Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold374
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: 461091
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 2 of 4
Found at i:164334 original size:23 final size:23
Alignment explanation
Indices: 164257--164334 Score: 61
Period size: 23 Copynumber: 3.3 Consensus size: 23
164247 TTATATGTGT
*
164257 TTAATTTATTTTTATTTGTAGAAGTA
1 TTAATTTATTTTTATTT-T-TAAG-A
* * *
164283 TAAATTT-GTTTTA-TTTTAAGG
1 TTAATTTATTTTTATTTTTAAGA
*
164304 TATGATTTATTTTTATTTTTAAGA
1 T-TAATTTATTTTTATTTTTAAGA
164328 TTAATTT
1 TTAATTT
164335 GATTAAAAGT
Statistics
Matches: 40, Mismatches: 9, Indels: 9
0.69 0.16 0.16
Matches are distributed among these distances:
21 1 0.03
22 7 0.17
23 11 0.28
24 10 0.25
25 5 0.12
26 6 0.15
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.60
Consensus pattern (23 bp):
TTAATTTATTTTTATTTTTAAGA
Found at i:164682 original size:8 final size:8
Alignment explanation
Indices: 164653--164729 Score: 68
Period size: 8 Copynumber: 9.4 Consensus size: 8
164643 AGGAGGGAGG
164653 AAAGAAGAA
1 AAAGAA-AA
*
164662 AAA-AAAT
1 AAAGAAAA
164669 AAAGAAAA
1 AAAGAAAA
164677 AAAGAAAGA
1 AAAGAAA-A
164686 AAGAGGAAAA
1 AA-A-GAAAA
*
164696 AAAG-GAA
1 AAAGAAAA
*
164703 AGAGAAAA
1 AAAGAAAA
*
164711 AAATAAAA
1 AAAGAAAA
164719 AAAGAAAA
1 AAAGAAAA
164727 AAA
1 AAA
164730 ATGGAAAAAG
Statistics
Matches: 55, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
7 9 0.16
8 31 0.56
9 7 0.13
10 4 0.07
11 4 0.07
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.03
Consensus pattern (8 bp):
AAAGAAAA
Found at i:164688 original size:32 final size:33
Alignment explanation
Indices: 164652--164731 Score: 96
Period size: 32 Copynumber: 2.5 Consensus size: 33
164642 GAGGAGGGAG
164652 GAAAGAAGAAAAAAAATAAAGA-AAAAAAGA-AA
1 GAAAGAAGAAAAAAAATAAAGAGAAAAAA-ATAA
* **
164684 GAAAGAGGAAAAAAAGGAAAGAGAAAAAAATAA
1 GAAAGAAGAAAAAAAATAAAGAGAAAAAAATAA
164717 -AAA-AAGAAAAAAAAT
1 GAAAGAAGAAAAAAAAT
164732 GGAAAAAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
31 9 0.22
32 23 0.57
33 8 0.20
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (33 bp):
GAAAGAAGAAAAAAAATAAAGAGAAAAAAATAA
Found at i:164738 original size:18 final size:18
Alignment explanation
Indices: 164671--164731 Score: 56
Period size: 17 Copynumber: 3.6 Consensus size: 18
164661 AAAAAAATAA
* *
164671 AGAAAAAAAGAAAGAAAG
1 AGAAAAAAATAAAAAAAG
* **
164689 AG-GAAAAA-AAGGAAAG
1 AGAAAAAAATAAAAAAAG
164705 AGAAAAAAATAAAAAAAG
1 AGAAAAAAATAAAAAAAG
164723 A-AAAAAAAT
1 AGAAAAAAAT
164732 GGAAAAAGGT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
16 9 0.25
17 18 0.50
18 9 0.25
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (18 bp):
AGAAAAAAATAAAAAAAG
Found at i:165306 original size:136 final size:138
Alignment explanation
Indices: 165026--165318 Score: 362
Period size: 136 Copynumber: 2.1 Consensus size: 138
165016 TATGTCAAAA
* * ** ** *
165026 TATGTTTAATATGTTTAAAATAAAAAGATTTAGTTTGACGTATTTTTTAGTTATATTTTTTGTTT
1 TATGTTTAATATGTTAAAAATAAAAAGACTTAGTTTGACGTATTTTGGAGTTATATTTCCTCTTT
* * *
165091 AATATGAAATACTCGTTTAAATACCTCTTAATATTATTTAAGATTTTTTATATTATTAATTTTTT
66 AATATGAAATACTCGTTTAAATACCTCTTAATATTATTTAAGATATCTGATATTATTAATTTTTT
*
165156 ATGGTATG
131 ATGGCATG
* *
165164 -ATTGTTTATTATGTTAAAAATAAAAAGACTT-GTTTTGACGTGGTTTTGGA-TTATA-TTCCTC
1 TA-TGTTTAATATGTTAAAAATAAAAAGACTTAG-TTTGACGT-ATTTTGGAGTTATATTTCCTC
* * * *
165225 TTTAATATGAAATGCTTGTTTAAATA-CTCTTAATGTTATTTGAGATATCTGATATTATTAATTT
63 TTTAATATGAAATACTCGTTTAAATACCTCTTAATATTATTTAAGATATCTGATATTATTAATTT
165289 TTTATGGCATG
128 TTTATGGCATG
*
165300 TATGTTTAATATGTCAAAA
1 TATGTTTAATATGTTAAAA
165319 TATGTTTAAT
Statistics
Matches: 132, Mismatches: 19, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
136 58 0.44
137 30 0.23
138 39 0.30
139 5 0.04
ACGTcount: A:0.32, C:0.06, G:0.12, T:0.50
Consensus pattern (138 bp):
TATGTTTAATATGTTAAAAATAAAAAGACTTAGTTTGACGTATTTTGGAGTTATATTTCCTCTTT
AATATGAAATACTCGTTTAAATACCTCTTAATATTATTTAAGATATCTGATATTATTAATTTTTT
ATGGCATG
Found at i:177961 original size:27 final size:25
Alignment explanation
Indices: 177904--177968 Score: 64
Period size: 27 Copynumber: 2.6 Consensus size: 25
177894 ATTTTAAATT
177904 TAAAAAATA-AATA-ATTTTTTTAA
1 TAAAAAATATAATATATTTTTTTAA
*
177927 -ATATAAATATAATATTATTTTTATTAA
1 TA-AAAAATATAATA-TATTTTT-TTAA
*
177954 TAAAAAATATCATAT
1 TAAAAAATATAATAT
177969 CAATATAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
22 1 0.03
23 6 0.18
24 4 0.12
26 7 0.21
27 14 0.42
28 1 0.03
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
TAAAAAATATAATATATTTTTTTAA
Found at i:178024 original size:12 final size:12
Alignment explanation
Indices: 177970--178030 Score: 52
Period size: 12 Copynumber: 5.1 Consensus size: 12
177960 ATATCATATC
177970 AATATAATTTAA
1 AATATAATTTAA
* * *
177982 ATTTTAAATTAA
1 AATATAATTTAA
* *
177994 TATATAA-TAAA
1 AATATAATTTAA
178005 AATATAATTTAA
1 AATATAATTTAA
*
178017 AATTTAATTATAA
1 AATATAATT-TAA
178030 A
1 A
178031 TTTTTTATTT
Statistics
Matches: 37, Mismatches: 10, Indels: 3
0.74 0.20 0.06
Matches are distributed among these distances:
11 9 0.24
12 24 0.65
13 4 0.11
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
AATATAATTTAA
Found at i:180937 original size:16 final size:15
Alignment explanation
Indices: 180896--180929 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
180886 AAGCCATATA
*
180896 TTTTT-AAAAATTAT
1 TTTTTCAAAAATAAT
180910 TTTTTCAAAAATAAT
1 TTTTTCAAAAATAAT
180925 TTTTT
1 TTTTT
180930 GGAAAAATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (15 bp):
TTTTTCAAAAATAAT
Found at i:181133 original size:21 final size:21
Alignment explanation
Indices: 181109--181149 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
181099 AAATTAATAA
181109 GTTAATTCTTGATCATGTCTT
1 GTTAATTCTTGATCATGTCTT
181130 GTTAATTCTTGATCATGTCT
1 GTTAATTCTTGATCATGTCT
181150 CCAAGAGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.20, C:0.15, G:0.15, T:0.51
Consensus pattern (21 bp):
GTTAATTCTTGATCATGTCTT
Found at i:181714 original size:3 final size:3
Alignment explanation
Indices: 181706--181732 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
181696 CATGGTACTC
181706 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
181733 AATTTCAGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:181985 original size:17 final size:16
Alignment explanation
Indices: 181968--182007 Score: 64
Period size: 16 Copynumber: 2.5 Consensus size: 16
181958 CTGAACACGA
181968 AAATAACTCGAACCCG
1 AAATAACTCGAACCCG
181984 AAATGAAC-CGAACCCG
1 AAAT-AACTCGAACCCG
182000 AAATAACT
1 AAATAACT
182008 TGAATAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 3 0.14
16 16 0.73
17 3 0.14
ACGTcount: A:0.47, C:0.28, G:0.12, T:0.12
Consensus pattern (16 bp):
AAATAACTCGAACCCG
Found at i:182767 original size:22 final size:21
Alignment explanation
Indices: 182726--182768 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
182716 ATCCAACTAT
*
182726 TAAACCTAATTGACTCAAACC
1 TAAACCTAAATGACTCAAACC
*
182747 TAAACCTAAAATGACTTAAACC
1 TAAACCT-AAATGACTCAAACC
182769 CGATTTAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.47, C:0.26, G:0.05, T:0.23
Consensus pattern (21 bp):
TAAACCTAAATGACTCAAACC
Found at i:182884 original size:16 final size:16
Alignment explanation
Indices: 182848--182897 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
182838 TTAAAATGAT
* *
182848 CCAAACCCGAAACAAT
1 CCAAACCCGAAATAAC
*
182864 TCAAACCCGAAATAAC
1 CCAAACCCGAAATAAC
* *
182880 CCAAACCCAAAATGAC
1 CCAAACCCGAAATAAC
182896 CC
1 CC
182898 GAACTTGAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.48, C:0.38, G:0.06, T:0.08
Consensus pattern (16 bp):
CCAAACCCGAAATAAC
Found at i:187907 original size:21 final size:21
Alignment explanation
Indices: 187883--187942 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
187873 TATTAAAAGT
