Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold223
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: 4172444
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 17292 characters in sequence are not A, C, G, or T
File 2 of 26
Found at i:177330 original size:15 final size:14
Alignment explanation
Indices: 177283--177331 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 14
177273 ATTTATATAC
*
177283 AAATATTTAAAAGAT
1 AAATTTTTAAAA-AT
*
177298 AAATTATTTAAAGAT
1 AAATT-TTTAAAAAT
177313 AAATTTTTAAAAATT
1 AAATTTTTAAAAA-T
177328 AAAT
1 AAAT
177332 AAATAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 7 0.24
15 16 0.55
16 6 0.21
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (14 bp):
AAATTTTTAAAAAT
Found at i:177631 original size:24 final size:24
Alignment explanation
Indices: 177599--177644 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
177589 TATTTAGTTT
177599 TTCATTAAATGTGGTTGATTATTG
1 TTCATTAAATGTGGTTGATTATTG
177623 TTCATTAAATGTGGTTGATTAT
1 TTCATTAAATGTGGTTGATTAT
177645 ACTAGCTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.26, C:0.04, G:0.20, T:0.50
Consensus pattern (24 bp):
TTCATTAAATGTGGTTGATTATTG
Found at i:180144 original size:23 final size:23
Alignment explanation
Indices: 180114--180159 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
180104 AGTCTTCTGT
180114 TTTCCACGAAGTGTGGTGACTCA
1 TTTCCACGAAGTGTGGTGACTCA
180137 TTTCCACGAAGTGTGGTGACTCA
1 TTTCCACGAAGTGTGGTGACTCA
180160 CTCACCTATG
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:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (23 bp):
TTTCCACGAAGTGTGGTGACTCA
Found at i:184133 original size:2 final size:2
Alignment explanation
Indices: 184126--184158 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
184116 GAATCTACTT
184126 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
184159 TTTACAAAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:185222 original size:2 final size:2
Alignment explanation
Indices: 185205--185256 Score: 70
Period size: 2 Copynumber: 25.0 Consensus size: 2
185195 CATTCAACTC
185205 TA TA -A TA TA CTA TA TA TA TA TA TA TA TA TA TA TA TCA TA TA TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA
185248 TCA TA TA TA
1 T-A TA TA TA
185257 ACTAGTAATC
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
1 1 0.02
2 39 0.85
3 6 0.13
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:187769 original size:20 final size:20
Alignment explanation
Indices: 187744--187781 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
187734 TTGTAATTAA
*
187744 TTAAAATGATAAAAATATAT
1 TTAAAATAATAAAAATATAT
187764 TTAAAATAATAAAAATAT
1 TTAAAATAATAAAAATAT
187782 TTTGAAAGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (20 bp):
TTAAAATAATAAAAATATAT
Found at i:188637 original size:2 final size:2
Alignment explanation
Indices: 188632--188656 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
188622 ATGTGTGTGA
188632 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 A
188657 AAGGTACTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:189213 original size:2 final size:2
Alignment explanation
Indices: 189206--189239 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
189196 ACTGAGAACG
189206 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
189240 TTGCGTGTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:189759 original size:2 final size:2
Alignment explanation
Indices: 189752--189788 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
189742 TCCAACACTA
*
189752 AT AT AT AT AT AT AG 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 AT A
189789 AAAGACCGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:195541 original size:129 final size:129
Alignment explanation
Indices: 195379--195643 Score: 512
Period size: 129 Copynumber: 2.1 Consensus size: 129
195369 ATGCTTTATA
*
195379 ATAACTTCATAAGTTGCATGCTGAAACAAAGCATCTAAAAGCAATATAGATGAACTCAATCAAAA
1 ATAATTTCATAAGTTGCATGCTGAAACAAAGCATCTAAAAGCAATATAGATGAACTCAATCAAAA
195444 GAAAAGCTCAAGAGATCATATGAAATACTTCCAGTCAGGAAAAAGCATCTAGATGGAACAAGTT
66 GAAAAGCTCAAGAGATCATATGAAATACTTCCAGTCAGGAAAAAGCATCTAGATGGAACAAGTT
195508 ATAATTTCATAAGTTGCATGCTGAAACAAAGCATCTAAAAGCAATATAGATGAACTCAATCAAAA
1 ATAATTTCATAAGTTGCATGCTGAAACAAAGCATCTAAAAGCAATATAGATGAACTCAATCAAAA
*
195573 GAAACGCTCAAGAGATCATATGAAATACTTCCAGTCAGGAAAAAGCATCTAGATGGAACAAGTT
66 GAAAAGCTCAAGAGATCATATGAAATACTTCCAGTCAGGAAAAAGCATCTAGATGGAACAAGTT
195637 ATAATTT
1 ATAATTT
195644 AGATAATCTA
Statistics
Matches: 134, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
129 134 1.00
ACGTcount: A:0.45, C:0.16, G:0.16, T:0.23
Consensus pattern (129 bp):
ATAATTTCATAAGTTGCATGCTGAAACAAAGCATCTAAAAGCAATATAGATGAACTCAATCAAAA
GAAAAGCTCAAGAGATCATATGAAATACTTCCAGTCAGGAAAAAGCATCTAGATGGAACAAGTT
Found at i:197177 original size:42 final size:42
Alignment explanation
Indices: 197126--197211 Score: 145
Period size: 42 Copynumber: 2.0 Consensus size: 42
197116 CCACCGCCAA
197126 CTCTGCCACCACGGTCTCCTCCTTGATAGCCTCCACCACCTC
1 CTCTGCCACCACGGTCTCCTCCTTGATAGCCTCCACCACCTC
* * *
197168 CTCTTCCACCACGGTCTCCTCCTTGATAGCCTGCACCGCCTC
1 CTCTGCCACCACGGTCTCCTCCTTGATAGCCTCCACCACCTC
197210 CT
1 CT
197212 GCATAATCCA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.13, C:0.49, G:0.13, T:0.26
Consensus pattern (42 bp):
CTCTGCCACCACGGTCTCCTCCTTGATAGCCTCCACCACCTC
Found at i:199539 original size:2 final size:2
Alignment explanation
Indices: 199532--199561 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
199522 CTGCTTAGCC
*
199532 AT AT AT AT AT GT 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
199562 CTTCTGAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:199918 original size:58 final size:59
Alignment explanation
Indices: 199803--199918 Score: 162
Period size: 58 Copynumber: 2.0 Consensus size: 59
199793 ATATATATAT
* * * *
199803 ATATAAAGAGTGGTGGGTCACAAATTTTGTGTACATTAGAAATGTTCCAACAGTACTAGC
1 ATATAAAGAGCGGTCGGTCACAAA-TTTGTGTACATTAAAAATGTTCCAACAATACTAGC
* *
199863 ATATAAAGAGCGGTCGGTCACAAA-TTGTGTTCATTAAAAATGTTCCAATAATACTA
1 ATATAAAGAGCGGTCGGTCACAAATTTGTGTACATTAAAAATGTTCCAACAATACTA
199919 ATATTTGTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
58 28 0.56
60 22 0.44
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (59 bp):
ATATAAAGAGCGGTCGGTCACAAATTTGTGTACATTAAAAATGTTCCAACAATACTAGC
Found at i:204948 original size:2 final size:2
Alignment explanation
Indices: 204941--204977 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
204931 GAGAACCGCC
*
204941 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
204978 ACTCATAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:206713 original size:25 final size:24
Alignment explanation
Indices: 206672--206781 Score: 84
Period size: 25 Copynumber: 4.5 Consensus size: 24
206662 AATATAAACA
*
206672 TAAAA-TTAAAAATATAAATATAT
1 TAAAATTTATAAATATAAATATAT
206695 TAAAATTTATATAATATAAAT-TAT
1 TAAAATTTATA-AATATAAATATAT
* *
206719 TAATAATTTA-AAATATTATATAAAT
1 TAA-AATTTATAAATA-TAAATATAT
*
206744 ATAATATTT-TAAATATAATAAATATAT
1 -TAAAATTTAT-AA-AT-ATAAATATAT
*
206771 AAAAATTTATA
1 TAAAATTTATA
206782 CAAACAACGA
Statistics
Matches: 68, Mismatches: 8, Indels: 19
0.72 0.08 0.20
Matches are distributed among these distances:
