Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007188.1 Hibiscus syriacus cultivar Beakdansim tig00018934_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 283786
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
File 1 of 2
Found at i:8299 original size:77 final size:79
Alignment explanation
Indices: 8159--8313 Score: 181
Period size: 77 Copynumber: 2.0 Consensus size: 79
8149 ATATAGTAAG
* **
8159 TAAACATTAAAAGAATGTGATTTTGATAACAACTCTTTTAATAGATATTTAATTCAAAATAATTA
1 TAAACATTAAAAGAATGTAATTCAGATAACAACTCTTTTAATAGATATTTAATTCAAAATAATTA
*
8224 AATAAGAGTTTAAA
66 AATAAGAATTTAAA
* * * * * *
8238 TAAACATT-AAAGAATGTAATTCAGATTATAAGTC-TTTAATGGATATTTAATAT-GAATTAATT
1 TAAACATTAAAAGAATGTAATTCAGATAACAACTCTTTTAATAGATATTTAAT-TCAAAATAATT
*
8300 AAATATGAATTTAA
65 AAATAAGAATTTAA
8314 TTAATTCGAA
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
77 35 0.55
78 21 0.33
79 8 0.12
ACGTcount: A:0.47, C:0.05, G:0.10, T:0.38
Consensus pattern (79 bp):
TAAACATTAAAAGAATGTAATTCAGATAACAACTCTTTTAATAGATATTTAATTCAAAATAATTA
AATAAGAATTTAAA
Found at i:8306 original size:15 final size:16
Alignment explanation
Indices: 8286--8317 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
8276 ATGGATATTT
8286 AATATGAA-TTAATTA
1 AATATGAATTTAATTA
8301 AATATGAATTTAATTA
1 AATATGAATTTAATTA
8317 A
1 A
8318 TTCGAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (16 bp):
AATATGAATTTAATTA
Found at i:9207 original size:14 final size:13
Alignment explanation
Indices: 9184--9235 Score: 56
Period size: 14 Copynumber: 4.1 Consensus size: 13
9174 TGTTTGTTTA
*
9184 TGTTCATTTATGT
1 TGTTCGTTTATGT
9197 TAGTTCGTTTATG-
1 T-GTTCGTTTATGT
9210 T-TT-GTTTATGT
1 TGTTCGTTTATGT
9221 TCGTTCGTTTATGT
1 T-GTTCGTTTATGT
9235 T
1 T
9236 TAGTCCAATC
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
10 7 0.21
11 3 0.09
13 4 0.12
14 19 0.58
ACGTcount: A:0.12, C:0.08, G:0.19, T:0.62
Consensus pattern (13 bp):
TGTTCGTTTATGT
Found at i:9236 original size:24 final size:24
Alignment explanation
Indices: 9179--9237 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
9169 CAATTTGTTT
*
9179 GTTTATGTTCATTTATGTTAGTTC
1 GTTTATGTTTATTTATGTTAGTTC
* *
9203 GTTTATGTTTGTTTATGTTCGTTC
1 GTTTATGTTTATTTATGTTAGTTC
9227 GTTTATGTTTA
1 GTTTATGTTTA
9238 GTCCAATCTC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.14, C:0.07, G:0.19, T:0.61
Consensus pattern (24 bp):
GTTTATGTTTATTTATGTTAGTTC
Found at i:9444 original size:10 final size:10
Alignment explanation
Indices: 9429--9453 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
9419 ATGTTCATTT
9429 GTTTATGTTC
1 GTTTATGTTC
9439 GTTTATGTTC
1 GTTTATGTTC
9449 GTTTA
1 GTTTA
9454 CATTTGTGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.12, C:0.08, G:0.20, T:0.60
Consensus pattern (10 bp):
GTTTATGTTC
Found at i:9644 original size:16 final size:16
Alignment explanation
Indices: 9623--9665 Score: 86
Period size: 16 Copynumber: 2.7 Consensus size: 16
9613 CAAAAAATTT
9623 TGTTTGTTTATGTTTG
1 TGTTTGTTTATGTTTG
9639 TGTTTGTTTATGTTTG
1 TGTTTGTTTATGTTTG
9655 TGTTTGTTTAT
1 TGTTTGTTTAT
9666 TTGTTTTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.07, C:0.00, G:0.23, T:0.70
Consensus pattern (16 bp):
TGTTTGTTTATGTTTG
Found at i:10734 original size:77 final size:77
Alignment explanation
Indices: 10639--10784 Score: 199
Period size: 77 Copynumber: 1.9 Consensus size: 77
10629 TTCGAATTAA
*
10639 TTAAGCTCTTATTTAATTAATTCA-AATTAAATATCCATT-AAAGACTTATAAT-ATGAATTACA
1 TTAAACTCTTATTTAATT-ATT-AGAATTAAATATCCATTAAAAGACTTATAATCA-GAATTACA
10701 CTCTTTACTGTTTAT
63 CTCTTTACTGTTTAT
* * *
10716 TTAAACTCTTATTTAATTATTATGAATTAAATATCCATTAAAAGAGTTGTAATCAGAATTACATT
1 TTAAACTCTTATTTAATTATTA-GAATTAAATATCCATTAAAAGACTTATAATCAGAATTACACT
10781 CTTT
65 CTTT
10785 TACTTACTAT
Statistics
Matches: 61, Mismatches: 4, Indels: 7
0.85 0.06 0.10
Matches are distributed among these distances:
75 1 0.02
76 3 0.05
77 32 0.52
78 24 0.39
79 1 0.02
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (77 bp):
TTAAACTCTTATTTAATTATTAGAATTAAATATCCATTAAAAGACTTATAATCAGAATTACACTC
TTTACTGTTTAT
Found at i:13281 original size:14 final size:14
Alignment explanation
Indices: 13248--13303 Score: 85
Period size: 14 Copynumber: 3.9 Consensus size: 14
13238 TCCAATCACC
*
13248 GAGTCAACTCGGTCT
1 GAGTCAACTC-GTTT
13263 GAGTCAACTCGTTT
1 GAGTCAACTCGTTT
13277 GAGTCAACTCGTTT
1 GAGTCAACTCGTTT
*
13291 GAGTCAACCCGTT
1 GAGTCAACTCGTT
13304 GACTTTGATC
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
14 29 0.74
15 10 0.26
ACGTcount: A:0.21, C:0.25, G:0.23, T:0.30
Consensus pattern (14 bp):
GAGTCAACTCGTTT
Found at i:15563 original size:24 final size:23
Alignment explanation
Indices: 15536--15591 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 23
15526 TTATTTCATT
*
15536 ATCACGGTTATGAGATATTACTGG
1 ATCACGGTTAT-AGATATTACAGG
* *
15560 ATCAC-GATCTAGATATTACAGG
1 ATCACGGTTATAGATATTACAGG