*
187883 TGCATTTTTTCATCCAAAAAA
1 TGCATTCTTTCATCCAAAAAA
**
187904 TGCATTCTTTCATCCAATCAA
1 TGCATTCTTTCATCCAAAAAA
*
187925 TGCA-TCATTTCATTCAAA
1 TGCATTC-TTTCATCCAAA
187943 GATACCTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
20 2 0.06
21 31 0.94
ACGTcount: A:0.33, C:0.23, G:0.05, T:0.38
Consensus pattern (21 bp):
TGCATTCTTTCATCCAAAAAA
Found at i:190196 original size:21 final size:22
Alignment explanation
Indices: 190164--190210 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
190154 TATTGATAAT
190164 TTAATAAAAAATTAGTTTTA-TA
1 TTAATAAAAAA-TAGTTTTATTA
*
190186 TTAAT-AAAAATATTTTTATTA
1 TTAATAAAAAATAGTTTTATTA
190207 TTAA
1 TTAA
190211 ATAGTATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 7 0.30
21 11 0.48
22 5 0.22
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
TTAATAAAAAATAGTTTTATTA
Found at i:190211 original size:18 final size:19
Alignment explanation
Indices: 190164--190221 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 19
190154 TATTGATAAT
*
190164 TTAATAAAAAATTAGTTTTATA
1 TTAATAAATAA-TA-TTTT-TA
190186 TTAATAAA-AATATTTTTA
1 TTAATAAATAATATTTTTA
* *
190204 TTATTAAATAGTATTTTT
1 TTAATAAATAATATTTTT
190222 TGTAAGACTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
18 9 0.27
19 12 0.36
20 2 0.06
21 2 0.06
22 8 0.24
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (19 bp):
TTAATAAATAATATTTTTA
Found at i:190489 original size:30 final size:29
Alignment explanation
Indices: 190427--190489 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 29
190417 TAATTTTTTT
190427 ATTATATATGAACCTTTAATTTTAATTAA
1 ATTATATATGAACCTTTAATTTTAATTAA
*
190456 ATTATATTATCGAA-CTTTTATTATTAA-TAA
1 ATTATA-TAT-GAACCTTTAATT-TTAATTAA
190486 ATTA
1 ATTA
190490 AATCATTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
29 6 0.20
30 17 0.57
31 7 0.23
ACGTcount: A:0.41, C:0.06, G:0.03, T:0.49
Consensus pattern (29 bp):
ATTATATATGAACCTTTAATTTTAATTAA
Found at i:191856 original size:7 final size:7
Alignment explanation
Indices: 191844--191868 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
191834 TCGTATTTAA
191844 TTTTATT
1 TTTTATT
191851 TTTTATT
1 TTTTATT
191858 TTTTATT
1 TTTTATT
191865 TTTT
1 TTTT
191869 TGACATACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTATT
Found at i:192842 original size:27 final size:27
Alignment explanation
Indices: 192772--192843 Score: 126
Period size: 27 Copynumber: 2.7 Consensus size: 27
192762 ACAAGCCACT
*
192772 ATTTTTGACAAACAAAAAGGAATCACC
1 ATTTTTGACAAACACAAAGGAATCACC
*
192799 ATTTTTGACAAATACAAAGGAATCACC
1 ATTTTTGACAAACACAAAGGAATCACC
192826 ATTTTTGACAAACACAAA
1 ATTTTTGACAAACACAAA
192844 TGGTGACTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.47, C:0.18, G:0.10, T:0.25
Consensus pattern (27 bp):
ATTTTTGACAAACACAAAGGAATCACC
Found at i:200466 original size:23 final size:24
Alignment explanation
Indices: 200437--200507 Score: 81
Period size: 27 Copynumber: 2.9 Consensus size: 24
200427 AATAAAAATT
200437 AGCCACCA-TTTTGACAAACAACA
1 AGCCACCATTTTTGACAAACAACA
* *
200460 AGCCACCATTTTTTACAAACAAAA
1 AGCCACCATTTTTGACAAACAACA
*
200484 AGGAACCACTATTTTTGACAAACA
1 A-G--CCACCATTTTTGACAAACA
200508 CAAAAAAACT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.20
24 14 0.35
25 1 0.03
27 17 0.43
ACGTcount: A:0.44, C:0.25, G:0.08, T:0.23
Consensus pattern (24 bp):
AGCCACCATTTTTGACAAACAACA
Found at i:200477 original size:24 final size:23
Alignment explanation
Indices: 200437--200481 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
200427 AATAAAAATT
200437 AGCCACCATTTTGACAAACAACA
1 AGCCACCATTTTGACAAACAACA
*
200460 AGCCACCATTTTTTACAAACAA
1 AGCCACCA-TTTTGACAAACAA
200482 AAAGGAACCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.42, C:0.29, G:0.07, T:0.22
Consensus pattern (23 bp):
AGCCACCATTTTGACAAACAACA
Found at i:200491 original size:24 final size:24
Alignment explanation
Indices: 200441--200512 Score: 65
Period size: 24 Copynumber: 2.9 Consensus size: 24
200431 AAAATTAGCC
* * *
200441 ACCA-TTTTGACAAACAACAAGCC
1 ACCATTTTTTACAAACAAAAAGCA
*
200464 ACCATTTTTTACAAACAAAAAGGA
1 ACCATTTTTTACAAACAAAAAGCA
200488 ACCACTATTTTTGACAAACACAAAA
1 ACCA-T-TTTTT-ACAAACA-AAAA
200513 AAACTACTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
23 4 0.10
24 19 0.47
25 1 0.03
26 5 0.12
27 7 0.17
28 4 0.10
ACGTcount: A:0.47, C:0.24, G:0.07, T:0.22
Consensus pattern (24 bp):
ACCATTTTTTACAAACAAAAAGCA
Found at i:200504 original size:27 final size:27
Alignment explanation
Indices: 200445--200540 Score: 101
Period size: 27 Copynumber: 3.7 Consensus size: 27
200435 TTAGCCACCA
* *
200445 TTTTGACAAACA-ACAAG--CCACCAT
1 TTTTGACAAACACAAAAGAACCACTAT
*
200469 TTTTTACAAACA-AAAAGGAACCACTAT
1 TTTTGACAAACACAAAA-GAACCACTAT
* *
200496 TTTTGACAAACACAAAAAAACTACTAT
1 TTTTGACAAACACAAAAGAACCACTAT
*
200523 TTTTGACAAACATAAAAG
1 TTTTGACAAACACAAAAG
200541 GGTGACTTTT
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
24 14 0.23
25 1 0.02
27 41 0.68
28 4 0.07
ACGTcount: A:0.48, C:0.20, G:0.07, T:0.25
Consensus pattern (27 bp):
TTTTGACAAACACAAAAGAACCACTAT
Found at i:200864 original size:14 final size:13
Alignment explanation
Indices: 200844--200884 Score: 55
Period size: 14 Copynumber: 3.0 Consensus size: 13
200834 AGATAAAAAA
200844 ATTTAATATTTAT
1 ATTTAATATTTAT
200857 ATTATAATATTATAT
1 ATT-TAATATT-TAT
*
200872 ATTTAATCTTTAT
1 ATTTAATATTTAT
200885 GTAATATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 6 0.24
14 13 0.52
15 6 0.24
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (13 bp):
ATTTAATATTTAT
Found at i:201614 original size:20 final size:20
Alignment explanation
Indices: 201570--201623 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
201560 ATTTCAACGA
201570 TTTGTATCGATACATAAAAT
1 TTTGTATCGATACATAAAAT
* ***
201590 GTTGTATCGATACATATTTT
1 TTTGTATCGATACATAAAAT
201610 TTTGTATCGATACA
1 TTTGTATCGATACA
201624 ATGTAAGTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.31, C:0.11, G:0.13, T:0.44
Consensus pattern (20 bp):
TTTGTATCGATACATAAAAT
Found at i:201687 original size:13 final size:13
Alignment explanation
Indices: 201669--201693 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
201659 ATTACTCACA
201669 TGTATCGATACAT
1 TGTATCGATACAT
201682 TGTATCGATACA
1 TGTATCGATACA
201694 CTGATTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:201758 original size:52 final size:52
Alignment explanation
Indices: 201702--201826 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
201692 CACTGATTTT
*
201702 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
201754 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
201806 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
201827 CTTTTCATAT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:206331 original size:21 final size:21
Alignment explanation
Indices: 206273--206362 Score: 80
Period size: 21 Copynumber: 4.3 Consensus size: 21
206263 AACATTTTTG
* *
206273 TAATTTTAGTAC-CTTTAATA
1 TAATTTTAATACTCTTTGATA
*
206293 TGATTTTGACA-ACT-TTTGATA
1 TAATTTT-A-ATACTCTTTGATA
206314 TAATTTTAATGA-TCTTTGATA
1 TAATTTTAAT-ACTCTTTGATA
* *
206335 TGATTTTAATACTCTTTAATA
1 TAATTTTAATACTCTTTGATA
206356 TAATTTT
1 TAATTTT
206363 GAAAACCTTT
Statistics
Matches: 56, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
19 1 0.02
20 9 0.16
21 46 0.82
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (21 bp):
TAATTTTAATACTCTTTGATA
Found at i:206373 original size:42 final size:42
Alignment explanation
Indices: 206273--206373 Score: 102
Period size: 42 Copynumber: 2.4 Consensus size: 42
206263 AACATTTTTG
* * *
206273 TAATTTTAGT-ACCTTTAATATGATTTTGACAACTTTTGATA
1 TAATTTTAATAACCTTTGATATGATTTTGACAACTTTTAATA
* *
206314 TAATTTTAATGATCTTTGATATGATTTT-A-ATACTCTTTAATA
1 TAATTTTAATAACCTTTGATATGATTTTGACA-ACT-TTTAATA
206356 TAATTTTGAA-AACCTTTG
1 TAATTTT-AATAACCTTTG
206374 TAACAGTTTC