23 9 0.13
24 15 0.22
25 21 0.31
26 12 0.18
27 10 0.15
28 1 0.01
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
TAAAATTTATAAATATAAATATAT
Found at i:206714 original size:16 final size:17
Alignment explanation
Indices: 206695--206761 Score: 70
Period size: 16 Copynumber: 4.2 Consensus size: 17
206685 ATAAATATAT
206695 TAAAAT-TTATATAATA
1 TAAAATATTATATAATA
* *
206711 TAAATTATTA-ATAATT
1 TAAAATATTATATAATA
206727 TAAAATATTATATAA-A
1 TAAAATATTATATAATA
* *
206743 TATAATATTTTA-AATA
1 TAAAATATTATATAATA
206759 TAA
1 TAA
206762 TAAATATATA
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
15 2 0.05
16 32 0.78
17 7 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TAAAATATTATATAATA
Found at i:208873 original size:3 final size:3
Alignment explanation
Indices: 208822--208854 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
208812 AGAAAAGAAA
208822 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
208855 GTGAGTAGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:210997 original size:6 final size:6
Alignment explanation
Indices: 210977--211010 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
210967 AATGTGAAGT
*
210977 TCCCAA T-CTAA TCCCAA TCCCAA TCCCAA TCCCA
1 TCCCAA TCCCAA TCCCAA TCCCAA TCCCAA TCCCA
211011 CTCGTTTAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 4 0.16
6 21 0.84
ACGTcount: A:0.32, C:0.47, G:0.00, T:0.21
Consensus pattern (6 bp):
TCCCAA
Found at i:212136 original size:2 final size:2
Alignment explanation
Indices: 212125--212153 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
212115 TCTAAAGAAA
212125 AG AG -G AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
212154 CCCATACTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
AG
Found at i:212988 original size:2 final size:2
Alignment explanation
Indices: 212981--213017 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
212971 GTCAATCATA
212981 AT 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 AT A
213018 ACTAAACTCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:214055 original size:2 final size:2
Alignment explanation
Indices: 214048--214074 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
214038 CCTTAATGTG
214048 CA CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA C
214075 TATTTTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:224965 original size:2 final size:2
Alignment explanation
Indices: 224958--224995 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
224948 CACTGCTTAC
224958 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
224996 GAGAGAGAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:225000 original size:2 final size:2
Alignment explanation
Indices: 224995--225022 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
224985 ATATATATAT
224995 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
225023 TAACTGTGGC
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:229402 original size:23 final size:24
Alignment explanation
Indices: 229348--229404 Score: 91
Period size: 23 Copynumber: 2.5 Consensus size: 24
229338 TGAATTTGCA
229348 GGATGATGATACAAACTACCACAT
1 GGATGATGATACAAACTACCACAT
*
229372 -GATGATGATACAAACTACCACGT
1 GGATGATGATACAAACTACCACAT
229395 GGAT-ATGATA
1 GGATGATGATA
229405 GCTGGGCTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
23 28 0.90
24 3 0.10
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.23
Consensus pattern (24 bp):
GGATGATGATACAAACTACCACAT
Found at i:230113 original size:34 final size:35
Alignment explanation
Indices: 230069--230143 Score: 100
Period size: 34 Copynumber: 2.2 Consensus size: 35
230059 GTTCAACCTA
*
230069 ACTTC-GGCTTCCAACATGATAATCTCACCCAATT
1 ACTTCGGGCTTCCAACAAGATAATCTCACCCAATT
* * *
230103 A-TTCGGGCTTCCAATAAGATATTCTCCCCCAATT
1 ACTTCGGGCTTCCAACAAGATAATCTCACCCAATT
230137 ACTTCGG
1 ACTTCGG
230144 TTTCGCTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
33 3 0.09
34 27 0.77
35 5 0.14
ACGTcount: A:0.27, C:0.31, G:0.12, T:0.31
Consensus pattern (35 bp):
ACTTCGGGCTTCCAACAAGATAATCTCACCCAATT
Found at i:232055 original size:34 final size:34
Alignment explanation
Indices: 232007--232073 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
231997 GATTCTAACA
*
232007 TTTCGTAAATTTTGGGTTACAA-TTATTAGGCACT
1 TTTCCTAAATTTTGGGTTACAACTT-TTAGGCACT
232041 TTTCCTAAATTTTGGGTTACAACTTTTAGGCAC
1 TTTCCTAAATTTTGGGTTACAACTTTTAGGCAC
232074 CGAAGCGAGC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 29 0.94
35 2 0.06
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (34 bp):
TTTCCTAAATTTTGGGTTACAACTTTTAGGCACT
Found at i:241355 original size:15 final size:15
Alignment explanation
Indices: 241331--241361 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
241321 AAAGGCCATT
241331 TGTTGCGTATGTGAA
1 TGTTGCGTATGTGAA
*
241346 TGTTGTGTATGTGAA
1 TGTTGCGTATGTGAA
241361 T
1 T
241362 AGTTTGGTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.03, G:0.32, T:0.45
Consensus pattern (15 bp):
TGTTGCGTATGTGAA
Found at i:241448 original size:1 final size:1
Alignment explanation
Indices: 241442--241466 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
241432 CAGTTGCCGC
241442 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
241467 CCCAAGCCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:242341 original size:50 final size:50
Alignment explanation
Indices: 242282--242551 Score: 224
Period size: 50 Copynumber: 5.4 Consensus size: 50
242272 AGTGTAAAAA
* * ** *
242282 AAGTGATCGTAATTGTTGATTATTTTTTATTAATCTTTGATAATCGAGAG
1 AAGTGATCGTAATTGTTGACTATTTTTCACAAATCTTTGACAATCGAGAG
* * * *
242332 AAGTGATCGTAATTGTTGATTACTTTTCACAAACCTTTGACAATCAAGAG
1 AAGTGATCGTAATTGTTGACTATTTTTCACAAATCTTTGACAATCGAGAG
* ** * *
242382 -AGATGACCGTAATTGTTGACTATTCCTCACCAATCTTTGACAACCGAGAG
1 AAG-TGATCGTAATTGTTGACTATTTTTCACAAATCTTTGACAATCGAGAG
* * * ** * * * *
242432 AGGTGATCATAATTATTGACTATTCCTCACCAACCCTTGACAATTGAGAG
1 AAGTGATCGTAATTGTTGACTATTTTTCACAAATCTTTGACAATCGAGAG
* * * *
242482 -AGTGGTCGTAATTATTGACTATTTTTCACCAA-CTTTTGACAATAGAGA-
1 AAGTGATCGTAATTGTTGACTATTTTTCACAAATC-TTTGACAATCGAGAG
* *
242530 AATGTGACCGTAATTATTGACT
1 AA-GTGATCGTAATTGTTGACT
242552 CTAAGCATCT
Statistics
Matches: 182, Mismatches: 33, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
48 1 0.01
49 42 0.23
50 138 0.76
51 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.35
Consensus pattern (50 bp):
AAGTGATCGTAATTGTTGACTATTTTTCACAAATCTTTGACAATCGAGAG
Found at i:242472 original size:100 final size:99
Alignment explanation
Indices: 242313--242551 Score: 259
Period size: 100 Copynumber: 2.4 Consensus size: 99
242303 ATTTTTTATT
* * * * *
242313 AATCTTTGATAATCGAGAGAAGTGATCGTAATTGTTGATTACTTTTCACAAACCTTTGACAATCA
1 AATCTTTGACAATCGAGAGAAGTGATCGTAATTATTGACTACTTCTCACAAACCCTTGACAATCA
*
242378 AGAGAGATGACCGTAATTGTTGACTATTCCTCACC
66 AGAGAG-TGACCGTAATTATTGACTATTCCTCACC
* * * * *
242413 AATCTTTGACAACCGAGAGAGGTGATCATAATTATTGACTA-TTCCTCACCAACCCTTGACAATT
1 AATCTTTGACAATCGAGAGAAGTGATCGTAATTATTGACTACTT-CTCACAAACCCTTGACAATC
* ** **
242477 GAGAGAGTGGTCGTAATTATTGACTATTTTTCACC
65 AAGAGAGTGACCGTAATTATTGACTATTCCTCACC
* *
242512 AA-CTTTTGACAATAGAGA-AATGTGACCGTAATTATTGACT
1 AATC-TTTGACAATCGAGAGAA-GTGATCGTAATTATTGACT
242552 CTAAGCATCT
Statistics