*
15582 ATTACGGTTA
1 ATCACGGTTA
15592 AAACTAATTT
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
22 15 0.60
23 5 0.20
24 5 0.20
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.32
Consensus pattern (23 bp):
ATCACGGTTATAGATATTACAGG
Found at i:22185 original size:2 final size:2
Alignment explanation
Indices: 22178--22206 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
22168 TGAGAAAGAA
22178 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 A
22207 GTTGTATTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:22543 original size:45 final size:46
Alignment explanation
Indices: 22448--22543 Score: 133
Period size: 45 Copynumber: 2.1 Consensus size: 46
22438 ATTCCAGCAG
* * *
22448 TTCCACGTTACAAATCCCATCAGCTTCTAGCACTGCCAGCAATCCC
1 TTCCACGTTACAAATCCCAACAGCTTCCAGCACTGCCAGCAAGCCC
* *
22494 -TCCACGTTGCAAATTCCAACAGCTTCCAGCACTGCCAGC-AGCCC
1 TTCCACGTTACAAATCCCAACAGCTTCCAGCACTGCCAGCAAGCCC
22538 TTCCAC
1 TTCCAC
22544 ATCCCCGTTC
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
44 4 0.09
45 40 0.91
ACGTcount: A:0.25, C:0.41, G:0.12, T:0.22
Consensus pattern (46 bp):
TTCCACGTTACAAATCCCAACAGCTTCCAGCACTGCCAGCAAGCCC
Found at i:25227 original size:36 final size:36
Alignment explanation
Indices: 25180--25248 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
25170 CTATGCACAC
* *
25180 AAAGATCCTGTTATATTAATACCAAAAGTATTCCAT
1 AAAGATCCTGTTAGATTAATACCAAAAGCATTCCAT
*
25216 AAAGATCCTGTTAGATTGATACCAAAAGCATTC
1 AAAGATCCTGTTAGATTAATACCAAAAGCATTC
25249 TATGGTAAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.30
Consensus pattern (36 bp):
AAAGATCCTGTTAGATTAATACCAAAAGCATTCCAT
Found at i:25769 original size:43 final size:44
Alignment explanation
Indices: 25702--25785 Score: 116
Period size: 43 Copynumber: 1.9 Consensus size: 44
25692 TGACTTTAGA
* *
25702 GAAGTTAGGAGGGAAAGTTATCCCCTATATGT-AAAGTTTTGTT
1 GAAGTTAGGACGGAAAGTTATCCCCTACATGTAAAAGTTTTGTT
* * *
25745 GAAGTTAGGACTGAAATTTGTCCCCTACATGTAAAAGTTTT
1 GAAGTTAGGACGGAAAGTTATCCCCTACATGTAAAAGTTTT
25786 ATTTGATGCA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
43 27 0.77
44 8 0.23
ACGTcount: A:0.31, C:0.12, G:0.23, T:0.35
Consensus pattern (44 bp):
GAAGTTAGGACGGAAAGTTATCCCCTACATGTAAAAGTTTTGTT
Found at i:26011 original size:35 final size:34
Alignment explanation
Indices: 25956--26025 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 34
25946 CATTCATATA
*
25956 TTTACATTTGCATTTGCATTTTGCATTTTTGCATT
1 TTTACATTTGCATTTACATTTT-CATTTTTGCATT
* * *
25991 TTTACGTTTGTATTTACATTTTCATTTTTGTATT
1 TTTACATTTGCATTTACATTTTCATTTTTGCATT
26025 T
1 T
26026 GCATCTTTGC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
34 12 0.39
35 19 0.61
ACGTcount: A:0.17, C:0.11, G:0.10, T:0.61
Consensus pattern (34 bp):
TTTACATTTGCATTTACATTTTCATTTTTGCATT
Found at i:31685 original size:118 final size:118
Alignment explanation
Indices: 31548--31844 Score: 454
Period size: 118 Copynumber: 2.5 Consensus size: 118
31538 ACAGAAATAG
* *
31548 AATGTTAGGG-CATCTTGAATGCCTAATTCAAATAGAAATGATCTGTGTGGGGTATTTTGAAGGC
1 AATGTT-GGGACATCTTGAATGCCTAATTCAAACAGAAATGATCTATGTGGGGTATTTTGAAGGC
* *
31612 TCCCAGCAATTGGAATATTTGGGCATTCTTGGAGGCTCATTTTAGCAAGAAGAA
65 TCACAGCAATAGGAATATTTGGGCATTCTTGGAGGCTCATTTTAGCAAGAAGAA
31666 AATGTTGGGACATCTTGAATGCCTAATTCAAACAGAAATGATCTATGTGGGGTATTTTGAAGGCT
1 AATGTTGGGACATCTTGAATGCCTAATTCAAACAGAAATGATCTATGTGGGGTATTTTGAAGGCT
* *
31731 CACAGTAATAGGAATATTTGGGCATTCTTGGAGGCTCATTTTAGCAAGAAGCA
66 CACAGCAATAGGAATATTTGGGCATTCTTGGAGGCTCATTTTAGCAAGAAGAA
* * * * **
31784 AATGTTGGGACATCTCGAAAGCCTATTTCAGACAGAAATGAT-TCATGTGAAGTATTTTGAA
1 AATGTTGGGACATCTTGAATGCCTAATTCAAACAGAAATGATCT-ATGTGGGGTATTTTGAA
31845 AGTTTATTTT
Statistics
Matches: 165, Mismatches: 12, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
117 4 0.02
118 161 0.98
ACGTcount: A:0.31, C:0.13, G:0.24, T:0.31
Consensus pattern (118 bp):
AATGTTGGGACATCTTGAATGCCTAATTCAAACAGAAATGATCTATGTGGGGTATTTTGAAGGCT
CACAGCAATAGGAATATTTGGGCATTCTTGGAGGCTCATTTTAGCAAGAAGAA
Found at i:33312 original size:36 final size:36
Alignment explanation
Indices: 33259--33459 Score: 186
Period size: 36 Copynumber: 5.5 Consensus size: 36
33249 TTTCAAATAG
33259 AAATTTATCTCACTTGAGATTGTTTTTCTTAAAACA
1 AAATTTATCTCACTTGAGATTGTTTTTCTTAAAACA
* *** * ** ** **
33295 AACTGCGTCTCCCTTGAGACAGTTTCACTCGAAACA
1 AAATTTATCTCACTTGAGATTGTTTTTCTTAAAACA
33331 GAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACA
1 -AAATTTATCTCACTTGAGATTGTTTTTCTTAAAACA
* * ** ** **
33368 AAATTTGTCTCGCTTGAGACAGTTTCACTCGAAACA
1 AAATTTATCTCACTTGAGATTGTTTTTCTTAAAACA
33404 ACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACA
1 A-AATTTATCTCACTTGAGATTGTTTTTCTTAAAACA
* * *
33441 AGATTCATCTCGCTTGAGA
1 AAATTTATCTCACTTGAGA
33460 CAGTTCACTA
Statistics
Matches: 122, Mismatches: 41, Indels: 4
0.73 0.25 0.02
Matches are distributed among these distances:
36 69 0.57
37 53 0.43