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
40 1 0.02
41 13 0.26
42 34 0.68
43 2 0.04
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.50
Consensus pattern (42 bp):
TAATTTTAATAACCTTTGATATGATTTTGACAACTTTTAATA
Found at i:206445 original size:20 final size:20
Alignment explanation
Indices: 206394--206450 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 20
206384 GGTAACTTAG
206394 ATTTTTGATAATATTTAATATA
1 ATTTTTGATAAT-TTT-ATATA
*
206416 A-TTTTCATAATTTT-TATA
1 ATTTTTGATAATTTTATATA
206434 ATTTTTTGATAATTTTA
1 A-TTTTTGATAATTTTA
206451 GATGTAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
18 5 0.17
20 15 0.50
21 9 0.30
22 1 0.03
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.60
Consensus pattern (20 bp):
ATTTTTGATAATTTTATATA
Found at i:206463 original size:21 final size:19
Alignment explanation
Indices: 206396--206506 Score: 73
Period size: 21 Copynumber: 5.5 Consensus size: 19
206386 TAACTTAGAT
206396 TTTTGATAATATTTAATATAA
1 TTTTGATAAT-TTT-ATATAA
*
206417 TTTTCATAATTTT-TATAA
1 TTTTGATAATTTTATATAA
*
206435 TTTTTTGATAATTTTAGATGTAA
1 --TTTTGATAATTTT--ATATAA
* *
206458 TTTTGAAAACTTTTGAAATAA
1 TTTTGATAA-TTTT-ATATAA
* *
206479 TTTTGATAACTTTT-TTTAG
1 TTTTGATAA-TTTTATATAA
206498 TTTTGATAA
1 TTTTGATAA
206507 CCTTTTATGA
Statistics
Matches: 74, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
18 5 0.07
19 11 0.15
20 15 0.20
21 35 0.47
22 4 0.05
23 4 0.05
ACGTcount: A:0.34, C:0.03, G:0.08, T:0.55
Consensus pattern (19 bp):
TTTTGATAATTTTATATAA
Found at i:206520 original size:19 final size:18
Alignment explanation
Indices: 206478--206520 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
206468 TTTTGAAATA
* *
206478 ATTTTGATAACTTTTTTT
1 ATTTTGATAACTTTTATG
206496 AGTTTTGATAACCTTTTATG
1 A-TTTTGATAA-CTTTTATG
206516 ATTTT
1 ATTTT
206521 AATAGTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 13 0.62
20 7 0.33
ACGTcount: A:0.23, C:0.07, G:0.09, T:0.60
Consensus pattern (18 bp):
ATTTTGATAACTTTTATG
Found at i:206985 original size:3 final size:3
Alignment explanation
Indices: 206977--207007 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
206967 TTAAGGAATA
206977 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
207008 GGCGCGTGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:207551 original size:11 final size:11
Alignment explanation
Indices: 207524--207584 Score: 54
Period size: 11 Copynumber: 5.4 Consensus size: 11
207514 TGATATAATT
207524 ATATAATATAAA
1 ATATAAT-TAAA
207536 A-ATAATTAAA
1 ATATAATTAAA
207546 ATATAATTAAA
1 ATATAATTAAA
* *
207557 AAATAACTTGAA
1 ATATAA-TTAAA
207569 ATA-AATATATAA
1 ATATAAT-TA-AA
207581 ATAT
1 ATAT
207585 TTTAAAATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
10 6 0.15
11 22 0.55
12 12 0.30
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (11 bp):
ATATAATTAAA
Found at i:207552 original size:22 final size:22
Alignment explanation
Indices: 207524--207600 Score: 70
Period size: 22 Copynumber: 3.5 Consensus size: 22
207514 TGATATAATT
207524 ATATAATATAAAAATAATTAAA
1 ATATAATATAAAAATAATTAAA
*
207546 ATATAAT-TAAAAAATAACTTGAA
1 ATATAATAT-AAAAATAA-TTAAA
* *
207569 ATA-AATATATAAATATTTTAAA
1 ATATAATATAAAAATA-ATTAAA
*
207591 AT-TTATATAA
1 ATATAATATAA
207601 TATAAATTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
21 1 0.02
22 35 0.80
23 8 0.18
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (22 bp):
ATATAATATAAAAATAATTAAA
Found at i:207607 original size:33 final size:34
Alignment explanation
Indices: 207569--207643 Score: 93
Period size: 32 Copynumber: 2.3 Consensus size: 34
207559 ATAACTTGAA
* * *
207569 ATAAATATATAAATATTTTAAAATTTATAT-AAT
1 ATAAATATATAAATATATCAAAATTTACATAAAT
*
207602 ATAAAT-TATTAATATATCAAAATTTACATAAAT
1 ATAAATATATAAATATATCAAAATTTACATAAAT
207635 ATAAA-ATAT
1 ATAAATATAT
207644 TTTATATATA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
32 19 0.53
33 17 0.47
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (34 bp):
ATAAATATATAAATATATCAAAATTTACATAAAT
Found at i:207745 original size:2 final size:2
Alignment explanation
Indices: 207738--207765 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
207728 AGTGTTAGAG
207738 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
207766 CACACCAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:208116 original size:16 final size:16
Alignment explanation
Indices: 208097--208157 Score: 63
Period size: 16 Copynumber: 3.9 Consensus size: 16
208087 GTCAACGTCT
208097 AATAATTTAAATTTAA
1 AATAATTTAAATTTAA
**
208113 AATAATTTAAA-ACAA
1 AATAATTTAAATTTAA
*
208128 AATAATTTAAATCTT-G
1 AATAATTTAAAT-TTAA
*
208144 AATAATCTAAATTT
1 AATAATTTAAATTT
208158 CTTTTTAATC
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
15 15 0.41
16 22 0.59
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (16 bp):
AATAATTTAAATTTAA
Found at i:208131 original size:15 final size:16
Alignment explanation
Indices: 208097--208139 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 16
208087 GTCAACGTCT
**
208097 AATAATTTAAATTTAA
1 AATAATTTAAATACAA
208113 AATAATTTAAA-ACAA
1 AATAATTTAAATACAA
208128 AATAATTTAAAT
1 AATAATTTAAAT
208140 CTTGAATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 13 0.54
16 11 0.46
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (16 bp):
AATAATTTAAATACAA
Found at i:210548 original size:3 final size:3
Alignment explanation
Indices: 210540--210576 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
210530 AACAAACAAC
210540 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
210577 TTCCCCACTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:210832 original size:15 final size:15
Alignment explanation
Indices: 210812--210866 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
210802 ATTACTCTTT
210812 TAATTTAATAAAAAA
1 TAATTTAATAAAAAA
* *
210827 TAATTTATTAATTAAA
1 TAATTTAATAA-AAAA
*
210843 TAA-TT-ATAAATAA
1 TAATTTAATAAAAAA
*
210856 TAATTAAATAA
1 TAATTTAATAA
210867 TTTTTAAAGA
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
13 5 0.16
14 4 0.13
15 16 0.52
16 6 0.19
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TAATTTAATAAAAAA
Found at i:210854 original size:10 final size:11
Alignment explanation
Indices: 210837--210874 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
210827 TAATTTATTA
210837 ATTAAATAATT
1 ATTAAATAATT
*
210848 A-TAAATAATA
1 ATTAAATAATT
210858 ATTAAATAATT
1 ATTAAATAATT
*
210869 TTTAAA
1 ATTAAA
210875 GAATATTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
10 9 0.39
11 14 0.61
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
ATTAAATAATT
Found at i:210882 original size:21 final size:21
Alignment explanation
Indices: 210835--210879 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
210825 AATAATTTAT
*
210835 TAATTAAATAATTATAAATAA
1 TAATTAAATAATTATAAAGAA
*
210856 TAATTAAATAATTTTTAAAGAA
1 TAATTAAATAA-TTATAAAGAA
210878 TA
1 TA
210880 TTATAACCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
TAATTAAATAATTATAAAGAA
Found at i:211737 original size:16 final size:16
Alignment explanation
Indices: 211713--211759 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
211703 ATAATCATAG
*
211713 ATATCAAATTTTAAAT
1 ATATAAAATTTTAAAT
211729 ATATAAAATATTTAAAT
1 ATATAAAAT-TTTAAAT
*
211746 -TAATTAAATTTTAA
1 AT-ATAAAATTTTAA
211760 TTTGATATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 14 0.52
17 13 0.48
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
ATATAAAATTTTAAAT
Found at i:213157 original size:34 final size:37
Alignment explanation
Indices: 213088--213172 Score: 106
Period size: 36 Copynumber: 2.4 Consensus size: 37
213078 TTAAAATATT
**
213088 AATAATAAT-TTTTATATTAATTTTATAATTAAATTTA
1 AATAA-AATATTTTATATTAATTAAATAATTAAATTTA
213125 AATAAAATATTTT-TATTAATTAAATAA-T-AATTTA
1 AATAAAATATTTTATATTAATTAAATAATTAAATTTA
213159 AATAAAAATATTTT
1 AAT-AAAATATTTT
213173 GGATTAAAGA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
