
1 GTAAACGTAATCATGCTGACGAGC
*
204788 GTAAACGTATTCATGCTGACGAGC
1 GTAAACGTAATCATGCTGACGAGC
204812 GTAAACGTAA
1 GTAAACGTAA
204822 AGAAGTCCTC
Statistics
Matches: 121, Mismatches: 28, Indels: 5
0.79 0.18 0.03
Matches are distributed among these distances:
23 41 0.34
24 80 0.66
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (24 bp):
GTAAACGTAATCATGCTGACGAGC
Found at i:204707 original size:47 final size:48
Alignment explanation
Indices: 204648--204821 Score: 210
Period size: 47 Copynumber: 3.7 Consensus size: 48
204638 GTAAATGAAG
* * *
204648 TAAATGTA-TCATGCTGACGAGCGTAAACATAATCATGCTGACAAGCA
1 TAAACGTATTCATGCTGACGAGCGTAAACGTAATCATGCTGACGAGCA
* * * *
204695 TAAACGTA-TCATGCTAACGAGTGTAAATGTAATCATGCTAACGAGCA
1 TAAACGTATTCATGCTGACGAGCGTAAACGTAATCATGCTGACGAGCA
** * * * *
204742 TAAACGTATTCATTTTTACGAGTGTGAACGT-ATCATGCTGACGAGCG
1 TAAACGTATTCATGCTGACGAGCGTAAACGTAATCATGCTGACGAGCA
204789 TAAACGTATTCATGCTGACGAGCGTAAACGTAA
1 TAAACGTATTCATGCTGACGAGCGTAAACGTAA
204822 AGAAGTCCTC
Statistics
Matches: 106, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
47 88 0.83
48 18 0.17
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (48 bp):
TAAACGTATTCATGCTGACGAGCGTAAACGTAATCATGCTGACGAGCA
Found at i:204818 original size:71 final size:70
Alignment explanation
Indices: 204647--204821 Score: 206
Period size: 71 Copynumber: 2.5 Consensus size: 70
204637 AGTAAATGAA
*
204647 GTAAATGTATCATGCTGACGAGCGTAAACATAATCATGCTGACAAGCATAAACGTATCATGCTAA
1 GTAAATGTATCATGCTGACGAGCGTAAACGTAATCATGCTGACAAGCATAAACGTATCATGCTAA
*
204712 CGAGT
66 CGAGC
* * * ** * * ** * *
204717 GTAAATGTAATCATGCTAACGAGCATAAACGTATTCATTTTTACGAGTGTGAACGTATCATGCTG
1 GTAAATGT-ATCATGCTGACGAGCGTAAACGTAATCATGCTGACAAGCATAAACGTATCATGCTA
204782 ACGAGC
65 ACGAGC
*
204788 GTAAACGTATTCATGCTGACGAGCGTAAACGTAA
1 GTAAATGTA-TCATGCTGACGAGCGTAAACGTAA
204822 AGAAGTCCTC
Statistics
Matches: 86, Mismatches: 17, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
70 9 0.10
71 77 0.90
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (70 bp):
GTAAATGTATCATGCTGACGAGCGTAAACGTAATCATGCTGACAAGCATAAACGTATCATGCTAA
CGAGC
Found at i:207886 original size:40 final size:40
Alignment explanation
Indices: 207831--207911 Score: 126
Period size: 40 Copynumber: 2.0 Consensus size: 40
207821 ACTTACCTTG
*
207831 GTCATAAGAACAAAATTCTGCATGCCAAGCCAGTTATGCA
1 GTCATAAGAACAAAATTCTGCATACCAAGCCAGTTATGCA
* * *
207871 GTCATAAGATCAAAATTTTGTATACCAAGCCAGTTATGCA
1 GTCATAAGAACAAAATTCTGCATACCAAGCCAGTTATGCA
207911 G
1 G
207912 AAATTATTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (40 bp):
GTCATAAGAACAAAATTCTGCATACCAAGCCAGTTATGCA
Found at i:217521 original size:43 final size:43
Alignment explanation
Indices: 217467--217563 Score: 124
Period size: 43 Copynumber: 2.3 Consensus size: 43
217457 ACAGAGGAAG
* * *
217467 CTACGTGGAAAAAGCCACATTT-AAGAAATGACAAAGGAGGAAA
1 CTACGTGGAAAAAACCAC-TTTCAAGAAATGACAAAGAAAGAAA
** *
217510 CTGTGTGGAAAAAACCACTTTCATGAAATGACAAAGAAAGAAA
1 CTACGTGGAAAAAACCACTTTCAAGAAATGACAAAGAAAGAAA
217553 CTACGTGGAAA
1 CTACGTGGAAA
217564 GCACCCACTA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