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (36 bp):
AAATTTATCTCACTTGAGATTGTTTTTCTTAAAACA
Found at i:33349 original size:37 final size:36
Alignment explanation
Indices: 33259--33482 Score: 162
Period size: 36 Copynumber: 6.2 Consensus size: 36
33249 TTTCAAATAG
** ** *
33259 AAATTTATCTCACTTGAGATTGTTTTTCTTAAAACA
1 AAATTTATCTCACTTGAGACAGTTTCACTCAAAACA
* *** * *
33295 AACTGCGTCTCCCTTGAGACAGTTTCACTCGAAACA
1 AAATTTATCTCACTTGAGACAGTTTCACTCAAAACA
** ** *
33331 GAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACA
1 -AAATTTATCTCACTTGAGACAGTTTCACTCAAAACA
* * *
33368 AAATTTGTCTCGCTTGAGACAGTTTCACTCGAAACA
1 AAATTTATCTCACTTGAGACAGTTTCACTCAAAACA
** ** *
33404 ACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACA
1 A-AATTTATCTCACTTGAGACAGTTTCACTCAAAACA
* * * *
33441 AGATTCATCTCGCTTGAGACAG-TTCACTAAAAACA
1 AAATTTATCTCACTTGAGACAGTTTCACTCAAAACA
33476 GAAATTT
1 -AAATTT
33483 CCATCACTCA
Statistics
Matches: 137, Mismatches: 48, Indels: 6
0.72 0.25 0.03
Matches are distributed among these distances:
35 10 0.07
36 74 0.54
37 53 0.39
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (36 bp):
AAATTTATCTCACTTGAGACAGTTTCACTCAAAACA
Found at i:33378 original size:73 final size:73
Alignment explanation
Indices: 33257--33482 Score: 357
Period size: 73 Copynumber: 3.1 Consensus size: 73
33247 GTTTTCAAAT
* * *
33257 AGAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTGCGTCTCCCTTGAGACAGTTTCA
1 AGAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTCGTCTCGCTTGAGACAGTTTCA
33322 CTCGAAAC
66 CTCGAAAC
*
33330 AGAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCA
1 AGAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTCGTCTCGCTTGAGACAGTTTCA
33395 CTCGAAAC
66 CTCGAAAC
* *
33403 A-ACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAGATTCATCTCGCTTGAGACAG-TTC
1 AGA-AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTCGTCTCGCTTGAGACAGTTTC
**
33466 ACTAAAAAC
65 ACTCGAAAC
33475 AGAAATTT
1 AGAAATTT
33483 CCATCACTCA
Statistics
Matches: 142, Mismatches: 9, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
72 17 0.12
73 125 0.88
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (73 bp):
AGAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTCGTCTCGCTTGAGACAGTTTCA
CTCGAAAC
Found at i:34063 original size:45 final size:45
Alignment explanation
Indices: 34009--34106 Score: 135
Period size: 45 Copynumber: 2.2 Consensus size: 45
33999 ATTCCAGCAG
* * *
34009 TTCCACGTTACAAATCCCATCAGTTTCTAGCACTGCCAGCAGCTCC
1 TTCCACGTTACAAATCCCAACAGCTTCCAGCACTGCCAGCAGC-CC
* *
34055 -TCCACGTTACAAATTCCAACAGCTTCCAGCACTGCCAGCTGCCC
1 TTCCACGTTACAAATCCCAACAGCTTCCAGCACTGCCAGCAGCCC
34099 TTCCACGT
1 TTCCACGT
34107 CCCCGTTCCA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
44 2 0.04
45 44 0.96
ACGTcount: A:0.23, C:0.39, G:0.13, T:0.24
Consensus pattern (45 bp):
TTCCACGTTACAAATCCCAACAGCTTCCAGCACTGCCAGCAGCCC
Found at i:35339 original size:2 final size:2
Alignment explanation
Indices: 35332--35364 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
35322 TCTTATTTAA
35332 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35365 TTTTCTAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35344 original size:137 final size:137
Alignment explanation
Indices: 35098--35345 Score: 376
Period size: 137 Copynumber: 1.8 Consensus size: 137
35088 AATTAAATAA
35098 TAATATTTATTTATTTTTAAATATTAAGAAAGGGGTTATCTTAAAGCACCTAAAAGTCATTTTCT
1 TAATATTTATTTATTTTTAAATATTAAGAAAGGGGTTATCTTAAAGCACCTAAAAGTCATTTTCT
**
35163 GATTTTCTTAAATAAATAAAATATTCTATTTTTATAAATTATATATTAATTTATTTTAAAGAAAT
66 GATTTTCTTAAATAAATAAAATATTCTATTTAAATAAATTATATATTAATTTATTTTAAAGAAAT
35228 GTTTTAT
131 GTTTTAT
* * * *
35235 TAATATTTATTTATTTTTTAATATTAAGAAATGGGTTGTCTTAAAGCACCTAGAAGTCATTTTCT
1 TAATATTTATTTATTTTTAAATATTAAGAAAGGGGTTATCTTAAAGCACCTAAAAGTCATTTTCT
* *
35300 GATATTTC-TAAGTAAAT-AAATA-TCTTATTTAAATATATATATATAT
66 GAT-TTTCTTAAATAAATAAAATATTC-TATTTAAATAAAT-TATATAT
35346 ATATATATAT
Statistics
Matches: 100, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
135 2 0.02
136 15 0.15
137 79 0.79
138 4 0.04
ACGTcount: A:0.39, C:0.06, G:0.08, T:0.47
Consensus pattern (137 bp):
TAATATTTATTTATTTTTAAATATTAAGAAAGGGGTTATCTTAAAGCACCTAAAAGTCATTTTCT
GATTTTCTTAAATAAATAAAATATTCTATTTAAATAAATTATATATTAATTTATTTTAAAGAAAT
GTTTTAT
Found at i:38179 original size:34 final size:34
Alignment explanation
Indices: 38136--38217 Score: 155
Period size: 34 Copynumber: 2.4 Consensus size: 34
38126 TTGATTCATT
38136 GAATGTAAGATTACCTTTGGGAATAACATTATTG
1 GAATGTAAGATTACCTTTGGGAATAACATTATTG
38170 GAATGTAAGATTACCTTTGGGAATAACATTATTG
1 GAATGTAAGATTACCTTTGGGAATAACATTATTG
*
38204 GAATGTAACATTAC
1 GAATGTAAGATTAC
38218 TATGGGAGTA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 47 1.00
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.34
Consensus pattern (34 bp):
GAATGTAAGATTACCTTTGGGAATAACATTATTG