34 9 0.20
35 11 0.25
36 15 0.34
37 9 0.20
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (37 bp):
AATAAAATATTTTATATTAATTAAATAATTAAATTTA
Found at i:213460 original size:27 final size:27
Alignment explanation
Indices: 213393--213501 Score: 89
Period size: 27 Copynumber: 3.9 Consensus size: 27
213383 GAAAATTTAT
213393 ATTATATTATATTATAATTATATTTTAAAA
1 ATTATA-TAT-TTAT-ATTATATTTTAAAA
* *
213423 ATTTTATATTTTTATTA-ATTTTAATAA
1 ATTATATATTTATATTATATTTTAA-AA
*
213450 ATTA-ATAATTTATATTATATAAATTTTAAA
1 ATTATAT-ATTTATATTATAT---TTTAAAA
*
213480 ATT-TATATTTATATTATTTTTT
1 ATTATATATTTATATTATATTTT
213502 TATTATTTTA
Statistics
Matches: 66, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
26 12 0.18
27 18 0.27
28 5 0.08
29 15 0.23
30 12 0.18
31 4 0.06
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (27 bp):
ATTATATATTTATATTATATTTTAAAA
Found at i:213508 original size:14 final size:14
Alignment explanation
Indices: 213481--213521 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
213471 AATTTTAAAA
213481 TTTATATTTA-TAT
1 TTTATATTTATTAT
*
213494 TATT-TTTTTATTAT
1 T-TTATATTTATTAT
213508 TTTATATTTATTAT
1 TTTATATTTATTAT
213522 ATTCATATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
13 8 0.35
14 15 0.65
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTATATTTATTAT
Found at i:213517 original size:56 final size:59
Alignment explanation
Indices: 213389--213518 Score: 135
Period size: 56 Copynumber: 2.3 Consensus size: 59
213379 TATCGAAAAT
* * *
213389 TTATATTATA-TTATATTATAATTATATTTTAAAAATTTTATATTTTTATTAATTTTAA
1 TTATTTTATATTTATATTATAATTAAATTTTAAAAATTTTATATTTATATTAATTTTAA
* * * * *
213447 TAAATTAATAATTTATATTAT-A-TAAATTTT-AAAA-TTTATATTTATATTATTTTTTTA
1 TTATTTTAT-ATTTATATTATAATTAAATTTTAAAAATTTTATATTTATATTA-ATTTTAA
213504 TTATTTTATATTTAT
1 TTATTTTATATTTAT
213519 TATATTCATA
Statistics
Matches: 58, Mismatches: 11, Indels: 8
0.75 0.14 0.10
Matches are distributed among these distances:
56 20 0.34
57 15 0.26
58 12 0.21
59 2 0.03
60 9 0.16
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (59 bp):
TTATTTTATATTTATATTATAATTAAATTTTAAAAATTTTATATTTATATTAATTTTAA
Found at i:216764 original size:14 final size:15
Alignment explanation
Indices: 216745--216786 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
216735 ATTTAATATT
216745 TAATAATATT-TTAA
1 TAATAATATTATTAA
*
216759 TAATAAATATTATTAT
1 TAAT-AATATTATTAA
216775 TAA-AATATTATT
1 TAATAATATTATT
216787 TTTTGAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 13 0.52
15 6 0.24
16 6 0.24
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATAATATTATTAA
Found at i:216826 original size:18 final size:17
Alignment explanation
Indices: 216803--216838 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
216793 AAATTAATAT
*
216803 TAATAATTAATAGTTTAA
1 TAATAAATAAT-GTTTAA
216821 TAATAAATAATGTTTAA
1 TAATAAATAATGTTTAA
216838 T
1 T
216839 TTTCAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (17 bp):
TAATAAATAATGTTTAA
Found at i:216944 original size:25 final size:26
Alignment explanation
Indices: 216864--216974 Score: 72
Period size: 28 Copynumber: 4.2 Consensus size: 26
216854 TAATTTCTAA
216864 ATATTAATATAATTAATGTTT---TATT
1 ATATTAATATAATT-AT-TTTAAATATT
* * *
216889 A-ATAAATATTATTATTTTAAGTATTT
1 ATATTAATATAATTATTTTAAATA-TT
216915 AATATTAATATAATT-TTTTAAATATT
1 -ATATTAATATAATTATTTTAAATATT
*
216941 ATATTAAAAT-ATTATTATGTGAAATATT
1 ATATTAATATAATTATT-T-T-AAATATT
216969 AATATT
1 -ATATT
216975 TTAATAATAA
Statistics
Matches: 69, Mismatches: 6, Indels: 18
0.74 0.06 0.19
Matches are distributed among these distances:
22 3 0.04
23 2 0.03
24 13 0.19
25 14 0.20
26 5 0.07
27 10 0.14
28 17 0.25
29 5 0.07
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (26 bp):
ATATTAATATAATTATTTTAAATATT
Found at i:217226 original size:26 final size:26
Alignment explanation
Indices: 217197--217283 Score: 61
Period size: 26 Copynumber: 3.2 Consensus size: 26
217187 TCAACTAGAT
217197 TATCTCATTTTTAAATAAGTCTAATA
1 TATCTCATTTTTAAATAAGTCTAATA
* * * *
217223 TATC-C-TTATATCATATATGTGTCAACTAAA
1 TATCTCATT-T-TTAAATAAGTCT-AA-T--A
217253 TTATCTCATTTTTAAATAAGTCTAATA
1 -TATCTCATTTTTAAATAAGTCTAATA
217280 TATC
1 TATC
217284 CTTTTTGTAT
Statistics
Matches: 44, Mismatches: 8, Indels: 18
0.63 0.11 0.26
Matches are distributed among these distances:
24 2 0.05
25 2 0.05
26 16 0.36
27 3 0.07
28 1 0.02
29 1 0.02
30 3 0.07
31 12 0.27
32 2 0.05
33 2 0.05
ACGTcount: A:0.37, C:0.14, G:0.05, T:0.45
Consensus pattern (26 bp):
TATCTCATTTTTAAATAAGTCTAATA
Found at i:218489 original size:2 final size:2
Alignment explanation
Indices: 218482--218513 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
218472 AGTGACCAGC
*
218482 TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
218514 GAGTACTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:221991 original size:30 final size:30
Alignment explanation
Indices: 221899--221993 Score: 111
Period size: 30 Copynumber: 3.2 Consensus size: 30
221889 TTTAAGGTTT
* * *
221899 TTTATATATAAATCAAAAGTTAAAAATTTA
1 TTTAAATATAAATTAAAAATTAAAAATTTA
* * *
221929 -TTAAGGTAAAAATTAAAAATTAAAAAATTA
1 TTTAA-ATATAAATTAAAAATTAAAAATTTA
*
221959 TTTAAATATAAATTAAAAATTAAAGATTTA
1 TTTAAATATAAATTAAAAATTAAAAATTTA
221989 TTTAA
1 TTTAA
221994 TTGTAAGAAA
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
29 3 0.06
30 46 0.87
31 4 0.08
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.38
Consensus pattern (30 bp):
TTTAAATATAAATTAAAAATTAAAAATTTA
Found at i:222495 original size:16 final size:16
Alignment explanation
Indices: 222460--222516 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
222450 TTATTATAAA
***
222460 AAAATTATTTATTGAA
1 AAAATTATTTATTTTT
222476 AAAATTATTTATTTTT
1 AAAATTATTTATTTTT
*
222492 AAAA-TATAATATTTTT
1 AAAATTAT-TTATTTTT
222508 -AAATTATTT
1 AAAATTATTT
222517 TATAAAATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
15 7 0.21
16 27 0.79
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (16 bp):
AAAATTATTTATTTTT
Found at i:222495 original size:17 final size:16
Alignment explanation
Indices: 222458--222488 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
222448 TTTTATTATA
222458 AAAAAATTATTTATTG
1 AAAAAATTATTTATTG
222474 AAAAAATTATTTATT
1 AAAAAATTATTTATT
222489 TTTAAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (16 bp):
AAAAAATTATTTATTG
Found at i:222846 original size:2 final size:2
Alignment explanation
Indices: 222841--222873 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
222831 TTATACACAC
222841 AT 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 AT A
222874 GAGAGAGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:222878 original size:2 final size:2
Alignment explanation
Indices: 222873--222911 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
222863 ATATATATAT
222873 AG AG AG AG AG AG 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 AG AG AG AG AG AG A
222912 TTATGGTTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:223300 original size:2 final size:2
Alignment explanation
Indices: 223293--223327 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
223283 GAAGAAATTA
223293 AT AT 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 AT AT A
223328 AGTATGCTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:223547 original size:23 final size:22
Alignment explanation
Indices: 223512--223571 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 22
223502 TTTTTAAATT
*
223512 TAATCATAA-AAATATATTAATAT
1 TAAT-ATAATAAATATATT-ATAA
* *
223535 TAATATATTAAATAATATTTTAA
1 TAATATAATAAAT-ATATTATAA
223558 TAATATAATAAATA
1 TAATATAATAAATA
223572 ACAAAATTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
22 4 0.13
23 22 0.71
24 5 0.16
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
TAATATAATAAATATATTATAA
Found at i:223561 original size:11 final size:12