42 3 0.07
43 42 0.93
ACGTcount: A:0.47, C:0.14, G:0.22, T:0.16
Consensus pattern (43 bp):
CTACGTGGAAAAAACCACTTTCAAGAAATGACAAAGAAAGAAA
Found at i:219168 original size:7 final size:6
Alignment explanation
Indices: 219141--219165 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
219131 CACTAAACAT
219141 CATCCC CATCCC CATCCC CATCCC C
1 CATCCC CATCCC CATCCC CATCCC C
219166 CATATATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.68, G:0.00, T:0.16
Consensus pattern (6 bp):
CATCCC
Found at i:226326 original size:20 final size:20
Alignment explanation
Indices: 226289--226328 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
226279 TATTATAACC
*
226289 CTTTCTTTCTATTTTCTTTT
1 CTTTCTTTCTATTCTCTTTT
226309 CTTTCTTT-TATTCCTCTTTT
1 CTTTCTTTCTATT-CTCTTTT
226329 TCCCCTCTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.05, C:0.23, G:0.00, T:0.72
Consensus pattern (20 bp):
CTTTCTTTCTATTCTCTTTT
Found at i:231146 original size:67 final size:67
Alignment explanation
Indices: 231060--231258 Score: 371
Period size: 67 Copynumber: 3.0 Consensus size: 67
231050 TGAATTTGTC
231060 GAGTGTTTTTCTGTGTGTCCTTTTAAATGGGTTAATTCCATGTATTTATATGATATCGTCACTGT
1 GAGTG-TTTTCTGTGTGTCCTTTTAAATGGGTTAATTCCATGTATTTATATGATATCGTCACTGT
231125 GTT
65 GTT
*
231128 GAGTGTTTTCTGTATGTCCTTTTAAATGGGTTAATTCCATGTATTTATATGATATCGTCACTGTG
1 GAGTGTTTTCTGTGTGTCCTTTTAAATGGGTTAATTCCATGTATTTATATGATATCGTCACTGTG
231193 TT
66 TT
*
231195 GAGTGTTTTCTGTGTGTCCTTTTAAATGGGTTAATTTCATGTATTTATATGATATCGTCACTGT
1 GAGTGTTTTCTGTGTGTCCTTTTAAATGGGTTAATTCCATGTATTTATATGATATCGTCACTGT
231259 TCATAGATGT
Statistics
Matches: 128, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
67 123 0.96
68 5 0.04
ACGTcount: A:0.20, C:0.12, G:0.20, T:0.48
Consensus pattern (67 bp):
GAGTGTTTTCTGTGTGTCCTTTTAAATGGGTTAATTCCATGTATTTATATGATATCGTCACTGTG
TT
Found at i:241288 original size:6 final size:6
Alignment explanation
Indices: 241277--241307 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
241267 TACAGACACC
241277 CCCACG CCCACG CCCACG CCCACG CCCACG C
1 CCCACG CCCACG CCCACG CCCACG CCCACG C
241308 ATGACAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.68, G:0.16, T:0.00
Consensus pattern (6 bp):
CCCACG
Found at i:241582 original size:22 final size:22
Alignment explanation
Indices: 241557--241620 Score: 119
Period size: 22 Copynumber: 2.9 Consensus size: 22
241547 AAGTTACAAT
241557 TTGATCATTTAATTATTTAAAA
1 TTGATCATTTAATTATTTAAAA
241579 TTGATCATTTAATTATTTAAAA
1 TTGATCATTTAATTATTTAAAA
241601 TTGATCATTTAAATTATTTA
1 TTGATCATTT-AATTATTTA
241621 TTTGATTATT
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 32 0.78
23 9 0.22
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.52
Consensus pattern (22 bp):
TTGATCATTTAATTATTTAAAA
Found at i:244373 original size:22 final size:23
Alignment explanation
Indices: 244334--244379 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
244324 AATCAGTTTA
244334 TAATTTTTCTTTTAAAAATCATT
1 TAATTTTTCTTTTAAAAATCATT
244357 TAATTTTTCTTTTAAAAATCATT
1 TAATTTTTCTTTTAAAAATCATT
244380 ATCAATGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.57