Found at i:38214 original size:16 final size:16
Alignment explanation
Indices: 38159--38216 Score: 57
Period size: 16 Copynumber: 3.5 Consensus size: 16
38149 CCTTTGGGAA
38159 TAACATTATTGGAATG
1 TAACATTATTGGAATG
*
38175 TAAGATTACCTTTGGGAA--
1 TAACATTA---TT-GGAATG
38193 TAACATTATTGGAATG
1 TAACATTATTGGAATG
38209 TAACATTA
1 TAACATTA
38217 CTATGGGAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
14 4 0.12
15 2 0.06
16 15 0.44
18 7 0.21
19 2 0.06
20 4 0.12
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (16 bp):
TAACATTATTGGAATG
Found at i:38289 original size:29 final size:29
Alignment explanation
Indices: 38256--38329 Score: 130
Period size: 29 Copynumber: 2.6 Consensus size: 29
38246 TTTGTTTAGT
*
38256 AGGAATGTAAGATTACAATGTTTGGTTGG
1 AGGAATGTAAGATTACAATGTTTGATTGG
38285 AGGAATGTAAGATTACAATGTTTGATTGG
1 AGGAATGTAAGATTACAATGTTTGATTGG
*
38314 AGGAATATAAGATTAC
1 AGGAATGTAAGATTAC
38330 TTGGATGCAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.36, C:0.04, G:0.27, T:0.32
Consensus pattern (29 bp):
AGGAATGTAAGATTACAATGTTTGATTGG
Found at i:38602 original size:16 final size:17
Alignment explanation
Indices: 38583--38619 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
38573 TAAAATATTA
38583 TTTTA-AATAATTAC-AT
1 TTTTACAATAA-TACTAT
38599 TTTTACAATAATACTAT
1 TTTTACAATAATACTAT
38616 TTTT
1 TTTT
38620 TATCCCATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (17 bp):
TTTTACAATAATACTAT
Found at i:41402 original size:29 final size:31
Alignment explanation
Indices: 41368--41489 Score: 139
Period size: 30 Copynumber: 4.1 Consensus size: 31
41358 TGTTACTTAC
*
41368 ATATA-TTTATTCTTTTTTTAATTT-AAAAT
1 ATATATTTTATTCTTATTTTAATTTAAAAAT
* * *
41397 ATATA-TTTACTCTTATCTT-ACTTAAAAAT
1 ATATATTTTATTCTTATTTTAATTTAAAAAT
*
41426 GTATATTTTATT-TTATTTTAATTTAAAAAT
1 ATATATTTTATTCTTATTTTAATTTAAAAAT
* *
41456 GTATATTTTATTCTT-TTTTAATTTCAAAAT
1 ATATATTTTATTCTTATTTTAATTTAAAAAT
41486 ATAT
1 ATAT
41490 TTTGTTTTTG
Statistics
Matches: 79, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
28 3 0.04
29 31 0.39
30 43 0.54
31 2 0.03
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.57
Consensus pattern (31 bp):
ATATATTTTATTCTTATTTTAATTTAAAAAT
Found at i:41558 original size:30 final size:30
Alignment explanation
Indices: 41427--41563 Score: 95
Period size: 30 Copynumber: 4.6 Consensus size: 30
41417 CTTAAAAATG
* * *
41427 TATATTTTA-TTTTATTTTAATTTA-AAAATG
1 TATATTTTATTTTTGTTTTAA-CTACAAAA-A
* * *
41457 TATATTTTATTCTT-TTTTAATTTC-AAAA
1 TATATTTTATTTTTGTTTTAACTACAAAAA
* * * *
41485 TATATTTTGTTTTTGTTTTACCTACATAGA
1 TATATTTTATTTTTGTTTTAACTACAAAAA
*
41515 TATATTTTATTTTTGTTTTAACTGCAAAAAA
1 TATATTTTATTTTTGTTTTAACTAC-AAAAA
* *
41546 TATATATT-TTTTTATTTT
1 TATATTTTATTTTTGTTTT
41564 TTTAATTGTA
Statistics
Matches: 85, Mismatches: 17, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
28 12 0.14
29 12 0.14
30 48 0.56
31 13 0.15
ACGTcount: A:0.31, C:0.05, G:0.04, T:0.60
Consensus pattern (30 bp):
TATATTTTATTTTTGTTTTAACTACAAAAA
Found at i:41684 original size:29 final size:29
Alignment explanation
Indices: 41635--41732 Score: 76
Period size: 30 Copynumber: 3.3 Consensus size: 29
41625 ATACTTTTTA
* * *
41635 ATAT-TTTTTAAGTTGAA-ATAATAAGAAT
1 ATATATTTTTAAATT-AAGATAAAAAAAAT
41663 ATATATTTTTAAATTAAGATAAGAATAAAAT
1 ATATATTTTTAAATTAAGATAA-AA-AAAAT
** *
41694 ATAT-TTAATAATTTAAGATAAAAATAAAGT
1 ATATATTTTTAAATTAAGATAAAAA-AAA-T
41724 ATATATTTT
1 ATATATTTT
41733 ATTTTTAAGA
Statistics
Matches: 55, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
28 7 0.13
29 18 0.33
30 20 0.36
31 10 0.18
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (29 bp):
ATATATTTTTAAATTAAGATAAAAAAAAT
Found at i:41712 original size:30 final size:29
Alignment explanation
Indices: 41663--41727 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 29
41653 TAATAAGAAT
* *
41663 ATATATTTTTAAATTAAGATAAGAATAAA
1 ATATATTTATAAATTAAGATAAAAATAAA
*
41692 ATATATTTAATAATTTAAGATAAAAATAAA
1 ATATATTT-ATAAATTAAGATAAAAATAAA
*
41722 GTATAT
1 ATATAT
41728 ATTTTATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 8 0.26
30 23 0.74
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.38
Consensus pattern (29 bp):
ATATATTTATAAATTAAGATAAAAATAAA
Found at i:41771 original size:18 final size:18
Alignment explanation
Indices: 41736--41779 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
41726 ATATTTTATT
* *
41736 TTTAAGATGTTAATTTAA
1 TTTAAGATGTGAAATTAA
*
41754 TTTAATATGTGAAATTAA
1 TTTAAGATGTGAAATTAA
*
41772 GTTAAGAT
1 TTTAAGAT
41780 ATATAAAATA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (18 bp):
TTTAAGATGTGAAATTAA
Found at i:45141 original size:603 final size:602
Alignment explanation
Indices: 43901--45709 Score: 3042
Period size: 603 Copynumber: 3.0 Consensus size: 602
43891 AATTATTACA
* *
43901 ATGCTTGGAAATGACTTCTATCACTTCAATTTCTCCTTTTAATTCACCATGCTTGTTGGTGAAAA