Alignment explanation
Indices: 223518--223572 Score: 60
Period size: 11 Copynumber: 4.6 Consensus size: 12
223508 AATTTAATCA
223518 TAAA-AATATAT
1 TAAATAATATAT
223529 TAATATTAATATAT
1 TAA-A-TAATATAT
223543 TAAATAATAT-T
1 TAAATAATATAT
* *
223554 TTAATAATATAA
1 TAAATAATATAT
223566 TAAATAA
1 TAAATAA
223573 CAAAATTAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
11 13 0.35
12 13 0.35
13 1 0.03
14 10 0.27
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TAAATAATATAT
Found at i:223562 original size:14 final size:14
Alignment explanation
Indices: 223517--223562 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
223507 AAATTTAATC
*
223517 ATAAAAATATATTA
1 ATAATAATATATTA
*
223531 ATATTAATATATT-
1 ATAATAATATATTA
*
223544 A-AATAATATTTTA
1 ATAATAATATATTA
223557 ATAATA
1 ATAATA
223563 TAATAAATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
12 9 0.35
13 2 0.08
14 15 0.58
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
ATAATAATATATTA
Found at i:224944 original size:16 final size:18
Alignment explanation
Indices: 224918--224955 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
224908 GTCGTCTCCA
224918 TTTGCATCTTC-ATTTTC
1 TTTGCATCTTCGATTTTC
*
224935 TTTG-ATCTTCGTTTTTC
1 TTTGCATCTTCGATTTTC
224952 TTTG
1 TTTG
224956 TCACTGTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.08, C:0.18, G:0.11, T:0.63
Consensus pattern (18 bp):
TTTGCATCTTCGATTTTC
Found at i:229805 original size:2 final size:2
Alignment explanation
Indices: 229798--229839 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
229788 GAAAACATAC
229798 AT AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT
229840 TCTTATCCAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:230255 original size:24 final size:25
Alignment explanation
Indices: 230228--230280 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
230218 AACTCACAAT
230228 TTTAAAAAAATTTT-AATTTTTTTA
1 TTTAAAAAAATTTTAAATTTTTTTA
****
230252 TTTAAATTTGTTTTAAATTTTTTTA
1 TTTAAAAAAATTTTAAATTTTTTTA
230277 TTTA
1 TTTA
230281 TATTTATTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 10 0.42
25 14 0.58
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (25 bp):
TTTAAAAAAATTTTAAATTTTTTTA
Found at i:230259 original size:14 final size:14
Alignment explanation
Indices: 230237--230298 Score: 51
Period size: 13 Copynumber: 4.6 Consensus size: 14
230227 TTTTAAAAAA
*
230237 ATTTTAATTTTTTT
1 ATTTAAATTTTTTT
*
230251 ATTTAAA--TTTGT
1 ATTTAAATTTTTTT
230263 -TTTAAATTTTTTT
1 ATTTAAATTTTTTT
* *
230276 ATTTATA-TTTATT
1 ATTTAAATTTTTTT
230289 ATTTATAATT
1 ATTTA-AATT
230299 AATAAAAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 9
0.71 0.12 0.17
Matches are distributed among these distances:
11 6 0.16
12 4 0.11
13 14 0.38
14 12 0.32
15 1 0.03
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (14 bp):
ATTTAAATTTTTTT
Found at i:230270 original size:25 final size:24
Alignment explanation
Indices: 230238--230285 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
230228 TTTAAAAAAA
230238 TTTTAATTTTTTTATTTAAATTTG
1 TTTTAATTTTTTTATTTAAATTTG
*
230262 TTTTAAATTTTTTTATTTATATTT
1 TTTT-AATTTTTTTATTTAAATTT
230286 ATTATTTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (24 bp):
TTTTAATTTTTTTATTTAAATTTG
Found at i:230344 original size:22 final size:20
Alignment explanation
Indices: 230318--230357 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
230308 TTAAAATAAT
230318 TATTTTTATATTAATATTTATA
1 TATTTTTA-ATTAA-ATTTATA
230340 TATTTTTAATTAAATTTA
1 TATTTTTAATTAAATTTA
230358 AATAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 5 0.28
22 8 0.44
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTTTTAATTAAATTTATA
Found at i:230366 original size:52 final size:50
Alignment explanation
Indices: 230268--230380 Score: 122
Period size: 51 Copynumber: 2.2 Consensus size: 50
230258 TTTGTTTTAA
* * *
230268 ATTTTTTTATTTATATTTATTATTTATAATTAATAAAAAATTAAAATAATT
1 ATTTTTATATTAATATTTATTATTTATAATTAATAAAAAATAAAAAT-ATT
* **
230319 ATTTTTATATTAATATTTATATATTTTTAATTAA-ATTTAAATAAAAATATT
1 ATTTTTATATTAATATTTAT-TATTTATAATTAATA-AAAAATAAAAATATT
*
230370 TTTTTTA-ATTA
1 ATTTTTATATTA
230381 TTAGATTTGA
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
50 4 0.08
51 28 0.53
52 21 0.40
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (50 bp):
ATTTTTATATTAATATTTATTATTTATAATTAATAAAAAATAAAAATATT
Found at i:230375 original size:51 final size:51
Alignment explanation
Indices: 230269--230380 Score: 126
Period size: 52 Copynumber: 2.3 Consensus size: 51
230259 TTGTTTTAAA
*
230269 TTTTTTTAT-TT-ATATTTATTATTTATAATTAATAAAAAATTAAAATAAT
1 TTTTTTTATATTAATATTTATTATTTATAATTAATAAAAAATAAAAATAAT
* * **
230318 TATTTTTATATTAATATTTATATATTTTTAATTAA-ATTTAAATAAAAAT-AT
1 TTTTTTTATATTAATATTTAT-TATTTATAATTAATA-AAAAATAAAAATAAT
230369 TTTTTTTA-ATTA
1 TTTTTTTATATTA
230381 TTAGATTTGA
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
49 8 0.15
50 6 0.11
51 18 0.34
52 21 0.40
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (51 bp):
TTTTTTTATATTAATATTTATTATTTATAATTAATAAAAAATAAAAATAAT
Found at i:231480 original size:15 final size:16
Alignment explanation
Indices: 231451--231484 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
231441 ATTTTGATCC
231451 TTTTAAATTTAAATTT
1 TTTTAAATTTAAATTT
231467 TTTTAAATTT-AATTT
1 TTTTAAATTTAAATTT
231482 TTT
1 TTT
231485 AAGTTTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTAAATTTAAATTT
Found at i:238479 original size:21 final size:21
Alignment explanation
Indices: 238455--238505 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
238445 GTATTTCAAT
238455 TTTTTTTAAGTTTGGATTTTA
1 TTTTTTTAAGTTTGGATTTTA
* * * *
238476 TTTTTTTGATTTTTGATTTTT
1 TTTTTTTAAGTTTGGATTTTA
238497 TTTATTTTA
1 TTT-TTTTA
238506 TGCTGACGTG
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.16, C:0.00, G:0.10, T:0.75
Consensus pattern (21 bp):
TTTTTTTAAGTTTGGATTTTA
Found at i:238483 original size:15 final size:16
Alignment explanation
Indices: 238471--238504 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
238461 TAAGTTTGGA
238471 TTTT-ATTTTTTTGAT
1 TTTTGATTTTTTTGAT
*
238486 TTTTGATTTTTTTTAT
1 TTTTGATTTTTTTGAT
238502 TTT
1 TTT
238505 ATGCTGACGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.82
Consensus pattern (16 bp):
TTTTGATTTTTTTGAT
Found at i:239477 original size:2 final size:2
Alignment explanation
Indices: 239464--239507 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
239454 ATCAAAACCC
*
239464 AT AT AC AT AT AT AT AT AT 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 AT AT AT AT AT AT
239506 AT
1 AT
239508 TGGTTACCAC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:244959 original size:30 final size:27
Alignment explanation
Indices: 244916--245002 Score: 88
Period size: 30 Copynumber: 3.1 Consensus size: 27
244906 TTTAATAATA
*
244916 AATTAATTTTATTTTTATATTTAATTTT
1 AATTAATTATATTTTTA-ATTTAATTTT
244944 GAACTTAATTATATTTATTAATTTTAA-TTT
1 -AA-TTAATTATATTT-TTAA-TTTAATTTT
*
244974 AATT-ATAATATTTTTAATATTAATTTT
1 AATTAATTATATTTTTAAT-TTAATTTT
245001 AA
1 AA
245003 AATAATAAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 12
0.78 0.03 0.18
Matches are distributed among these distances:
25 1 0.02
26 8 0.16
27 13 0.25
28 2 0.04
29 4 0.08
30 15 0.29
31 8 0.16
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (27 bp):
AATTAATTATATTTTTAATTTAATTTT
Found at i:245007 original size:26 final size:27
Alignment explanation
Indices: 244949--245009 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 27
244939 ATTTTGAACT
* *
244949 TAATTATATTTATTAATTTTAATTTAA
1 TAATAATATTTATTAATATTAATTTAA
*
244976 TTATAATATTT-TTAATATTAATTTTAA
1 TAATAATATTTATTAATATTAA-TTTAA
245003 -AATAATA
1 TAATAATA
245010 AAAAAATTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 15 0.52
27 14 0.48
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