Matches: 115, Mismatches: 21, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
98 2 0.02
99 56 0.49
100 57 0.50
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (99 bp):
AATCTTTGACAATCGAGAGAAGTGATCGTAATTATTGACTACTTCTCACAAACCCTTGACAATCA
AGAGAGTGACCGTAATTATTGACTATTCCTCACC
Found at i:243812 original size:21 final size:21
Alignment explanation
Indices: 243788--243829 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
243778 GACTTCTAGA
243788 AGAGAGTGGTTCCAATAATAC
1 AGAGAGTGGTTCCAATAATAC
243809 AGAGAGTGGTTCCAATAATAC
1 AGAGAGTGGTTCCAATAATAC
243830 GAACCTATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.24
Consensus pattern (21 bp):
AGAGAGTGGTTCCAATAATAC
Found at i:246985 original size:50 final size:50
Alignment explanation
Indices: 246929--247141 Score: 311
Period size: 50 Copynumber: 4.3 Consensus size: 50
246919 AGAGGTAGTT
246929 GTAATTGTTGACTATTCTTCACCAATCTTTGACAATCGAAAGAGGTGACC
1 GTAATTGTTGACTATTCTTCACCAATCTTTGACAATCGAAAGAGGTGACC
* * * *
246979 GTAATTGTTGACTATTCTTCACTAACCTTTGACAATCGAGAGAGGTGATC
1 GTAATTGTTGACTATTCTTCACCAATCTTTGACAATCGAAAGAGGTGACC
* * * *
247029 GTAATTATTGACTATTCCTCACCAA-CTTTTGACAATCGAGAGAGGTGATC
1 GTAATTGTTGACTATTCTTCACCAATC-TTTGACAATCGAAAGAGGTGACC
* *
247079 GTAATTGTTGACTATTCTTCACCAATCTTTGACAATAGAAAAAGGTGACC
1 GTAATTGTTGACTATTCTTCACCAATCTTTGACAATCGAAAGAGGTGACC
*
247129 GTAATTATTGACT
1 GTAATTGTTGACT
247142 CTAAGCATCT
Statistics
Matches: 147, Mismatches: 14, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
49 1 0.01
50 145 0.99
51 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (50 bp):
GTAATTGTTGACTATTCTTCACCAATCTTTGACAATCGAAAGAGGTGACC
Found at i:254128 original size:18 final size:17
Alignment explanation
Indices: 254097--254141 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
254087 TATATAAAAT
254097 TAATTTA-A-TTTTATA
1 TAATTTATATTTTTATA
254112 TAATTTTATATTTTTATA
1 TAA-TTTATATTTTTATA
*
254130 TGATTTATATTT
1 TAATTTATATTT
254142 ATTTATATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 3 0.12
16 4 0.15
17 10 0.38
18 9 0.35
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (17 bp):
TAATTTATATTTTTATA
Found at i:254147 original size:10 final size:9
Alignment explanation
Indices: 254106--254166 Score: 54
Period size: 10 Copynumber: 6.8 Consensus size: 9
254096 TTAATTTAAT
*
254106 TTTATATAA
1 TTTATATTA
254115 TTTTATATT-
1 -TTTATATTA
*
254124 TTTATATGA
1 TTTATATTA
254133 TTTATATTTA
1 TTTATA-TTA
254143 TTTATATT-
1 TTTATATTA
*
254151 TTTTTATTA
1 TTTATATTA
*
254160 TGTATAT
1 TTTATAT
254167 CAAATTTTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
8 14 0.33
9 13 0.31
10 15 0.36
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (9 bp):
TTTATATTA
Found at i:256839 original size:2 final size:2
Alignment explanation
Indices: 256832--256861 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
256822 CATGATCAAA
*
256832 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
256862 CAACTTTAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:257025 original size:29 final size:29
Alignment explanation
Indices: 256964--257027 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
256954 ATTGCTTAGT
*
256964 AAAATATAAATAAATTTTAACGATCGATC
1 AAAATATAAATAAATTTTAACAATCGATC
* * * *
256993 AAAATATAAATTAATTTTAATAATTGATG
1 AAAATATAAATAAATTTTAACAATCGATC
257022 AAAATA
1 AAAATA
257028 ACTGTAATAG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.55, C:0.05, G:0.06, T:0.34
Consensus pattern (29 bp):
AAAATATAAATAAATTTTAACAATCGATC
Found at i:260347 original size:2 final size:2
Alignment explanation
Indices: 260335--260365 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
260325 AACACGTAAG
*
260335 CT CT CT AT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
260366 AAATATTAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.03, C:0.48, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:269455 original size:23 final size:21
Alignment explanation
Indices: 269414--269457 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
269404 TACAAAAATT
269414 ATAAAATATTTTAAATAATAA
1 ATAAAATATTTTAAATAATAA
*
269435 ATAAAATAATTCTTAATTAATAA
1 ATAAAAT-ATT-TTAAATAATAA
269458 TTATAAAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 3 0.15
23 10 0.50
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (21 bp):
ATAAAATATTTTAAATAATAA
Found at i:270274 original size:16 final size:16
Alignment explanation
Indices: 270235--270276 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
270225 ATGTATGTAT
270235 ATATATTTAAAAAATA
1 ATATATTTAAAAAATA
*
270251 AAATTATTTAAAAAATA
1 ATA-TATTTAAAAAATA
*
270268 TTATATTTA
1 ATATATTTA
270277 TATTTAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATATTTAAAAAATA
Found at i:276717 original size:2 final size:2
Alignment explanation
Indices: 276710--276742 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
276700 TCCTTTGCAA
276710 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
276743 TTGATAAGTT
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:278648 original size:2 final size:2
Alignment explanation
Indices: 278643--278673 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
278633 TATATACACA
278643 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 A
278674 TTGTGGAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:279280 original size:2 final size:2
Alignment explanation
Indices: 279273--279306 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
279263 ATAGACGGAC
279273 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
279307 GCGTTTTGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:281441 original size:15 final size:15
Alignment explanation
Indices: 281412--281440 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
281402 TTTGCAGATC
281412 CTCTTTTCTTTTTTT
1 CTCTTTTCTTTTTTT
281427 CTCTTTT-TTTTTTT
1 CTCTTTTCTTTTTTT
281441 TTTCTGGGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
CTCTTTTCTTTTTTT
Found at i:285090 original size:2 final size:2
Alignment explanation
Indices: 285085--285126 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
285075 TTCCCTGAAA
285085 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
285127 CGTAAACATC
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:286688 original size:3 final size:3
Alignment explanation
Indices: 286680--286706 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
286670 TATTCCAACA
286680 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
286707 GGTTAAATTT
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:297046 original size:14 final size:14
Alignment explanation
Indices: 297024--297070 Score: 67
Period size: 14 Copynumber: 3.4 Consensus size: 14
297014 ATAAAAATAA
297024 ATATTTTAATTTTT
1 ATATTTTAATTTTT
* * *
297038 ATATATTAAATTTA
1 ATATTTTAATTTTT
297052 ATATTTTAATTTTT
1 ATATTTTAATTTTT
297066 ATATT
1 ATATT
297071 AAAATAGAGA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
ATATTTTAATTTTT
Found at i:297334 original size:14 final size:14
Alignment explanation
Indices: 297315--297364 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
297305 TTATAATTTA
297315 AAAATATAAAAATT
1 AAAATATAAAAATT
* *
297329 AAAATACACAAATTT
1 AAAATATA-AAAATT
297344 AATAATAT-AAAATT
1 AA-AATATAAAAATT
297358 AAAATAT
1 AAAATAT