1 ATGCTTGGAAAGGACTTCTATCTCTTCAATTTCTCCTTTTAATTCACCATGCTTGTTGGTGAAAA
43966 GGTTTGTCTCTTGGTTGCAGTCATCACGTCACTTGGTGAAGATAATTGTTCTTTGAATGACTCTT
66 GGTTTGTCTCTTGGTTGCAGTCATCAC-TCACTTGGTGAAGATAATTGTTCTTTGAATGACTCTT
* * *
44031 TGGTGTTGTTTGTAACCAATATGTCCTTTGCCCGAAACATTATATCTTTTGGAAAAGGTACTTAT
130 TGGTGTTGTTTGTAACCAACATGTCCTTTGCCTGAAACATTATGTCTTTTGGAAAAGGTACTTAT
*
44096 CCCTTCAAATTCTCTTTGGTGATGGTTTGAAACATCATGTGCTTTCGCCTTTGTATCTTTCCAAA
195 CCCTTCAACTTCTCTTTGGTGATGGTTTGAAACATCATGTGCTTTCGCCTTTGTATCTTTCCAAA
* *
44161 TGATCACCTTTGATTCAATGTAAACAATCATTAAAAAGCTAAGCATGGTAGAAATTTTTTTGATT
260 TGATCACCTTTGATTCAATGTAAACAATCATTAAAAAACTAGGCATGGTAGAAA-TTTTTTGATT
44226 CATTTTCTTTGTTTCCTCTCATCTTCTGGTGTAATTCTTTCTTTAACTTATGCCTTCTTTCATTT
324 CATTTTCTTTGTTTCCTCTCATCTTCTGGTGTAATTCTTTCTTTAACTTATGCCTTCTTTCATTT
* *
44291 CCTACAA-CACAATCAGATTAGTAGAAAAAGAAAATCAATTCCAAAAGAGTAGAGAAACCAAACC
389 CCTACAACCACAATCAGATTAGTA-AAAAAGAAAATCAATTCCAAAAGAGTAGAGAAAACAAATC
* * *
44355 CAATAGTACTTGTGAGTGGCATTGAATGCTTGTTCTTGATGAACAGTTGTATTGGTTCATCCTTT
453 CAATAGTGCTTGTGAGTGGCATTGAACGCTTGTTCTTGATGAACAATTGTATTGGTTCATCCTTT
*
44420 GAAACCCTTTATC-GAAACATGGTTGTTGTTTGATAATATTTATGATTGGCAACATGATTAGATC
518 GAAACCCTTTATCAG-AACATGGTTGTTGTTTGATAATATTTATGATTGGCAACATGATTGGATC
*
44484 ATCCCTTGAAGTATTTTCATT
582 ATCCCTTGAAGTCTTTTCATT
*
44505 ATGCTTGGAAAGGACTTCTATCTCTTCAATTTCTCCTTTTAATTCACCACGCTTGTTGGTGAAAA
1 ATGCTTGGAAAGGACTTCTATCTCTTCAATTTCTCCTTTTAATTCACCATGCTTGTTGGTGAAAA
44570 GGTTTGTCTCTTGGTTGCAGTCATCACATCACTTGGTGAAGATAATTGTTCTTTGAATGACTCTT
66 GGTTTGTCTCTTGGTTGCAGTCATCAC-TCACTTGGTGAAGATAATTGTTCTTTGAATGACTCTT
* *
44635 TGGTGTTGTTTGTAACTAACATGTCATTTGCCTGAAACATTATGTCTTTTGGAAAAGGTACTTAT
130 TGGTGTTGTTTGTAACCAACATGTCCTTTGCCTGAAACATTATGTCTTTTGGAAAAGGTACTTAT
44700 CCCTTCAACTTCTCTTTGGTGATGGTTTGAAACATCATGTGCTTTCGCCTTTGTATCTTTCCAAA
195 CCCTTCAACTTCTCTTTGGTGATGGTTTGAAACATCATGTGCTTTCGCCTTTGTATCTTTCCAAA
44765 TGATCACCTTTGATTCAATGTAAACAATCATTAAAAAACTAGGCATGGTAGAAATTTTTTGATTC
260 TGATCACCTTTGATTCAATGTAAACAATCATTAAAAAACTAGGCATGGTAGAAATTTTTTGATTC
44830 ATTTTCTTTGTTTCCTCTCATCTTCTGGTGTAATTCTTTCTTTAACTTATGCCTTCTTTCATTTC
325 ATTTTCTTTGTTTCCTCTCATCTTCTGGTGTAATTCTTTCTTTAACTTATGCCTTCTTTCATTTC
44895 CTACAACCACAATCAGATTAGTAAAAAAGAAAATCAATTCCAAAAGAGTAGAGAAAACAAATCCA
390 CTACAACCACAATCAGATTAGTAAAAAAGAAAATCAATTCCAAAAGAGTAGAGAAAACAAATCCA
* * *
44960 ATAGTGCTTGTGAGTGCCATTGAACGCTTATTCTTGATGAACAATTGTATTGGTTCATTCTTTGA
455 ATAGTGCTTGTGAGTGGCATTGAACGCTTGTTCTTGATGAACAATTGTATTGGTTCATCCTTTGA
45025 AACCCTTTATCAGAACATGGTTGTTGTTTGATAATATTTATGATTGGCAACATGATTGGATCATC
520 AACCCTTTATCAGAACATGGTTGTTGTTTGATAATATTTATGATTGGCAACATGATTGGATCATC
45090 CCTTGAAGTCTTTTCATT
585 CCTTGAAGTCTTTTCATT
*
45108 ATGCTTGGAAAGGACTTCTATCTCTTCAATTTCTCCTTTTAATTCACCATACTTGTTGGTGAAAA
1 ATGCTTGGAAAGGACTTCTATCTCTTCAATTTCTCCTTTTAATTCACCATGCTTGTTGGTGAAAA
* * *
45173 GGTTTGTCTATTGGTTAG-AGTC-T---TCACGTGGTGAAGATAATTGTTCTTTGAATGACTCAT
66 GGTTTGTCTCTTGGTT-GCAGTCATCACTCACTTGGTGAAGATAATTGTTCTTTGAATGACTCTT
*
45233 TGGTGTTGTTTGTAACCAACATGTCCTTTGCCTAAAACATTATGTCTTTTGGAAAAGGTACTTAT
130 TGGTGTTGTTTGTAACCAACATGTCCTTTGCCTGAAACATTATGTCTTTTGGAAAAGGTACTTAT
* * * *
45298 ACCTTTAACTTCTCTTTGGTGATGGTTGGAAACATCATGTGCTTTCTCCTTTGTATCTTTCCAAA
195 CCCTTCAACTTCTCTTTGGTGATGGTTTGAAACATCATGTGCTTTCGCCTTTGTATCTTTCCAAA
****
45363 TGATCACCTTTGATTCAATGTAAACAATCATTAAAAAACTAGGCATGGTAGAAAAAAAATTGATT
260 TGATCACCTTTGATTCAATGTAAACAATCATTAAAAAACTAGGCATGGTAG-AAATTTTTTGATT
* ** *
45428 CATTTTCTTTGTTTCCTCTCATCTT-TCGGTGTAATTATTTCTCAAACTTATGGCTTC-TTCAAT
324 CATTTTCTTTGTTTCCTCTCATCTTCT-GGTGTAATTCTTTCTTTAACTTATGCCTTCTTTC-AT
* * * * * *
45491 TTCCTAGAACCACAATCAAATTAGTAGAAAATAAAATCAATTTCAAAAGAGTACAGAAAACAAAT
387 TTCCTACAACCACAATCAGATTAGTAAAAAAGAAAATCAATTCCAAAAGAGTAGAGAAAACAAAT
* *
45556 CCATTAGTGCTTGTGAGTGGCATTGAACGCTTGTTCTTGATGAACAATTGTATTGATTCATCCTT
452 CCAATAGTGCTTGTGAGTGGCATTGAACGCTTGTTCTTGATGAACAATTGTATTGGTTCATCCTT
45621 TGAAACTCCTTTATCAGAACATGGTTGTTGTTTGATAATATTTATGATTGGCAACATGATTGGAT
517 TGAAAC-CCTTTATCAGAACATGGTTGTTGTTTGATAATATTTATGATTGGCAACATGATTGGAT
*
45686 CATCCCTTGAAGTCTTTTCGTT
581 CATCCCTTGAAGTCTTTTCATT
45708 AT
1 AT
45710 CCTACATCAA
Statistics
Matches: 1144, Mismatches: 54, Indels: 18
0.94 0.04 0.01
Matches are distributed among these distances:
598 213 0.19
599 187 0.16
600 81 0.07
602 1 0.00
603 342 0.30
604 320 0.28
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39
Consensus pattern (602 bp):
ATGCTTGGAAAGGACTTCTATCTCTTCAATTTCTCCTTTTAATTCACCATGCTTGTTGGTGAAAA
GGTTTGTCTCTTGGTTGCAGTCATCACTCACTTGGTGAAGATAATTGTTCTTTGAATGACTCTTT
GGTGTTGTTTGTAACCAACATGTCCTTTGCCTGAAACATTATGTCTTTTGGAAAAGGTACTTATC
CCTTCAACTTCTCTTTGGTGATGGTTTGAAACATCATGTGCTTTCGCCTTTGTATCTTTCCAAAT
GATCACCTTTGATTCAATGTAAACAATCATTAAAAAACTAGGCATGGTAGAAATTTTTTGATTCA
TTTTCTTTGTTTCCTCTCATCTTCTGGTGTAATTCTTTCTTTAACTTATGCCTTCTTTCATTTCC
TACAACCACAATCAGATTAGTAAAAAAGAAAATCAATTCCAAAAGAGTAGAGAAAACAAATCCAA