Consensus pattern (23 bp):
TAATTTTTCTTTTAAAAATCATT
Found at i:246225 original size:28 final size:27
Alignment explanation
Indices: 246180--246258 Score: 83
Period size: 28 Copynumber: 2.9 Consensus size: 27
246170 TAAGATGATT
*
246180 ATATACAAAATTTT-AATAAATAAATA
1 ATATATAAAATTTTAAATAAATAAATA
*
246206 ATATATAAAATTATTAAAT-ATTAAAATA
1 ATATATAAAATT-TTAAATAAAT-AAATA
246234 ATATAATATAAATTTTAAA-AAATAA
1 ATAT-ATA-AAATTTTAAATAAATAA
246259 TATTGGCTGG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
26 11 0.25
27 4 0.09
28 14 0.32
29 10 0.23
30 5 0.11
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (27 bp):
ATATATAAAATTTTAAATAAATAAATA
Found at i:246241 original size:16 final size:17
Alignment explanation
Indices: 246197--246243 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
246187 AAATTTTAAT
246197 AAATAA-ATAATATATA
1 AAATAATATAATATATA
*
246213 AAATTAT-TAA-ATATTA
1 AAATAATATAATATA-TA
246229 AAATAATATAATATA
1 AAATAATATAATATA
246244 AATTTTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 3 0.12
16 16 0.64
17 3 0.12
18 3 0.12
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AAATAATATAATATATA
Found at i:256354 original size:36 final size:36
Alignment explanation
Indices: 256307--256378 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
256297 AAGACTCCCA
256307 AGAGTTTCAACCTATCCTTGTGATGGACATGTGATT
1 AGAGTTTCAACCTATCCTTGTGATGGACATGTGATT
256343 AGAGTTTCAACCTATCCTTGTGATGGACATGTGATT
1 AGAGTTTCAACCTATCCTTGTGATGGACATGTGATT
256379 TATTGAATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (36 bp):
AGAGTTTCAACCTATCCTTGTGATGGACATGTGATT
Found at i:267916 original size:24 final size:24
Alignment explanation
Indices: 267880--267941 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
267870 TATAAGCACC
267880 CAGA-CTACCGATACTTCTATGAA
1 CAGATCTACCGATACTTCTATGAA
*
267903 CAGATCTACTGATACTTCTATGAA
1 CAGATCTACCGATACTTCTATGAA
* *
267927 TAGATCTAGCGATAC
1 CAGATCTACCGATAC
267942 CTACTATGCA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 4 0.12
24 30 0.88
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.29
Consensus pattern (24 bp):
CAGATCTACCGATACTTCTATGAA
Found at i:270511 original size:21 final size:23
Alignment explanation
Indices: 270485--270530 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
270475 GGTTTTTTAT
*
270485 AAATGGTGTTTTG-AAGA-AGAA
1 AAATGGTGTTTGGCAAGAGAGAA
270506 AAATGGTGTTTGGCAAGAGAGAA
1 AAATGGTGTTTGGCAAGAGAGAA
270529 AA
1 AA
270531 TGAGAGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 12 0.55
22 4 0.18
23 6 0.27
ACGTcount: A:0.43, C:0.02, G:0.30, T:0.24
Consensus pattern (23 bp):
AAATGGTGTTTGGCAAGAGAGAA
Found at i:272556 original size:19 final size:19
Alignment explanation
Indices: 272534--272578 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
272524 AAAAATTATG
*
272534 AATTTTTGAAA-ATTCATTA
1 AATTTTT-AAATATTCATAA
*
272553 AATTTTTAAATATTTATAA
1 AATTTTTAAATATTCATAA
272572 AATTTTT
1 AATTTTT
272579 TATGAAATAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 3 0.13
19 20 0.87
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (19 bp):
AATTTTTAAATATTCATAA
Done.