TAATAATATTTATTAATATTAATTTAA
Found at i:246854 original size:18 final size:18
Alignment explanation
Indices: 246818--246853 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
246808 AAATATAATA
*
246818 TAAAAATAATTAAAATTT
1 TAAAAAAAATTAAAATTT
246836 TAAAAAAAATT-AAATTT
1 TAAAAAAAATTAAAATTT
246853 T
1 T
246854 TTTTAAATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAAAAAAATTAAAATTT
Found at i:246926 original size:17 final size:18
Alignment explanation
Indices: 246893--246976 Score: 61
Period size: 21 Copynumber: 4.7 Consensus size: 18
246883 AATAATATAA
246893 ATTAT-TAATTTATTAAAAT
1 ATTATATAA-TTA-TAAAAT
246912 -TTATATAATTATAAAAT
1 ATTATATAATTATAAAAT
246929 ATT-T-TAATTA-AAAAT
1 ATTATATAATTATAAAAT
* *
246944 ATAATATAATAAAATATAAAT
1 ATTATATAAT--TATA-AAAT
*
246965 ATAATATAATTA
1 ATTATATAATTA
246977 ATCTAATTTA
Statistics
Matches: 54, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
15 7 0.13
16 7 0.13
17 11 0.20
18 9 0.17
19 5 0.09
20 1 0.02
21 14 0.26
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTATATAATTATAAAAT
Found at i:246951 original size:5 final size:5
Alignment explanation
Indices: 246941--246983 Score: 52
Period size: 5 Copynumber: 8.6 Consensus size: 5
246931 TTTAATTAAA
* *
246941 AATAT AATAT AATAA AATAT AAATAT AATAT AAT-T AATCT AAT
1 AATAT AATAT AATAT AATAT -AATAT AATAT AATAT AATAT AAT
246984 TTAGTGGGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
4 4 0.12
5 25 0.74
6 5 0.15
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (5 bp):
AATAT
Found at i:246956 original size:16 final size:17
Alignment explanation
Indices: 246937--246970 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
246927 ATATTTTAAT
246937 TAAAAATAT-AATATAA
1 TAAAAATATAAATATAA
246953 T-AAAATATAAATATAA
1 TAAAAATATAAATATAA
246969 TA
1 TA
246971 TAATTAATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 3
0.84 0.00 0.16
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
TAAAAATATAAATATAA
Found at i:247147 original size:8 final size:8
Alignment explanation
Indices: 247134--247258 Score: 62
Period size: 8 Copynumber: 15.1 Consensus size: 8
247124 GTAATGTTAA
*
247134 ATATAATT
1 ATATAAAT
247142 ATATAAAT
1 ATATAAAT
247150 ATATAAAT
1 ATATAAAT
*
247158 ATTTTAAAAT
1 A-TAT-AAAT
*
247168 TTATATAAT
1 ATATA-AAT
247177 A-A-AAAT
1 ATATAAAT
*
247183 -TATTAAT
1 ATATAAAT
247190 ATATTAAAAT
1 ATA-T-AAAT
*
247200 TTATAAAT
1 ATATAAAT
*
247208 ATAAAAAT
1 ATATAAAT
**
247216 AT-TTTAT
1 ATATAAAT
247223 ATAT-AAT
1 ATATAAAT
247230 ATAATAAAAT
1 AT-AT-AAAT
247240 ATATAATAT
1 ATATAA-AT
247249 AATATAAAT
1 -ATATAAAT
247258 A
1 A
247259 AAAATATTAT
Statistics
Matches: 89, Mismatches: 14, Indels: 28
0.68 0.11 0.21
Matches are distributed among these distances:
6 4 0.04
7 12 0.13
8 38 0.43
9 15 0.17
10 20 0.22
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (8 bp):
ATATAAAT
Found at i:247183 original size:15 final size:16
Alignment explanation
Indices: 247163--247228 Score: 64
Period size: 17 Copynumber: 4.1 Consensus size: 16
247153 TAAATATTTT
247163 AAAATTTATATA-ATA
1 AAAATTTATATATATA
*
247178 AAAA-TTATTAATATATT
1 AAAATTTA-T-ATATATA
*
247195 AAAATTTATAAATATA
1 AAAATTTATATATATA
*
247211 AAAATATTTTATATATA
1 AAAAT-TTATATATATA
247228 A
1 A
247229 TATAATAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
14 3 0.07
15 5 0.12
16 13 0.32
17 17 0.41
18 3 0.07
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AAAATTTATATATATA
Found at i:247197 original size:32 final size:34
Alignment explanation
Indices: 247135--247217 Score: 107
Period size: 32 Copynumber: 2.5 Consensus size: 34
247125 TAATGTTAAA
* * *
247135 TATAATTATATAAATATATAAATATTTTAAAATT
1 TATAAATATAAAAATATATAAATATATTAAAATT
* *
247169 TATATA-ATAAAAAT-TATTAATATATTAAAATT
1 TATAAATATAAAAATATATAAATATATTAAAATT
247201 TATAAATATAAAAATAT
1 TATAAATATAAAAATAT
247218 TTTATATATA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
32 21 0.51
33 15 0.37
34 5 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (34 bp):
TATAAATATAAAAATATATAAATATATTAAAATT
Found at i:247210 original size:18 final size:18
Alignment explanation
Indices: 247146--247210 Score: 66
Period size: 18 Copynumber: 3.8 Consensus size: 18
247136 ATAATTATAT
* *
247146 AAATATATAAATATTTTA
1 AAATTTATAAATATATTA
247164 AAATTTAT--ATA-A-TA
1 AAATTTATAAATATATTA
* *
247178 AAAATTATTAATATATTA
1 AAATTTATAAATATATTA
247196 AAATTTATAAATATA
1 AAATTTATAAATATA
247211 AAAATATTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
14 9 0.24
16 6 0.16
17 1 0.03
18 22 0.58
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AAATTTATAAATATATTA
Found at i:247241 original size:17 final size:18
Alignment explanation
Indices: 247221--247258 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
247211 AAAATATTTT
247221 ATATATAATATAATA-AA
1 ATATATAATATAATATAA
247238 ATATATAATATAATATAA
1 ATATATAATATAATATAA
247256 ATA
1 ATA
247259 AAAATATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
ATATATAATATAATATAA
Found at i:247245 original size:12 final size:12
Alignment explanation
Indices: 247228--247265 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
247218 TTTATATATA
247228 ATATAATAAAAT
1 ATATAATAAAAT
*
247240 ATATAATATAAT
1 ATATAATAAAAT
247252 ATA-AATAAAA-
1 ATATAATAAAAT
247262 ATAT
1 ATAT
247266 TATTATATCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
10 3 0.13
11 6 0.26
12 14 0.61
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
ATATAATAAAAT
Found at i:247264 original size:17 final size:17
Alignment explanation
Indices: 247221--247265 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
247211 AAAATATTTT
*
247221 ATATATAATATAATAAA
1 ATATAAAATATAATAAA
*
247238 ATATATAATATAATATAA
1 ATATAAAATATAATA-AA
247256 ATA-AAAATAT
1 ATATAAAATAT
247266 TATTATATCT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 21 0.81
18 5 0.19
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
ATATAAAATATAATAAA
Found at i:248376 original size:19 final size:17
Alignment explanation
Indices: 248354--248395 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
248344 TAATGTGAAT
248354 ATTTATTTTATTATTTAAA
1 ATTTATTTTA-TA-TTAAA
*
248373 ATTTATTTTATATTAAT
1 ATTTATTTTATATTAAA
248390 ATTTAT
1 ATTTAT
248396 ATATTTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 10 0.45
18 2 0.09
19 10 0.45
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTTATTTTATATTAAA
Found at i:249382 original size:15 final size:16
Alignment explanation
Indices: 249350--249384 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
249340 TAATTTATGT
*
249350 AATTATTTTTATAAAA
1 AATTATATTTATAAAA
249366 AATTATATTTA-AAAA
1 AATTATATTTATAAAA
249381 AATT
1 AATT
249385 TAATATCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
AATTATATTTATAAAA
Found at i:250008 original size:24 final size:24
Alignment explanation
Indices: 249968--250036 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 24
249958 AAAATTTATT
*
249968 TTATTA-TTTATAATAATATTAAA
1 TTATTATTTTATATTAATATTAAA
*
249991 TTATTATTTTATATTAATATT-TA
1 TTATTATTTTATATTAATATTAAA
250014 -TA-TATTTTATAATTAAT-TTAAA
1 TTATTATTTTAT-ATTAATATTAAA
250036 T
1 T
250037 AATAAAATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
21 10 0.26
22 9 0.23
23 7 0.18
24 13 0.33
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
TTATTATTTTATATTAATATTAAA
Found at i:250845 original size:20 final size:20
Alignment explanation
Indices: 250820--250859 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
250810 TATATCTCTG
250820 TTAATTCAATT-TAAATTAAA
1 TTAATT-AATTATAAATTAAA
*
250840 TTAATTTATTATAAATTAAA
1 TTAATTAATTATAAATTAAA
250860 ATTTTTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (20 bp):
TTAATTAATTATAAATTAAA
Found at i:251970 original size:22 final size:22
Alignment explanation
Indices: 251945--251991 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 22