TAGTGCTTGTGAGTGGCATTGAACGCTTGTTCTTGATGAACAATTGTATTGGTTCATCCTTTGAA
ACCCTTTATCAGAACATGGTTGTTGTTTGATAATATTTATGATTGGCAACATGATTGGATCATCC
CTTGAAGTCTTTTCATT
Found at i:46740 original size:17 final size:18
Alignment explanation
Indices: 46700--46734 Score: 54
Period size: 17 Copynumber: 1.9 Consensus size: 18
46690 TAGAATAGGT
46700 AATGAA-TAAAGAAAAGG
1 AATGAAGTAAAGAAAAGG
46717 AATGAAGTAAAGAGAAAG
1 AATGAAGTAAAGA-AAAG
46735 ATGAAGATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 6 0.38
19 4 0.25
ACGTcount: A:0.63, C:0.00, G:0.26, T:0.11
Consensus pattern (18 bp):
AATGAAGTAAAGAAAAGG
Found at i:46955 original size:10 final size:10
Alignment explanation
Indices: 46940--46987 Score: 62
Period size: 10 Copynumber: 4.8 Consensus size: 10
46930 GATGTATGAG
*
46940 TTCTTTTCTT
1 TTCTTTTTTT
46950 TTCTTTTTTT
1 TTCTTTTTTT
*
46960 TT-TGTTTTTC
1 TTCT-TTTTTT
46970 TTCTTTTTTT
1 TTCTTTTTTT
46980 TTCTTTTT
1 TTCTTTTT
46988 GTTGTAACAC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
9 1 0.03
10 31 0.94
11 1 0.03
ACGTcount: A:0.00, C:0.12, G:0.02, T:0.85
Consensus pattern (10 bp):
TTCTTTTTTT
Found at i:50922 original size:21 final size:20
Alignment explanation
Indices: 50882--50923 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
50872 TCTCACTAAA
*
50882 TTTTATTATCTTTCTTATTT
1 TTTTATTATCTTTCTAATTT
50902 TTTTAATTATACTTT-TAATTT
1 TTTT-ATTAT-CTTTCTAATTT
50923 T
1 T
50924 ATATTTTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 4 0.21
21 11 0.58
22 4 0.21
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTTATTATCTTTCTAATTT
Found at i:52424 original size:31 final size:32
Alignment explanation
Indices: 52380--52444 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 32
52370 TCCTTCCAGA
*
52380 TAAAACTTGCATCAATTTCTAATTTTCATTAT
1 TAAAACTTGCATCAATTTCTAATTATCATTAT
52412 TAAAACTT-CATCAATTTCTAATTATCATTAT
1 TAAAACTTGCATCAATTTCTAATTATCATTAT
52443 TA
1 TA
52445 CCTGTCAGTA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 24 0.75
32 8 0.25
ACGTcount: A:0.37, C:0.15, G:0.02, T:0.46
Consensus pattern (32 bp):
TAAAACTTGCATCAATTTCTAATTATCATTAT
Found at i:53555 original size:18 final size:20
Alignment explanation
Indices: 53534--53579 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 20
53524 TTTAAATTGC
53534 AAAAATTACAT-AAA-TAAA
1 AAAAATTACATCAAACTAAA
53552 AAAAA-T-CATCAAACTAAA
1 AAAAATTACATCAAACTAAA
53570 AATAAATTAC
1 AA-AAATTAC
53580 TTCGTTACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
16 3 0.13
17 4 0.17
18 11 0.48
19 3 0.13
20 1 0.04
21 1 0.04
ACGTcount: A:0.67, C:0.11, G:0.00, T:0.22
Consensus pattern (20 bp):
AAAAATTACATCAAACTAAA
Found at i:57663 original size:22 final size:22
Alignment explanation
Indices: 57629--57674 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
57619 AATTTTTACA
*
57629 TATACATACATATGTATGTATG
1 TATACATACATATATATGTATG
* *
57651 TATATATATATATATATGTATG
1 TATACATACATATATATGTATG
57673 TA
1 TA
57675 GTTAATTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.39, C:0.04, G:0.11, T:0.46
Consensus pattern (22 bp):
TATACATACATATATATGTATG
Found at i:59106 original size:2 final size:2
Alignment explanation
Indices: 59101--59204 Score: 52
Period size: 2 Copynumber: 57.5 Consensus size: 2
59091 TTTTAAAATG
* * *
59101 TA TA TA TA T- TA TA TA T- TGA AA AA TA TA TA TA T- TT TA -A TA
1 TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA
* *
59140 TA TA TA TA TA TA -A TA TT TA T- TA TA TA T- TA TG TA T- TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
59177 TA T- TT TA TA -A TA TA TA -A TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
59205 TTATTTTATT
Statistics
Matches: 79, Mismatches: 10, Indels: 26
0.69 0.09 0.23
Matches are distributed among these distances:
1 12 0.15
2 67 0.85
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (2 bp):
TA
Found at i:59117 original size:43 final size:42
Alignment explanation
Indices: 59064--59205 Score: 112
Period size: 41 Copynumber: 3.3 Consensus size: 42
59054 AGTATTTTAT
* * *
59064 TATTTTATATTATTATAATATATATCTTTTTAAAATGTATATA
1 TATTATATATTATTATAATATATAT-ATTTTAAAATATATATA
* *
59107 TATTATATATTGA--AAAATATATATATTTTAATATATATATA
1 TATTATATATT-ATTATAATATATATATTTTAAAATATATATA
* *
59148 TATAATAT-TTATTATATATTATGTATTATTATTTTATAATATATAATA
1 TATTATATATTATTATA-A-TA--TA-TA-TATTTTAAAATATAT-ATA
59196 TATT-TATATT
1 TATTATATATT
59206 TATTTTATTA
Statistics
Matches: 78, Mismatches: 10, Indels: 17
0.74 0.10 0.16
Matches are distributed among these distances:
39 1 0.01
40 2 0.03
41 23 0.29
42 11 0.14
43 12 0.15
44 1 0.01
45 2 0.03
46 2 0.03
47 16 0.21
48 8 0.10
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (42 bp):
TATTATATATTATTATAATATATATATTTTAAAATATATATA
Found at i:59148 original size:20 final size:20
Alignment explanation
Indices: 59073--59192 Score: 77
Period size: 20 Copynumber: 5.9 Consensus size: 20
59063 TTATTTTATA
*