297365 TTTTCACTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
13 5 0.17
14 14 0.47
15 7 0.23
16 4 0.13
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (14 bp):
AAAATATAAAAATT
Found at i:298412 original size:2 final size:2
Alignment explanation
Indices: 298405--298431 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
298395 ATAATAACTT
298405 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
298432 CCCAAATCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:298506 original size:2 final size:2
Alignment explanation
Indices: 298499--298529 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
298489 GTAATTTGTT
298499 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
298530 CTGTGGTCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:298833 original size:20 final size:21
Alignment explanation
Indices: 298788--298833 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
298778 GATAAATATG
* *
298788 ATTAATAATTTGACATAAAAA
1 ATTAATAATATGAAATAAAAA
298809 A-TAATAATAT-AAATAAAAA
1 ATTAATAATATGAAATAAAAA
298828 ATTAAT
1 ATTAAT
298834 TTTTTATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 9 0.41
20 12 0.55
21 1 0.05
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (21 bp):
ATTAATAATATGAAATAAAAA
Found at i:298930 original size:29 final size:28
Alignment explanation
Indices: 298873--298938 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 28
298863 ATAAAAAATT
*
298873 AATAAAAATATAATAAATTTCAAACTGAA
1 AATAAAAATATAAAAAATTT-AAACTGAA
*
298902 AATAAAAATATATAAAACATTT-AAGTGAA
1 AATAAAAATATA-AAAA-ATTTAAACTGAA
*
298931 AAAAAAAA
1 AATAAAAA
298939 ATTGAGGTCC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 25 0.78
30 3 0.09
31 4 0.12
ACGTcount: A:0.67, C:0.05, G:0.05, T:0.24
Consensus pattern (28 bp):
AATAAAAATATAAAAAATTTAAACTGAA
Found at i:303516 original size:12 final size:12
Alignment explanation
Indices: 303499--303525 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
303489 GTGTTGGAGA
303499 AGATAAGTCTCC
1 AGATAAGTCTCC
303511 AGATAAGTCTCC
1 AGATAAGTCTCC
303523 AGA
1 AGA
303526 GCAACCTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (12 bp):
AGATAAGTCTCC
Found at i:305305 original size:111 final size:111
Alignment explanation
Indices: 305111--305332 Score: 444
Period size: 111 Copynumber: 2.0 Consensus size: 111
305101 CAAAAACATG
305111 TAAGAATGATTACTTGAAGCATTTCAATTACTACTACGAAATTGTAATATAAAACTTAGTTGATA
1 TAAGAATGATTACTTGAAGCATTTCAATTACTACTACGAAATTGTAATATAAAACTTAGTTGATA
305176 TTTAATTAACCTTTAAGGCTCATTTTAAAAAGGGTCTCATCTCATT
66 TTTAATTAACCTTTAAGGCTCATTTTAAAAAGGGTCTCATCTCATT
305222 TAAGAATGATTACTTGAAGCATTTCAATTACTACTACGAAATTGTAATATAAAACTTAGTTGATA
1 TAAGAATGATTACTTGAAGCATTTCAATTACTACTACGAAATTGTAATATAAAACTTAGTTGATA
305287 TTTAATTAACCTTTAAGGCTCATTTTAAAAAGGGTCTCATCTCATT
66 TTTAATTAACCTTTAAGGCTCATTTTAAAAAGGGTCTCATCTCATT
305333 GGCAACTTAA
Statistics
Matches: 111, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
111 111 1.00
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.38
Consensus pattern (111 bp):
TAAGAATGATTACTTGAAGCATTTCAATTACTACTACGAAATTGTAATATAAAACTTAGTTGATA
TTTAATTAACCTTTAAGGCTCATTTTAAAAAGGGTCTCATCTCATT
Found at i:306657 original size:27 final size:26
Alignment explanation
Indices: 306627--306710 Score: 66
Period size: 27 Copynumber: 3.2 Consensus size: 26
306617 ATGGTTGCTT
306627 GTGGCATAGATTGAGGTGGTGGTGATG
1 GTGGCATAGATTGAGGTGGTGGTG-TG
** * * **
306654 GTGG-AGGCGCTTGTGGTCCT--TGTG
1 GTGGCA-TAGATTGAGGTGGTGGTGTG
306678 GTGGCATAGATTGAGGTGGTGGTGCTG
1 GTGGCATAGATTGAGGTGGTGGTG-TG
306705 GTGGCA
1 GTGGCA
306711 GTTGGGGTTG
Statistics
Matches: 40, Mismatches: 12, Indels: 10
0.65 0.19 0.16
Matches are distributed among these distances:
24 14 0.35
25 3 0.08
26 3 0.08
27 20 0.50
ACGTcount: A:0.13, C:0.10, G:0.48, T:0.30
Consensus pattern (26 bp):
GTGGCATAGATTGAGGTGGTGGTGTG
Found at i:312114 original size:36 final size:37
Alignment explanation
Indices: 312068--312148 Score: 112
Period size: 38 Copynumber: 2.2 Consensus size: 37
312058 TTTTACTAAA
*
312068 AAAATCTTAATTTAAA-AATAAAAA-ATTATAAATATT
1 AAAATCTTAATTTAAAGAA-AAAAAGAGTATAAATATT
*
312104 AAAATCTTAATTTAAAGTAAAAAAAGCGTATAAATATT
1 AAAATCTTAATTTAAAG-AAAAAAAGAGTATAAATATT
312142 AAAATCT
1 AAAATCT
312149 AAACTAAGGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
36 16 0.40
37 5 0.12
38 19 0.47
ACGTcount: A:0.58, C:0.05, G:0.04, T:0.33
Consensus pattern (37 bp):
AAAATCTTAATTTAAAGAAAAAAAGAGTATAAATATT
Found at i:316056 original size:14 final size:14
Alignment explanation
Indices: 316033--316065 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
316023 ACAATATTAA
316033 TATAAA-AATAATT
1 TATAAATAATAATT
316046 TATAAATAATAATT
1 TATAAATAATAATT
316060 TA-AAAT
1 TATAAAT
316066 TTTAAATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TATAAATAATAATT
Found at i:319224 original size:18 final size:19
Alignment explanation
Indices: 319183--319225 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
319173 TTTCCCCTTT
*
319183 TTTTTCCTTAAGAATTTTC
1 TTTTTCCTTAAGAATTTCC
*
319202 TTTTTCCTT-GGAATTTCC
1 TTTTTCCTTAAGAATTTCC
319220 TTTTTC
1 TTTTTC
319226 AACTAACAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.14, C:0.19, G:0.07, T:0.60
Consensus pattern (19 bp):
TTTTTCCTTAAGAATTTCC
Found at i:325345 original size:11 final size:11
Alignment explanation
Indices: 325317--325347 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
325307 CATTCATGTA
325317 TTTATATTATT
1 TTTATATTATT
325328 TTT-TATTATT
1 TTTATATTATT
325338 TTTATATTAT
1 TTTATATTAT
325348 AATTATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTATATTATT
Found at i:331334 original size:10 final size:10
Alignment explanation
Indices: 331316--331346 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
331306 TTTTATATAA
331316 AAATTTAAAT
1 AAATTTAAAT
*
331326 AAATATAAAT
1 AAATTTAAAT
331336 AAATTTAAAT
1 AAATTTAAAT
331346 A
1 A
331347 TTATTTTATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (10 bp):
AAATTTAAAT
Found at i:335280 original size:50 final size:49
Alignment explanation
Indices: 335186--335281 Score: 149
Period size: 49 Copynumber: 2.0 Consensus size: 49
335176 ATATGGAATT
*
335186 GGAATTGTCTTTTTAACGCCGTCACGTGCAAGGGTATGAAAAAAAAAAA
1 GGAATTGTCTTTTTAACGCCGTCACGTGCAAGGGTAGGAAAAAAAAAAA
* *
335235 GGAATTTTCCTTTTT-ACGCCGTCACGTGCAAGGGTAGGGAAAAAAAA
1 GGAATTGT-CTTTTTAACGCCGTCACGTGCAAGGGTAGGAAAAAAAAA
335282 GGCATATACA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
49 37 0.86
50 6 0.14
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (49 bp):
GGAATTGTCTTTTTAACGCCGTCACGTGCAAGGGTAGGAAAAAAAAAAA
Found at i:336549 original size:3 final size:3
Alignment explanation
Indices: 336541--336574 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
336531 ACCCTGATTC
*
336541 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTT TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
336575 ATTTTTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:344980 original size:2 final size:2
Alignment explanation
Indices: 344973--345023 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
344963 TGGATAGTGT
344973 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
345015 TA TA TA TA T
1 TA TA TA TA T