251935 ATGATATATT
251945 TAAAA-TTATAAAAAT-TAAATAA
1 TAAAAGTT-TAAAAATATAAA-AA
251967 TAAAAGTTTAAAAATATAAAAA
1 TAAAAGTTTAAAAATATAAAAA
251989 TAA
1 TAA
251992 TTAAAAGGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (22 bp):
TAAAAGTTTAAAAATATAAAAA
Found at i:254044 original size:18 final size:18
Alignment explanation
Indices: 254021--254070 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 18
254011 ATAATGTCTA
*
254021 TAAATATTATTAATTAAT
1 TAAATAATATTAATTAAT
* *
254039 TAAATAATATTATTTTAT
1 TAAATAATATTAATTAAT
254057 TAAA-AATA-TAATTA
1 TAAATAATATTAATTA
254071 TTTATATTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
16 4 0.15
17 4 0.15
18 19 0.70
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TAAATAATATTAATTAAT
Found at i:254069 original size:30 final size:28
Alignment explanation
Indices: 254035--254109 Score: 73
Period size: 30 Copynumber: 2.6 Consensus size: 28
254025 TATTATTAAT
254035 TAATTAAATAATATTATTTTATTAAAAATA
1 TAATTAAATAATATTATTTTA--AAAAATA
* *
254065 TAATT-ATTTATATTTATTTTAAAAAATA
1 TAATTAAATAATA-TTATTTTAAAAAATA
*
254093 TGATATAAATAAT-TTAT
1 TAAT-TAAATAATATTAT
254110 ATATTATCAA
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
28 14 0.38
29 6 0.16
30 17 0.46
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (28 bp):
TAATTAAATAATATTATTTTAAAAAATA
Found at i:254107 original size:28 final size:28
Alignment explanation
Indices: 254035--254109 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 28
254025 TATTATTAAT
254035 TAATTAAATAATATTATTTTATTAAAAATA
1 TAATTAAATAAT-TTATTTTA-TAAAAATA
**
254065 TAATTATTTATATTTATTTTA-AAAAATA
1 TAATTAAATA-ATTTATTTTATAAAAATA
*
254093 TGATATAAATAATTTAT
1 TAAT-TAAATAATTTAT
254110 ATATTATCAA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
28 16 0.42
29 4 0.11
30 16 0.42
31 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (28 bp):
TAATTAAATAATTTATTTTATAAAAATA
Found at i:255591 original size:11 final size:11
Alignment explanation
Indices: 255576--255637 Score: 60
Period size: 10 Copynumber: 5.8 Consensus size: 11
255566 ATTTAAAATA
255576 TATATTTATAAT
1 TATATTTAT-AT
*
255588 ATATAATT-T-T
1 -TATATTTATAT
255598 TATA-TTATAT
1 TATATTTATAT
255608 TATATTTATAT
1 TATATTTATAT
255619 TATATTT-TAT
1 TATATTTATAT
*
255629 TAAATTTAT
1 TATATTTAT
255638 TTTTAAACTT
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
8 2 0.05
9 5 0.12
10 15 0.35
11 14 0.33
12 1 0.02
13 6 0.14
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TATATTTATAT
Found at i:255605 original size:5 final size:5
Alignment explanation
Indices: 255597--255630 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
255587 TATATAATTT
*
255597 TTATA TTATA TTATA TTTATA TTATA TTTTA TTA
1 TTATA TTATA TTATA -TTATA TTATA TTATA TTA
255631 AATTTATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (5 bp):
TTATA
Found at i:255621 original size:21 final size:21
Alignment explanation
Indices: 255597--255637 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
255587 TATATAATTT
*
255597 TTATATTATATTATATTTATA
1 TTATATTATATTAAATTTATA
*
255618 TTATATTTTATTAAATTTAT
1 TTATATTATATTAAATTTAT
255638 TTTTAAACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TTATATTATATTAAATTTATA
Found at i:255624 original size:16 final size:16
Alignment explanation
Indices: 255576--255629 Score: 72
Period size: 16 Copynumber: 3.4 Consensus size: 16
255566 ATTTAAAATA
*
255576 TATATTTATAATATAT
1 TATATTTATATTATAT
* *
255592 AATTTTTATATTATAT
1 TATATTTATATTATAT
255608 TATATTTATATTATAT
1 TATATTTATATTATAT
*
255624 TTTATT
1 TATATT
255630 AAATTTATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TATATTTATATTATAT
Found at i:255851 original size:20 final size:20
Alignment explanation
Indices: 255808--255894 Score: 56
Period size: 20 Copynumber: 4.3 Consensus size: 20
255798 TATTTTATAA
*
255808 TTAAATTA-AAAATATT--T
1 TTAAATTATTAAATATTAAT
*
255825 TTTAATTATTAAATATTAAT
1 TTAAATTATTAAATATTAAT
*
255845 TTAAATTAATATAA-ATTAAT
1 TTAAATTATTA-AATATTAAT
** *
255865 AAAAAATATATTTAATATTTAAT
1 -TTAAAT-TATTAAATA-TTAAT
255888 TTAAATT
1 TTAAATT
255895 TATCAAATTA
Statistics
Matches: 52, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
17 7 0.13
18 7 0.13
20 16 0.31
21 9 0.17
22 8 0.15
23 5 0.10
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TTAAATTATTAAATATTAAT
Found at i:257025 original size:12 final size:13
Alignment explanation
Indices: 256992--257023 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
256982 TAATTTTAAA
256992 AAATTTTAAAATT
1 AAATTTTAAAATT
*
257005 AAATTTTAAATTT
1 AAATTTTAAAATT
257018 AAATTT
1 AAATTT
257024 AACTTAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
AAATTTTAAAATT
Found at i:257432 original size:10 final size:10
Alignment explanation
Indices: 257407--257470 Score: 58
Period size: 10 Copynumber: 6.2 Consensus size: 10
257397 AATTAGAATC
257407 TTAAATTTTAT
1 TTAAA-TTTAT
*
257418 CTAAATTTAT
1 TTAAATTTAT
257428 TTAAATTTAT
1 TTAAATTTAT
* *
257438 ATATTATTTGAT
1 TTA-AATTT-AT
*
257450 TTAAAATTAT
1 TTAAATTTAT
257460 TTAAA-TTAT
1 TTAAATTTAT
257469 TT
1 TT
257471 TTTATAAAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
9 6 0.14
10 23 0.52
11 11 0.25
12 4 0.09
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (10 bp):
TTAAATTTAT
Found at i:264763 original size:19 final size:19
Alignment explanation
Indices: 264739--264782 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
264729 AAATAATTAA
264739 TTAAAAAT-AGTTATAATTT
1 TTAAAAATAAGTTATAA-TT
* *
264758 TTAAAAGTAATTTATAATT
1 TTAAAAATAAGTTATAATT
264777 TTAAAA
1 TTAAAA
264783 TGTTAATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (19 bp):
TTAAAAATAAGTTATAATT
Found at i:266953 original size:16 final size:16
Alignment explanation
Indices: 266932--266963 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
266922 AGGAAAAATA
266932 CAATTAATGTATGATT
1 CAATTAATGTATGATT
*
266948 CAATTAATGTGTGATT
1 CAATTAATGTATGATT
266964 TTGTTTAAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.06, G:0.16, T:0.44
Consensus pattern (16 bp):
CAATTAATGTATGATT
Found at i:267244 original size:335 final size:336
Alignment explanation
Indices: 266633--267278 Score: 1240
Period size: 335 Copynumber: 1.9 Consensus size: 336
266623 AGAATTCACA
266633 TAAGCATATTCTCAAAGCATAAAATGGATGCAAAGGTGGGGGACATTGTATGATCCTTTGTCGTT
1 TAAGCATATTCTCAAAGCATAAAATGGATGCAAAGGTGGGGGACATTGTATGATCCTTTGTCGTT
266698 TGCAATTCTTGACTATGCTTATGTTGACAACACAATGGCCTATGAAATCTCCCCCCTTACCATAT
66 TGCAATTCTTGACTATGCTTATGTTGACAACACAATGGCCTATGAAATCTCCCCCCTTACCATAT
266763 GGATATTGAGGCATACAAACCACAATGGTCATGCCTTTGTTCTATCCTTGTTATTGATAGGAATT
131 GGATATTGAGGCATACAAACCACAATGGTCATGCCTTTGTTCTATCCTTGTTATTGATAGGAATT
*
266828 AATTTAATATTTAATTCTATGATTAGTGTCTCTATATTTTTTTGTAAATAGATTCAAATCTTTTT
196 AATTAAATATTTAATTCTATGATTAGTGTCTCTATATTTTTTTGTAAATAGATTCAAATCTTTTT
266893 GTTTAATACATTAGTTAAGGTGATTTTTTAGGAAAAATACAATTAATGTATGATTCAATTAATGT
261 GTTTAATACATTAGTTAAGGTGATTTTTTAGGAAAAATACAATTAATGTATGATTCAATTAATGT
266958 GTGATTTTGTT
326 GTGATTTTGTT
266969 TAAGCATATTCTCAAAGCATAAAATGGATGCAAAGGTGGGGGACATTGTATGATCCTTTGTCGTT
1 TAAGCATATTCTCAAAGCATAAAATGGATGCAAAGGTGGGGGACATTGTATGATCCTTTGTCGTT
*
267034 TGCAATTCTTGACTATGCTTGTGTTGACAACACAATGGCCTATGAAATCT-CCCCCTTACCATAT
66 TGCAATTCTTGACTATGCTTATGTTGACAACACAATGGCCTATGAAATCTCCCCCCTTACCATAT
*
267098 GGATATTGAGGCATACAAACCACATTGGTCATGCCTTTGTTCTATCCTTGTTATTGATAGGAATT
131 GGATATTGAGGCATACAAACCACAATGGTCATGCCTTTGTTCTATCCTTGTTATTGATAGGAATT
267163 AATTAAATATTTAATTCTATGATTAGTGTCTCTATATTTTTTTGTAAATAGATTCAAATCTTTTT
196 AATTAAATATTTAATTCTATGATTAGTGTCTCTATATTTTTTTGTAAATAGATTCAAATCTTTTT
* *
267228 GTTTAATACATTAGTTAATGTGATTTTTTAGGAAAAATCCAATTAATGTAT
261 GTTTAATACATTAGTTAAGGTGATTTTTTAGGAAAAATACAATTAATGTAT
267279 TATTTTTTTT
Statistics
Matches: 305, Mismatches: 5, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
335 191 0.63
336 114 0.37