59073 TTATTATA-ATATATATCTT
1 TTATTATATATATATATATT
* * *
59092 TT-TAAAATGTATATATATT
1 TTATTATATATATATATATT
* *
59111 ATATATTGAAAAATATATATATT
1 -T-TATT-ATATATATATATATT
*
59134 TTAATATATATATATATAATAT
1 TTATTATATATATATAT-AT-T
*
59156 TTATTATATAT-TATGTATT
1 TTATTATATATATATATATT
*
59175 ATTATTTTATA-ATATATA
1 -TTATTATATATATATATA
59193 ATATATTTAT
Statistics
Matches: 78, Mismatches: 14, Indels: 17
0.72 0.13 0.16
Matches are distributed among these distances:
18 3 0.04
19 12 0.15
20 27 0.35
21 10 0.13
22 13 0.17
23 13 0.17
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (20 bp):
TTATTATATATATATATATT
Found at i:59215 original size:47 final size:49
Alignment explanation
Indices: 59135--59229 Score: 126
Period size: 49 Copynumber: 2.0 Consensus size: 49
59125 ATATATATTT
59135 TAATATATATATATATAATATTTATTATATATT-ATGTATTATTATTTTA
1 TAATATATATATATATAATATTTATTATATATTAAT-TATTATTATTTTA
* *
59184 TAATATATA-ATATATTTATATTTATT-T-TATTAATTTTTATTATTTT
1 TAATATATATATATA-TAATATTTATTATATATTAATTATTATTATTTT
59230 TCAGGTTTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
47 15 0.36
48 8 0.19
49 19 0.45
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (49 bp):
TAATATATATATATATAATATTTATTATATATTAATTATTATTATTTTA
Found at i:60077 original size:18 final size:18
Alignment explanation
Indices: 60054--60096 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
60044 GGAGTCAATC
60054 GTCGTCGAAAATCGAGAA
1 GTCGTCGAAAATCGAGAA
60072 GTCGTCGAAAATCGAGAA
1 GTCGTCGAAAATCGAGAA
60090 GTCGTCG
1 GTCGTCG
60097 GAGAAGGTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.33, C:0.19, G:0.30, T:0.19
Consensus pattern (18 bp):
GTCGTCGAAAATCGAGAA
Found at i:80028 original size:15 final size:15
Alignment explanation
Indices: 80008--80040 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
79998 ATCCAACCTG
80008 AATAACACT-TATCCA
1 AATAACA-TATATCCA
80023 AATAACATATATCCA
1 AATAACATATATCCA
80038 AAT
1 AAT
80041 TCTGATATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 1 0.06
15 16 0.94
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.27
Consensus pattern (15 bp):
AATAACATATATCCA
Found at i:80974 original size:16 final size:16
Alignment explanation
Indices: 80953--80984 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
80943 TCAAAGTTAG
80953 TTTTTTTAGTTTAATA
1 TTTTTTTAGTTTAATA
80969 TTTTTTTAGTTTAATA
1 TTTTTTTAGTTTAATA
80985 CTAACATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (16 bp):
TTTTTTTAGTTTAATA
Found at i:82131 original size:2 final size:2
Alignment explanation
Indices: 82124--82155 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
82114 AATGAGTAGA
82124 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
82156 GTATTAAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:87347 original size:55 final size:55
Alignment explanation
Indices: 87087--87404 Score: 386
Period size: 55 Copynumber: 5.7 Consensus size: 55
87077 TTTATACAGC
* * **
87087 TAGTATGAATTTCCT-AGTTTTTCACATAAAGTGCCCATACAAAAATTCATCCACT
1 TAGTATGAATTTCTTAAG-TTTACACATAAAGTGCCCATACGGAAATTCATCCACT
* ** *
87142 TAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACGAAAATTCATAAACA
1 TAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACGGAAATTCATCCACT
* * * * * *
87197 AATTATGAATTTATTAAGTTTACACATAAAGTGTCCATTCAGAAATTCATCCACT
1 TAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACGGAAATTCATCCACT
87252 TAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACGGAAATTCATCCACT
1 TAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACGGAAATTCATCCACT
* * ** *
87307 TAGTATGAATTTCTTAAGTTTACACATAAAGTGGCCATACGGAAATCCATAAACA
1 TAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACGGAAATTCATCCACT
* * * * *
87362 AATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCATACG
1 TAGTATGAATTTCTTAA--GTTTACACATAAAGTGCCCATACG
87405 ATAATCACCA
Statistics
Matches: 227, Mismatches: 33, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
55 205 0.90
56 2 0.01
57 20 0.09
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (55 bp):
TAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACGGAAATTCATCCACT
Found at i:89408 original size:66 final size:66
Alignment explanation
Indices: 89299--89584 Score: 328
Period size: 66 Copynumber: 4.3 Consensus size: 66
89289 ATTGAGAGTC
** *
89299 ATAGGTGCA-TATCGGCATAAAAGGTGTAACTAATGAAATTTATCGATCGATTTTGATTAATGCA
1 ATAGG-GCATTATCGGCATAAAAGGTGCCACTAATGAAAATTATCGATCGATTTTGATTAATGCA
89363 TA
65 TA
* * * * *
89365 ATAGGGTATTATTGGCATAAAATGTGCTACTAATGAAAATTATCGATCGA-TTTGATTAATGCAA
1 ATAGGGCATTATCGGCATAAAAGGTGCCACTAATGAAAATTATCGATCGATTTTGATTAATGCAT
89429 A
66 A
* * * *
89430 AT-GATGCAATATCGGCATAAAAGCTGCCACTAATGAAAATTATCGATCGATTTTGATTAATACA
1 ATAG-GGCATTATCGGCATAAAAGGTGCCACTAATGAAAATTATCGATCGATTTTGATTAATGCA
89494 TA
65 TA
* * ** *
89496 A-CGGTGCATTACCTACATAAAAGGAGCCACTAATGAAAATTATCGATCGATTTTGATTAATGCA