345024 TTGTACTGAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:345411 original size:28 final size:28
Alignment explanation
Indices: 345359--345413 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
345349 TATTAAAATA
*
345359 AATTTTTAAATAATTTTAATTATATTAT
1 AATTTTTAAATAATTTTAATAATATTAT
345387 AATTATTTAAAT-ATTTT-ATGAATATTA
1 AATT-TTTAAATAATTTTAAT-AATATTA
345414 AAAAAATCCG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 2 0.08
28 15 0.62
29 7 0.29
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (28 bp):
AATTTTTAAATAATTTTAATAATATTAT
Found at i:347603 original size:2 final size:2
Alignment explanation
Indices: 347596--347623 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
347586 ACATTTTTAC
347596 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
347624 ATCTGTGTGT
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:347956 original size:29 final size:30
Alignment explanation
Indices: 347910--347966 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
347900 TTATTTTTAA
347910 TAAAAATAAAATAATATTTTTAA-AATTTT
1 TAAAAATAAAATAATATTTTTAATAATTTT
*
347939 TAAAAATTAAAAT-TTATTTTTAATAATT
1 TAAAAA-TAAAATAATATTTTTAATAATT
347967 ATCTTTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (30 bp):
TAAAAATAAAATAATATTTTTAATAATTTT
Found at i:348798 original size:2 final size:2
Alignment explanation
Indices: 348791--348818 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
348781 ATCAAAGACT
348791 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
348819 TGGGGAGGGC
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:354289 original size:2 final size:2
Alignment explanation
Indices: 354282--354308 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
354272 CATTTCGTAT
354282 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
354309 TAATTCATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:357799 original size:16 final size:16
Alignment explanation
Indices: 357780--357820 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 16
357770 CACCTAAATA
357780 ATAAT-TAAAATATAAT
1 ATAATATAAAA-ATAAT
357796 ATAATATAAAAATAAT
1 ATAATATAAAAATAAT
357812 ATAAATATA
1 AT-AATATA
357821 TTATATTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 12 0.52
17 11 0.48
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
ATAATATAAAAATAAT
Found at i:357825 original size:11 final size:11
Alignment explanation
Indices: 357788--357825 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
357778 TAATAATTAA
357788 AATAT-AATAT
1 AATATAAATAT
*
357798 AATATAAAAAT
1 AATATAAATAT
357809 AATATAAATAT
1 AATATAAATAT
*
357820 ATTATA
1 AATATA
357826 TTAATAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
10 5 0.21
11 19 0.79
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
AATATAAATAT
Found at i:357862 original size:34 final size:35
Alignment explanation
Indices: 357798--357919 Score: 98
Period size: 34 Copynumber: 3.5 Consensus size: 35
357788 AATATAATAT
* *
357798 AATATAAAAATAATATAAATAT--ATTA-TATTAATA
1 AATATTAAAAT-ATATAAATATAAAATATTATTAA-A
*
357832 AATTTTAAAATATATAAA-ATAAAAT-TTATT-AA
1 AATATTAAAATATATAAATATAAAATATTATTAAA
*
357864 AATATTAAATTTTATATAAATATAAAATATT-TTAAA
1 AATATTAAA--ATATATAAATATAAAATATTATTAAA
357900 AATCA-TATAAATATATAAAT
1 AAT-ATTA-AAATATATAAAT
357920 TATCAATTTC
Statistics
Matches: 72, Mismatches: 6, Indels: 19
0.74 0.06 0.20
Matches are distributed among these distances:
32 11 0.15
33 8 0.11
34 23 0.32
35 18 0.25
36 9 0.12
37 3 0.04
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (35 bp):
AATATTAAAATATATAAATATAAAATATTATTAAA
Found at i:357902 original size:18 final size:19
Alignment explanation
Indices: 357833--357913 Score: 60
Period size: 18 Copynumber: 4.1 Consensus size: 19
357823 ATATTAATAA
357833 ATTT-TAAAATATATAAAAT
1 ATTTATAAAA-ATATAAAAT
* *
357852 AAAATTTATTAAAATATTAAAT
1 ---ATTTATAAAAATATAAAAT
*
357874 -TTTATATAAATATAAAAT
1 ATTTATAAAAATATAAAAT
357892 ATTT-TAAAAATCATATAAAT
1 ATTTATAAAAAT-ATA-AAAT
357912 AT
1 AT
357914 ATAAATTATC
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
18 21 0.43
19 6 0.12
20 6 0.12
22 12 0.24
23 4 0.08
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (19 bp):
ATTTATAAAAATATAAAAT
Found at i:357915 original size:35 final size:32
Alignment explanation
Indices: 357839--357919 Score: 85
Period size: 35 Copynumber: 2.4 Consensus size: 32
357829 ATAAATTTTA
357839 AAATATATAAA-ATAAAATTTATTAAAATATT
1 AAATATATAAATATAAAATTTATTAAAATATT
357870 AAATTTTATATAAATATAAAATATT-TTAAAAATCATAT
1 AAA---TATATAAATATAAAAT-TTATT-AAAAT-AT-T
357908 AAATATATAAAT
1 AAATATATAAAT
357920 TATCAATTTC
Statistics
Matches: 42, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
31 3 0.07
34 8 0.19
35 18 0.43
36 7 0.17
37 2 0.05
38 4 0.10
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (32 bp):
AAATATATAAATATAAAATTTATTAAAATATT
Found at i:358128 original size:44 final size:45
Alignment explanation
Indices: 358075--358163 Score: 110
Period size: 44 Copynumber: 2.0 Consensus size: 45
358065 AATTTAGAAC
*
358075 AAAATTATTTATAAAAAAAT-TACTTTT-AAAAATTTTAAAAATAA
1 AAAATTATTT-TAAAAAAATATACTTTTAAAAAAATTTAAAAATAA
* * * *
358119 AAAATTATTTTTAATAATTATATTTTTAAAAAAATTTAAAAATAA
1 AAAATTATTTTAAAAAAATATACTTTTAAAAAAATTTAAAAATAA
358164 TATTTATTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
43 6 0.16
44 16 0.42
45 16 0.42
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (45 bp):
AAAATTATTTTAAAAAAATATACTTTTAAAAAAATTTAAAAATAA
Found at i:358171 original size:44 final size:43
Alignment explanation
Indices: 358098--358182 Score: 118
Period size: 44 Copynumber: 2.0 Consensus size: 43
358088 AAAAAATTAC
*
358098 TTTTAAAAATTTTAAAAATAAAAAATTATTTTTAATAATTATAT
1 TTTTAAAAAATTTAAAAATAAAAAATTATTTTTAAT-ATTATAT
* *
358142 TTTTAAAAAAATTTAAAAAT-AATATTTATTTTTAATATTAT
1 TTTT-AAAAAATTTAAAAATAAAAAATTATTTTTAATATTAT
358183 CATATTAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
43 5 0.14
44 18 0.49
45 14 0.38
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (43 bp):
TTTTAAAAAATTTAAAAATAAAAAATTATTTTTAATATTATAT
Found at i:358227 original size:33 final size:33
Alignment explanation
Indices: 358150--358242 Score: 107
Period size: 33 Copynumber: 2.8 Consensus size: 33
358140 ATTTTTAAAA
* *
358150 AAATTTAAAAATAATATTTATTTTTAATATTATC
1 AAATTT-AAAATAATATTAATTTTTAATATCATC
* * *
358184 ATATTAAAAATAATATTAATTTTTAATATCATT
1 AAATTTAAAATAATATTAATTTTTAATATCATC
*
358217 AAATTTAAAATAA-ATGATATTTTTAA
1 AAATTTAAAATAATATTA-ATTTTTAA
358243 ATTTTTATTT
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
32 3 0.06
33 43 0.86
34 4 0.08
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.47
Consensus pattern (33 bp):
AAATTTAAAATAATATTAATTTTTAATATCATC
Found at i:359077 original size:17 final size:19
Alignment explanation
Indices: 359055--359096 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
359045 ATTATATTTT
359055 TATTTAA-AA-TTTTAATA
1 TATTTAATAATTTTTAATA
*
359072 TATTTAATAATTTTTATTA
1 TATTTAATAATTTTTAATA
359091 TATTTA
1 TATTTA
359097 TATTTATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.32
18 2 0.09
19 13 0.59
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TATTTAATAATTTTTAATA
Found at i:361516 original size:80 final size:80
Alignment explanation
Indices: 361378--361529 Score: 207
Period size: 80 Copynumber: 1.9 Consensus size: 80