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.39
Consensus pattern (336 bp):
TAAGCATATTCTCAAAGCATAAAATGGATGCAAAGGTGGGGGACATTGTATGATCCTTTGTCGTT
TGCAATTCTTGACTATGCTTATGTTGACAACACAATGGCCTATGAAATCTCCCCCCTTACCATAT
GGATATTGAGGCATACAAACCACAATGGTCATGCCTTTGTTCTATCCTTGTTATTGATAGGAATT
AATTAAATATTTAATTCTATGATTAGTGTCTCTATATTTTTTTGTAAATAGATTCAAATCTTTTT
GTTTAATACATTAGTTAAGGTGATTTTTTAGGAAAAATACAATTAATGTATGATTCAATTAATGT
GTGATTTTGTT
Found at i:267464 original size:21 final size:22
Alignment explanation
Indices: 267422--267482 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 22
267412 TTTTTCAATT
267422 TAAATTATTATTTAATTCATTTAA
1 TAAATTATTATTTAA-T-ATTTAA
*
267446 TAAATTTTTATTTAA-ATTTAA
1 TAAATTATTATTTAATATTTAA
267467 TTAAAATTATATATTT
1 -T-AAATTAT-TATTT
267483 TTTTAATATT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
21 6 0.19
22 1 0.03
23 6 0.19
24 19 0.59
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
TAAATTATTATTTAATATTTAA
Found at i:268444 original size:16 final size:16
Alignment explanation
Indices: 268401--268445 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 16
268391 AAATAAATTT
*
268401 TAATATTTATCTTTTA
1 TAATATTTATTTTTTA
*
268417 TCATTATTTATTTTTTA
1 T-AATATTTATTTTTTA
*
268434 TAATATATATTT
1 TAATATTTATTT
268446 AAAAATAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
16 10 0.42
17 14 0.58
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.64
Consensus pattern (16 bp):
TAATATTTATTTTTTA
Found at i:268698 original size:24 final size:24
Alignment explanation
Indices: 268671--268716 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
268661 TATCTTTATT
268671 AATAAATTCAA-AATAATATATAAA
1 AATAAATT-AATAATAATATATAAA
* *
268695 AATACATTAATATTAATATATA
1 AATAAATTAATAATAATATATA
268717 TCAACTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 2 0.11
24 17 0.89
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (24 bp):
AATAAATTAATAATAATATATAAA
Found at i:269763 original size:19 final size:20
Alignment explanation
Indices: 269700--269768 Score: 54
Period size: 19 Copynumber: 3.5 Consensus size: 20
269690 TAATATAAAT
* *
269700 AATAATATATATTATAATTTAA
1 AATAATTTATA-TA-AATATAA
* **
269722 ATTAATTT-TATAAATATTT
1 AATAATTTATATAAATATAA
269741 AATAATTTATA-AAATATAA
1 AATAATTTATATAAATATAA
269760 AAT-ATTTAT
1 AATAATTTAT
269769 TTACATTAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
18 6 0.16
19 20 0.53
20 4 0.11
21 2 0.05
22 6 0.16
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
AATAATTTATATAAATATAA
Found at i:269929 original size:20 final size:19
Alignment explanation
Indices: 269906--269943 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
269896 AAGAAGATAA
269906 AATGAAAAAAAAGAAAATTT
1 AATGAAAAAAAA-AAAATTT
*
269926 AATGAAACAAAAAAAATT
1 AATGAAAAAAAAAAAATT
269944 AATTTTTAGA
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:0.71, C:0.03, G:0.08, T:0.18
Consensus pattern (19 bp):
AATGAAAAAAAAAAAATTT
Found at i:270979 original size:25 final size:25
Alignment explanation
Indices: 270942--270993 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
270932 AATAAAAAAT
*
270942 ATTTTTATTTAAAT-TTAATTATAAA
1 ATTTTTATATAAATATTAA-TATAAA
270967 ATTTTTATATAAATATTAATATAAA
1 ATTTTTATATAAATATTAATATAAA
270992 AT
1 AT
270994 AATATTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 21 0.84
26 4 0.16
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
ATTTTTATATAAATATTAATATAAA
Found at i:271415 original size:17 final size:17
Alignment explanation
Indices: 271393--271428 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
271383 GCTTTGACAA
271393 GGGATGTAAGAAAATTT
1 GGGATGTAAGAAAATTT
271410 GGGATGTAAGAAAATTT
1 GGGATGTAAGAAAATTT
271427 GG
1 GG
271429 ATAGTAGCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.33, T:0.28
Consensus pattern (17 bp):
GGGATGTAAGAAAATTT
Found at i:290206 original size:36 final size:36
Alignment explanation
Indices: 290023--290196 Score: 242
Period size: 36 Copynumber: 4.8 Consensus size: 36
290013 GAAGTTTCTT
* *
290023 GTGATTTTTGTTGGGCCCAAGAACCATT-ATTTGTAG
1 GTGATTTTTGTTGGTCCCAAGAACTATTCA-TTGTAG
* *
290059 GGGAATTTTGTTGGTCCCAAGAACTATTCATTGTAG
1 GTGATTTTTGTTGGTCCCAAGAACTATTCATTGTAG
* *
290095 GTGATTTTTGTTGGTCCCCAGAACTATTCGTTGTAG
1 GTGATTTTTGTTGGTCCCAAGAACTATTCATTGTAG
** *
290131 GTGATTTTTGTTGGTCCCAAGAACTATTTGTTGTTG
1 GTGATTTTTGTTGGTCCCAAGAACTATTCATTGTAG
*
290167 GTGATTTTTGTAGGTCCCAAGAACTATTCA
1 GTGATTTTTGTTGGTCCCAAGAACTATTCA
290197 CTACAGGTGA
Statistics
Matches: 123, Mismatches: 14, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
36 122 0.99
37 1 0.01
ACGTcount: A:0.21, C:0.14, G:0.24, T:0.40
Consensus pattern (36 bp):
GTGATTTTTGTTGGTCCCAAGAACTATTCATTGTAG
Found at i:300789 original size:2 final size:2
Alignment explanation
Indices: 300782--300814 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
300772 CACATGTGAA
300782 AG AG AG 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 AG AG AG A
300815 ACTTGTTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:302389 original size:2 final size:2
Alignment explanation
Indices: 302382--302416 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
302372 AGCAAAACAA
302382 AG AG AG AG 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 AG AG AG AG A
302417 ATTCAATCCG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:303688 original size:16 final size:16
Alignment explanation
Indices: 303667--303700 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
303657 GAGGAAGATA
303667 GACAAAGAAA-ATGCAT
1 GACAAA-AAACATGCAT
303683 GACAAAAAACATGCAT
1 GACAAAAAACATGCAT
303699 GA
1 GA
303701 TTTACAAGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.18
16 14 0.82
ACGTcount: A:0.56, C:0.15, G:0.18, T:0.12
Consensus pattern (16 bp):
GACAAAAAACATGCAT
Found at i:305510 original size:17 final size:17
Alignment explanation
Indices: 305471--305512 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
305461 AATTAAAAAT
*
305471 AAAAATAATTTTATAGTT
1 AAAAAT-ATTTTATAGTA
305489 AAAAATATTTTAT-GTA
1 AAAAATATTTTATAGTA
305505 AGAAAATA
1 A-AAAATA
305513 AAAGAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 3 0.14
17 13 0.59
18 6 0.27
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (17 bp):
AAAAATATTTTATAGTA
Found at i:305858 original size:32 final size:33
Alignment explanation
Indices: 305813--305892 Score: 101
Period size: 32 Copynumber: 2.5 Consensus size: 33
305803 ATTTACTCAT
*
305813 TATATATAT-TTATATAAATTTTAATATATTAA
1 TATATCTATATTATATAAATTTTAATATATTAA
* * *
305845 TA-ATGTATATTATATAAATTTTGATATATTCA
1 TATATCTATATTATATAAATTTTAATATATTAA
*
305877 TATATCTATACTATAT
1 TATATCTATATTATAT
305893 TTATTTATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
31 5 0.12
32 25 0.61
33 11 0.27
ACGTcount: A:0.42, C:0.04, G:0.03, T:0.51
Consensus pattern (33 bp):
TATATCTATATTATATAAATTTTAATATATTAA
Found at i:306412 original size:10 final size:10
Alignment explanation
Indices: 306370--306418 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
306360 AAATTGGTTA
306370 AAAAAT-TA-
1 AAAAATATAT
306378 AAAATATATAT
1 AAAA-ATATAT
*
306389 AAAAAGAGTA-
1 AAAAATA-TAT
306399 AAAAATATAT
1 AAAAATATAT
306409 AAAAATATAT
1 AAAAATATAT
306419 TTTATATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
8 4 0.12
9 4 0.12
10 20 0.59
11 6 0.18
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (10 bp):
AAAAATATAT
Found at i:308747 original size:26 final size:26
Alignment explanation
Indices: 308700--308750 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
308690 TAATAAATTG
*
308700 ATCTACATATTAAATAGGAATATACA
1 ATCTACATATTAAATAGAAATATACA
*
308726 ATCTACATATTATATTA-AAATATAC
1 ATCTACATATTA-AATAGAAATATAC
308751 GAGCATGTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 19 0.86
27 3 0.14
ACGTcount: A:0.49, C:0.12, G:0.04, T:0.35
Consensus pattern (26 bp):
ATCTACATATTAAATAGAAATATACA
Done.