361368 ATTTATAATT
* * * * *
361378 TTGTATTAGTGAATTTAAAAATCAAGTCAACATAAGAAATCAAATGCAAAGAGTGTTCTTTCAAG
1 TTGTATTAGTAAATTCAAAAATCAAGTCAACATAAGAAATCAAATACAAAGAGAGTTCTCTCAAG
*
361443 AAGTGTTATATAGTC
66 AAATGTTATATAGTC
* * *
361458 TTGTATTTGTAAATTCAAAAATC-AGGCTAAGATAAGAAATCAAATACAAAGAGAGTTCTCTCAA
1 TTGTATTAGTAAATTCAAAAATCAAGTC-AACATAAGAAATCAAATACAAAGAGAGTTCTCTCAA
361522 GAAATGTT
65 GAAATGTT
361530 TGAGTGTTCT
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
79 3 0.05
80 59 0.95
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.31
Consensus pattern (80 bp):
TTGTATTAGTAAATTCAAAAATCAAGTCAACATAAGAAATCAAATACAAAGAGAGTTCTCTCAAG
AAATGTTATATAGTC
Found at i:363918 original size:3 final size:3
Alignment explanation
Indices: 363912--363942 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
363902 CTGCTGCTAC
363912 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG T
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG T
363943 AAGATGGAAG
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:0.00, C:0.00, G:0.65, T:0.35
Consensus pattern (3 bp):
TGG
Found at i:364025 original size:21 final size:21
Alignment explanation
Indices: 363987--364034 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
363977 AACCTGAATA
**
363987 TGGATACATGCCTGGTTACTCC
1 TGGATACATGCCAAGTTA-TCC
364009 -GGATACATGCCAAGTTATCC
1 TGGATACATGCCAAGTTATCC
364029 TGGATA
1 TGGATA
364035 TGGGCACCCG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (21 bp):
TGGATACATGCCAAGTTATCC
Found at i:366349 original size:12 final size:13
Alignment explanation
Indices: 366331--366367 Score: 58
Period size: 12 Copynumber: 2.8 Consensus size: 13
366321 TGTTCATGAT
366331 ATCTTAAAATTTC
1 ATCTTAAAATTTC
366344 -TCTTAAAATTTC
1 ATCTTAAAATTTC
366356 ATGCTTAAAATT
1 AT-CTTAAAATT
366368 AAATCAAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 12 0.55
13 1 0.05
14 9 0.41
ACGTcount: A:0.38, C:0.14, G:0.03, T:0.46
Consensus pattern (13 bp):
ATCTTAAAATTTC
Found at i:373948 original size:22 final size:23
Alignment explanation
Indices: 373891--373948 Score: 64
Period size: 22 Copynumber: 2.4 Consensus size: 23
373881 TTTTACTATA
373891 AAAATAATTAAAATATTATAAATTTT
1 AAAATAATT-AAATATTAT--ATTTT
* *
373917 AAATTTATTAAATATTAT-TTTT
1 AAAATAATTAAATATTATATTTT
373939 AAAATAATTA
1 AAAATAATTA
373949 TATAAATGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
22 12 0.43
25 9 0.32
26 7 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
AAAATAATTAAATATTATATTTT
Found at i:374376 original size:18 final size:19
Alignment explanation
Indices: 374346--374387 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
374336 CATATATTAT
374346 TTAAAATATATTTATAAAA
1 TTAAAATATATTTATAAAA
*
374365 TTAAAA-ATATTTTTAAAA
1 TTAAAATATATTTATAAAA
*
374383 ATAAA
1 TTAAA
374388 TAAAATATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TTAAAATATATTTATAAAA
Found at i:380693 original size:17 final size:17
Alignment explanation
Indices: 380667--380705 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
380657 ATAGAAAATA
380667 ATTTAATGAAT-TTGAAT
1 ATTTAATGAATGTT-AAT
*
380684 ATTTAGTGAATGTTAAT
1 ATTTAATGAATGTTAAT
380701 ATTTA
1 ATTTA
380706 TTTATTGTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 18 0.90
18 2 0.10
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (17 bp):
ATTTAATGAATGTTAAT
Found at i:380826 original size:17 final size:20
Alignment explanation
Indices: 380788--380827 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 20
380778 ATAAATTGAG
380788 ATTTTAAATATATTAAACAA
1 ATTTTAAATATATTAAACAA
380808 ATTTT-AATAT-TTAAA-AA
1 ATTTTAAATATATTAAACAA
380825 ATT
1 ATT
380828 GCAAATATAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 5 0.25
19 5 0.25
20 5 0.25
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTTTAAATATATTAAACAA
Found at i:381614 original size:2 final size:2
Alignment explanation
Indices: 381607--381639 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
381597 TTTAAAAATC
381607 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
381640 CCCCCCATCA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:383097 original size:78 final size:78
Alignment explanation
Indices: 383007--383163 Score: 305
Period size: 78 Copynumber: 2.0 Consensus size: 78
382997 CAATTACAGG
*
383007 TGCACTGAATAATTGATGGTACTTGTGAAATTGTATTGTTCATAGAGGGCTAATTTGAAATTTAC
1 TGCACTGAATAATTGATGGTACTTGTGAAATTGTATTGTTCATAGAGGGCTAATATGAAATTTAC
383072 CCGACGGCAAAGA
66 CCGACGGCAAAGA
383085 TGCACTGAATAATTGATGGTACTTGTGAAATTGTATTGTTCATAGAGGGCTAATATGAAATTTAC
1 TGCACTGAATAATTGATGGTACTTGTGAAATTGTATTGTTCATAGAGGGCTAATATGAAATTTAC
383150 CCGACGGCAAAGA
66 CCGACGGCAAAGA
383163 T
1 T
383164 AAGAGACTTG
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 78 1.00
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.32
Consensus pattern (78 bp):
TGCACTGAATAATTGATGGTACTTGTGAAATTGTATTGTTCATAGAGGGCTAATATGAAATTTAC
CCGACGGCAAAGA
Found at i:385840 original size:3 final size:3
Alignment explanation
Indices: 385834--385867 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
385824 TAATAATGAG
385834 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
385868 CTAGGATTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:391886 original size:22 final size:22
Alignment explanation
Indices: 391855--391896 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
391845 AAAAATATAT
*
391855 TATTTTTTTAATGTTTTAAAAA
1 TATTTATTTAATGTTTTAAAAA
* *
391877 TATTTATTTATTTTTTTAAA
1 TATTTATTTAATGTTTTAAA
391897 GTTGGATAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (22 bp):
TATTTATTTAATGTTTTAAAAA
Found at i:392083 original size:11 final size:10
Alignment explanation
Indices: 392043--392086 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
392033 GATTTAGTTA
392043 ATTTTCAAATT
1 ATTTT-AAATT
*
392054 ATTTTTAATT
1 ATTTTAAATT
*
392064 ACTTTAAATT
1 ATTTTAAATT
392074 ATTATTAAATT
1 ATT-TTAAATT
392085 AT
1 AT
392087 AATTTAATTC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
10 14 0.50
11 14 0.50
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.57
Consensus pattern (10 bp):
ATTTTAAATT
Found at i:396586 original size:2 final size:2
Alignment explanation
Indices: 396581--396615 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
396571 GTATACATAC
396581 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
396616 GGTTGGAAGC
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:403302 original size:2 final size:2
Alignment explanation
Indices: 403295--403322 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
403285 CCATATAGAC
403295 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
403323 TGTTGAGCAA
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):
AT
Found at i:404552 original size:2 final size:2
Alignment explanation
Indices: 404545--404569 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
404535 TGAACATTAC
404545 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 A
404570 CAAATTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:407356 original size:56 final size:57
Alignment explanation
Indices: 407282--407390 Score: 166
Period size: 56 Copynumber: 1.9 Consensus size: 57
407272 AAATAAGATT
407282 CATTCCTATACTTGGCAGATCTTTGA-TTTCCATTATTTCATCAAAGATTTTTCCTC
1 CATTCCTATACTTGGCAGATCTTTGATTTTCCATTATTTCATCAAAGATTTTTCCTC
* * ** *
407338 CATTCTTATACTTTGCAGATCTTTGATTTTTGATTATTTCATTAAAGATTTTT
1 CATTCCTATACTTGGCAGATCTTTGATTTTCCATTATTTCATCAAAGATTTTT
407391 GCTTGCGGGA
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
56 24 0.51
57 23 0.49
ACGTcount: A:0.24, C:0.17, G:0.09, T:0.50
Consensus pattern (57 bp):
CATTCCTATACTTGGCAGATCTTTGATTTTCCATTATTTCATCAAAGATTTTTCCTC
Found at i:412096 original size:19 final size:21
Alignment explanation
Indices: 412061--412099 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
412051 AAAAAATTAA
412061 AATATGATATAATATAAATAC
1 AATATGATATAATATAAATAC
412082 AATATG-TAT-ATATAAATA
1 AATATGATATAATATAAATA
412100 TTTTAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.50
20 3 0.17
21 6 0.33
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.36
Consensus pattern (21 bp):
AATATGATATAATATAAATAC
Found at i:412896 original size:2 final size:2
Alignment explanation
Indices: 412889--412922 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
412879 CAAATTTTAA
412889 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
412923 ATATATATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:413212 original size:22 final size:21
Alignment explanation
Indices: 413177--413217 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
413167 AAGTTAAGTT
*
413177 ATTCATGAATTATTTGAATTCG
1 ATTCATGAAATATTT-AATTCG
*
413199 ATTCATTAAATATTTAATT
1 ATTCATGAAATATTTAATT
413218 AAATTTGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.49
Consensus pattern (21 bp):
ATTCATGAAATATTTAATTCG
Found at i:413421 original size:20 final size:20
Alignment explanation
Indices: 413393--413434 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
413383 TTACAATTAC
*
413393 TTAATAAATTATAATTTTAT
1 TTAAAAAATTATAATTTTAT
413413 TTAAAAAATTATAATTTTAT
1 TTAAAAAATTATAATTTTAT
413433 TT
1 TT
413435 TTTATTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTAAAAAATTATAATTTTAT
Found at i:424425 original size:16 final size:15
Alignment explanation
Indices: 424404--424434 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
424394 TATCTGCTTT
424404 TTTTTTTCTTTATTTA
1 TTTTTTTCTTT-TTTA
424420 TTTTTTTCTTTTTTA
1 TTTTTTTCTTTTTTA
424435 ATGCAACTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.10, C:0.06, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTTTTTCTTTTTTA
Found at i:425657 original size:31 final size:32
Alignment explanation
Indices: 425594--425662 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 32
425584 TTATAAAATA
* * *
425594 TATAAATATTAAAATTAAATTTTTAATATATT
1 TATAAAAAATAAAATTAAATTTTAAATATATT
*
425626 T-TAAAAAATAAAATT-AATTTGTAAATTTATT
1 TATAAAAAATAAAATTAAATTT-TAAATATATT
425657 TATAAA
1 TATAAA
425663 TATTTTTAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
30 5 0.16
31 21 0.68
32 5 0.16
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (32 bp):
TATAAAAAATAAAATTAAATTTTAAATATATT
Found at i:426240 original size:2 final size:2
Alignment explanation
Indices: 426233--426272 Score: 71
Period size: 2 Copynumber: 19.5 Consensus size: 2
426223 AAATCGATTC
426233 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AGT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A
426273 GTTTGCAAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 35 0.95
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:426645 original size:21 final size:23
Alignment explanation
Indices: 426619--426661 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
426609 ATCTGTATTT
426619 ATAATTA-TAAA-TATTAATATA
1 ATAATTATTAAATTATTAATATA
*
426640 ATAATTATTAAATTATTTATAT
1 ATAATTATTAAATTATTAATAT
426662 TCGATTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
22 4 0.21
23 8 0.42
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
ATAATTATTAAATTATTAATATA
Found at i:426798 original size:2 final size:2
Alignment explanation
Indices: 426791--426830 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
426781 TAAAGCAAGA
426791 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
426831 GAAAAGGAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:428469 original size:2 final size:2
Alignment explanation
Indices: 428462--428494 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
428452 GATTGGCCTC
428462 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
428495 GTGAAGCAGC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:429049 original size:2 final size:2
Alignment explanation
Indices: 429042--429069 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
429032 TTCTTTACAA
429042 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
429070 TCGAGCCTGC
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):
AT
Found at i:435383 original size:363 final size:354
Alignment explanation
Indices: 434727--435433 Score: 1024
Period size: 363 Copynumber: 2.0 Consensus size: 354
434717 CACCACTGTA
* * * *
434727 ACTGAAACCCTTGCACATAGTAAAATGCAAGAGCCTGTTGAGGCACAGAAAATCTGCAGCATTGA
1 ACTGAAACCCTTGAACATAGTAAAATGCAAGAGCCAGTTGAGGCACAGAAAATCTCCAGCACTGA
* *
434792 AGACCTTAACAAGATTGTGCCACGAAAAGAAGGTGACTATGAGAAGCGAAAGAAGAAGAAACAAA
66 AAACATTAACAAGATTGTGCCACGAAAAGAAGGTGACTATGAGAAGCGAAAGAAGAAGAAACAAA
* * * * ** *
434857 AGCTGGAGAAGTTGACTGGTAATGTCGGTGGTCGTATTGCAGTTAGTACTGATGGAAATGAAACT
131 AGCTGGAGAAGGTGAATGCTAATGTCGATGGTCGTATTGCAGCAAGCACTGATGGAAATGAAACT
* *
434922 GGTAAAGAGGATTCAACTGGCAGTAAAGGAGAATGCAGAAAATTAGGAGGTGATGGTGGTGATGC
196 GCTAAAGAGGATTCAACTGGCAGTAAAGGAGAATGCAGAAAATTAGGAGGTGATGGCGGTGATGC
* *
434987 TGAAGATGGTAACAGAAGCAGGAAAAAGAAATCTAAATCAGGGAAAAATGGGTCTGAGGGTAAAC
261 TGAAGATGGTAACAGAAGCAGGAAAAAGAAATCTAAATCAGGGAAAAATGGATCTCAGGGTAAAC
*
435052 GTCATAAAGGTGATGCAGGCACTATTGTG
326 ATCATAAAGGTGATGCAGGCACTATTGTG
* * *
435081 ACTGAAACCCTTGAACATGGTAAAATGCAAGAGCCAGTTGAGGCA-ATGAAAATCTCCGGTACTG
1 ACTGAAACCCTTGAACATAGTAAAATGCAAGAGCCAGTTGAGGCACA-GAAAATCTCCAGCACTG
* * *
435145 AAAACATTAATAAGATTGTGCCAGGGAAAGAAGGTGAAC-ATGAGAAGCAAAAGAAGAAGAAGAA
65 AAAACATTAACAAGATTGTGCCACGAAAAGAAGGTG-ACTATGAGAAGC-------G-A-AAGAA
* *
435209 GAAGAAACAAAAGCTGGAGAAGGTGAATGCTAATGTTGATGGTCGTATTGCAGCAAGCATTGATG
120 GAAGAAACAAAAGCTGGAGAAGGTGAATGCTAATGTCGATGGTCGTATTGCAGCAAGCACTGATG
*
435274 GAAATGATACTGCTAAAGAGGATTCAACTGGCAGT-AAGGTAGAATGCAGAAAATTAGGAGGTGA
185 GAAATGAAACTGCTAAAGAGGATTCAACTGGCAGTAAAGG-AGAATGCAGAAAATTAGGAGGTGA
* *
435338 TGGCGGTGATGCTGAAGATGGTAACAGAGGCAGGAAAAAGAAATCTAAATCAGTGAAAAATGGAT
249 TGGCGGTGATGCTGAAGATGGTAACAGAAGCAGGAAAAAGAAATCTAAATCAGGGAAAAATGGAT
435403 CTCAGGGTAAACATCATAAAGGTGATGCAGG
314 CTCAGGGTAAACATCATAAAGGTGATGCAGG
435434 AACCAGAAAA
Statistics
Matches: 312, Mismatches: 29, Indels: 15
0.88 0.08 0.04
Matches are distributed among these distances:
353 1 0.00
354 95 0.30
355 2 0.01
361 1 0.00
362 5 0.02
363 208 0.67
ACGTcount: A:0.39, C:0.12, G:0.29, T:0.20
Consensus pattern (354 bp):
ACTGAAACCCTTGAACATAGTAAAATGCAAGAGCCAGTTGAGGCACAGAAAATCTCCAGCACTGA
AAACATTAACAAGATTGTGCCACGAAAAGAAGGTGACTATGAGAAGCGAAAGAAGAAGAAACAAA
AGCTGGAGAAGGTGAATGCTAATGTCGATGGTCGTATTGCAGCAAGCACTGATGGAAATGAAACT
GCTAAAGAGGATTCAACTGGCAGTAAAGGAGAATGCAGAAAATTAGGAGGTGATGGCGGTGATGC
TGAAGATGGTAACAGAAGCAGGAAAAAGAAATCTAAATCAGGGAAAAATGGATCTCAGGGTAAAC
ATCATAAAGGTGATGCAGGCACTATTGTG
Found at i:436905 original size:17 final size:17
Alignment explanation
Indices: 436879--436911 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
436869 ACATACAACT
436879 GATGGATGATTTGATGG
1 GATGGATGATTTGATGG
*
436896 GATGGGTGATTTGATG
1 GATGGATGATTTGATG
436912 AATTATAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.42, T:0.36
Consensus pattern (17 bp):
GATGGATGATTTGATGG
Found at i:437175 original size:2 final size:2
Alignment explanation
Indices: 437168--437216 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
437158 AGCAGCATGA
437168 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
437210 AT AT AT A
1 AT AT AT A
437217 AGATTGGAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:440110 original size:2 final size:2
Alignment explanation
Indices: 440103--440142 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
440093 TTAATCATCA
440103 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
440143 CTAACTCCCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:442306 original size:17 final size:18
Alignment explanation
Indices: 442279--442312 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
442269 AAAGATAGAT
442279 TTAATAAAAAAATTTAAA
1 TTAATAAAAAAATTTAAA
*
442297 TTAA-AAAAAACTTTAA
1 TTAATAAAAAAATTTAA
442313 TCAAGCAAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (18 bp):
TTAATAAAAAAATTTAAA
Found at i:442857 original size:21 final size:21
Alignment explanation
Indices: 442817--442858 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
442807 TCATATCAGT
*
442817 ATATTTTATTATTTTTTTAAA
1 ATATTTTATTATTTTATTAAA
442838 ATATTTTATT-TTTATATTAAA
1 ATATTTTATTATTT-TATTAAA
442859 TTTAATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
ATATTTTATTATTTTATTAAA
Found at i:442918 original size:11 final size:11
Alignment explanation
Indices: 442818--442921 Score: 52
Period size: 11 Copynumber: 9.3 Consensus size: 11
442808 CATATCAGTA
442818 TATTTTATTATT
1 TATTTTA-TATT
**
442830 T-TTTTA-AAA
1 TATTTTATATT
*
442839 TATTTTATTTT
1 TATTTTATATT
* *
442850 TATATTAAATT
1 TATTTTATATT
*
442861 TAATTATTATATA
1 T-ATT-TTATATT
* * *
442874 AATTTTAAAATA
1 TATTTT-ATATT
*
442886 TATATTATATT
1 TATTTTATATT
442897 ATATTTT-TATT
1 -TATTTTATATT
442908 TATTTTATATT
1 TATTTTATATT
442919 TAT
1 TAT
442922 ATAATAATAT
Statistics
Matches: 67, Mismatches: 18, Indels: 15
0.67 0.18 0.15
Matches are distributed among these distances:
9 2 0.03
10 11 0.16
11 30 0.45
12 19 0.28
13 5 0.07
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
TATTTTATATT
Found at i:444179 original size:2 final size:2
Alignment explanation
Indices: 444172--444214 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
444162 ACAAAACGTG
444172 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
444214 G
1 G
444215 GTATGATTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:445264 original size:14 final size:14
Alignment explanation
Indices: 445245--445282 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
445235 TACATACATT
445245 TATATATATATATG
1 TATATATATATATG
445259 TATATATATATATG
1 TATATATATATATG
*
445273 TATGTATATA
1 TATATATATA
445283 CATGCAAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (14 bp):
TATATATATATATG
Found at i:459533 original size:38 final size:36
Alignment explanation
Indices: 459487--459598 Score: 113
Period size: 35 Copynumber: 3.1 Consensus size: 36
459477 AATTAGGTTA
459487 TTTAGTTAAATTTAAATATAGAAATAGATCACGTAC
1 TTTAGTTAAATTTAAATATAGAAATAGATCACGTAC
* * ** * *
459523 TTCCTTGTTAAATTTAAATTTA-ATGTTA-ATTAGGTTA-
1 TT--TAGTTAAATTTAAATATAGA-AATAGATCACG-TAC
459560 TTTAGTTAAATTTAAATATAGAAATAGATCACGTAC
1 TTTAGTTAAATTTAAATATAGAAATAGATCACGTAC
459596 TTT
1 TTT
459599 CACTTCATCA
Statistics
Matches: 57, Mismatches: 12, Indels: 14
0.69 0.14 0.17
Matches are distributed among these distances:
35 20 0.35
36 10 0.18
37 7 0.12
38 20 0.35
ACGTcount: A:0.39, C:0.07, G:0.11, T:0.43
Consensus pattern (36 bp):
TTTAGTTAAATTTAAATATAGAAATAGATCACGTAC
Found at i:461152 original size:16 final size:16
Alignment explanation
Indices: 461107--461154 Score: 62
Period size: 17 Copynumber: 3.0 Consensus size: 16
461097 TAATATTTTT
**
461107 AATA-AAAATTTATTA
1 AATATAAAATTTAAAA
461122 AATATAAATATTTAAAA
1 AATATAAA-ATTTAAAA
461139 AATATAAAATTTAAAA
1 AATATAAAATTTAAAA
461155 TAACCTGTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 4 0.14
16 11 0.38
17 14 0.48
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AATATAAAATTTAAAA
Found at i:462354 original size:23 final size:24
Alignment explanation
Indices: 462307--462351 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
462297 ATTTTTAAAT
462307 TTTAAATATAAAAATTTAATATTCA
1 TTTAAATAT-AAAATTTAATATTCA
462332 TTTAAATAT-AAATTT-ATATT
1 TTTAAATATAAAATTTAATATT
462352 TCAAGCTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 5 0.25
23 6 0.30
25 9 0.45
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (24 bp):
TTTAAATATAAAATTTAATATTCA
Found at i:463016 original size:2 final size:2
Alignment explanation
Indices: 463009--463040 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
462999 AGTGAATAGG
*
463009 TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
463041 CACTTGCAAA
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:463159 original size:25 final size:25
Alignment explanation
Indices: 463131--463202 Score: 64
Period size: 25 Copynumber: 3.0 Consensus size: 25
463121 CCCACTCTTC
463131 AATATAATTATTAAAATATAATATA
1 AATATAATTATTAAAATATAATATA
* * *
463156 AATAAAATAATTTAAATAT-ATATTA
1 AATATAATTATTAAAATATAATA-TA
463181 AA-AT--TTA-TATAAATATAATATA
1 AATATAATTATTA-AAATATAATATA
463203 TTTTAAATAT
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
21 1 0.03
22 10 0.26
23 3 0.08
24 4 0.11
25 20 0.53
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
AATATAATTATTAAAATATAATATA
Found at i:463175 original size:20 final size:20
Alignment explanation
Indices: 463150--463236 Score: 58
Period size: 20 Copynumber: 4.4 Consensus size: 20
463140 ATTAAAATAT
463150 AATATAAATAAAATAATTTA
1 AATATAAATAAAATAATTTA
* *
463170 AATATATAT-TAA-AATTT-
1 AATATAAATAAAATAATTTA
*
463187 -ATATAAATATAATATATTTTA
1 AATATAAATA-AA-ATAATTTA
* *
463208 AATATAATTATAAT-ATTATAA
1 AATATAAATAAAATAATT-T-A
463229 AATATAAA
1 AATATAAA
463237 AATATAACAT
Statistics
Matches: 50, Mismatches: 9, Indels: 15
0.68 0.12 0.20
Matches are distributed among these distances:
16 7 0.14
18 6 0.12
19 5 0.10
20 15 0.30
21 9 0.18
22 8 0.16
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AATATAAATAAAATAATTTA
Found at i:463212 original size:22 final size:21
Alignment explanation
Indices: 463137--463236 Score: 66
Period size: 22 Copynumber: 4.7 Consensus size: 21
463127 CTTCAATATA
463137 ATTATTAAAATAT-AATATAA-
1 ATTA-TAAAATATAAATATAAT
* *
463157 A-TAAAATAATTTAAATAT-AT
1 ATTATAA-AATATAAATATAAT
463177 ATTA-AAATTTATATAAATATAAT
1 ATTATAAA---ATATAAATATAAT
* * *
463200 ATATTTTAAATATAATTATAAT
1 AT-TATAAAATATAAATATAAT
463222 ATTATAAAATATAAA
1 ATTATAAAATATAAA
463237 AATATAACAT
Statistics
Matches: 61, Mismatches: 9, Indels: 19
0.69 0.10 0.21
Matches are distributed among these distances:
18 2 0.03
19 8 0.13
20 9 0.15
21 12 0.20
22 23 0.38
23 4 0.07
24 1 0.02
25 2 0.03
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
ATTATAAAATATAAATATAAT
Done.