1 ATAGG-GCATTATCGGCATAAAAGGTGCCACTAATGAAAATTATCGATCGATTTTGATTAATGCA
*
89560 TC
65 TA
* * *
89562 ACAGTGAATTATCGGCATAAAAG
1 ATAGGGCATTATCGGCATAAAAG
89585 CTGCATGATA
Statistics
Matches: 183, Mismatches: 31, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
64 1 0.01
65 57 0.31
66 124 0.68
67 1 0.01
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (66 bp):
ATAGGGCATTATCGGCATAAAAGGTGCCACTAATGAAAATTATCGATCGATTTTGATTAATGCAT
A
Found at i:89541 original size:131 final size:130
Alignment explanation
Indices: 89307--89589 Score: 358
Period size: 131 Copynumber: 2.2 Consensus size: 130
89297 TCATAGGTGC
* * * * *
89307 ATATCGGCATAAAAGGTGTAACTAATGAAATTTATCGATCGATTTTGATTAATGCATAATAGGGT
1 ATATCGGCATAAAAGCTGCAACTAATGAAAATTATCGATCGATTTTGATTAATACATAATAGGGC
* * * * *
89372 ATTATTGGCATAAAATGTGCTACTAATGAAAATTATCGATCGA-TTTGATTAATGCA-AAATGAT
66 ATTACTGACATAAAAGGAGCCACTAATGAAAATTATCGATCGATTTTGATTAATGCACAAA-G-T
89435 GCA
129 G-A
* *
89438 ATATCGGCATAAAAGCTGCCACTAATGAAAATTATCGATCGATTTTGATTAATACATAA-CGGTG
1 ATATCGGCATAAAAGCTGCAACTAATGAAAATTATCGATCGATTTTGATTAATACATAATAGG-G
*
89502 CATTACCT-ACATAAAAGGAGCCACTAATGAAAATTATCGATCGATTTTGATTAATGCATCACAG
65 CATTA-CTGACATAAAAGGAGCCACTAATGAAAATTATCGATCGATTTTGATTAATGCA-CAAAG
89566 TGA
128 TGA
89569 ATTATCGGCATAAAAGCTGCA
1 A-TATCGGCATAAAAGCTGCA
89590 TGATACAAGT
Statistics
Matches: 132, Mismatches: 14, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
130 2 0.02
131 93 0.70
132 34 0.26
133 1 0.01
134 2 0.02
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (130 bp):
ATATCGGCATAAAAGCTGCAACTAATGAAAATTATCGATCGATTTTGATTAATACATAATAGGGC
ATTACTGACATAAAAGGAGCCACTAATGAAAATTATCGATCGATTTTGATTAATGCACAAAGTGA
Found at i:94000 original size:19 final size:19
Alignment explanation
Indices: 93976--94020 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
93966 AATAGCCATA
93976 GTGCATCGATACATGGCTG
1 GTGCATCGATACATGGCTG
*
93995 GTGCATCGATGCATGGCTG
1 GTGCATCGATACATGGCTG
94014 GTGCATC
1 GTGCATC
94021 AAATGCATTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.18, C:0.22, G:0.33, T:0.27
Consensus pattern (19 bp):
GTGCATCGATACATGGCTG
Found at i:94067 original size:76 final size:76
Alignment explanation
Indices: 93939--94085 Score: 183
Period size: 76 Copynumber: 1.9 Consensus size: 76
93929 AGTGCATCGA
* *
93939 TGCATCAAGTGCATTTTGATGTTTCAAAATAGCCATAGTGCATCGATACATGGCT-GGTGCATCG
1 TGCATCAAATGCATTTCGATGTTTCAAAATAGCCATAGTGCATCGATACATGG-TAGGTGCATCG
94003 ATGCATGGCTGG
65 ATGCATGGCTGG
* * * * *
94015 TGCATCAAATGCA-TTCGATGTTTTCATAAA-ATCCTTAGTGCATCGGTGCATGGTATGTGCATC
1 TGCATCAAATGCATTTCGATG-TTTCA-AAATAGCCATAGTGCATCGATACATGGTAGGTGCATC
94078 GATGCATG
64 GATGCATG
94086 AAATGCATTC
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
75 7 0.11
76 51 0.84
77 3 0.05
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.32
Consensus pattern (76 bp):
TGCATCAAATGCATTTCGATGTTTCAAAATAGCCATAGTGCATCGATACATGGTAGGTGCATCGA
TGCATGGCTGG
Found at i:94590 original size:2 final size:2
Alignment explanation
Indices: 94583--94613 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
94573 AATTGATTAA
94583 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
94614 GCTTAAGTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:95225 original size:21 final size:21
Alignment explanation
Indices: 95201--95244 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
95191 CCGAAGGAGG
*
95201 AGGAGGAGCACGAGAAGAGCT
1 AGGAGCAGCACGAGAAGAGCT
* *
95222 AGGAGCAGCTCGTGAAGAGCT
1 AGGAGCAGCACGAGAAGAGCT
95243 AG
1 AG
95245 CTCCTGAGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.16, G:0.41, T:0.09
Consensus pattern (21 bp):
AGGAGCAGCACGAGAAGAGCT
Found at i:97577 original size:17 final size:17
Alignment explanation
Indices: 97552--97591 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
97542 GCTAAACTAG
*
97552 AGTCTTTAGGATACCAA
1 AGTCCTTAGGATACCAA
97569 AGTCCTTAGGATACCAA
1 AGTCCTTAGGATACCAA
97586 AGTCCT
1 AGTCCT
97592 AAACTAGGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.28
Consensus pattern (17 bp):
AGTCCTTAGGATACCAA
Found at i:100670 original size:22 final size:21
Alignment explanation
Indices: 100628--100667 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
100618 GAGTTTATTT
*
100628 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
100649 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
100668 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:102753 original size:65 final size:64
Alignment explanation
Indices: 102612--102771 Score: 180
Period size: 65 Copynumber: 2.5 Consensus size: 64
102602 TTCACTAAAA
* * *
102612 GTGCATTGATGCATCAAGTGCATTCGATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGAAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGAAT
* * * * * * *
102675 GTTGCATCAATGCATCAAATCCATTCGATGTTTTCATAAA-ATCCTCAGTGTATCGGTGCATGGT
1 G-TGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAGCCACAGTGCATCGATGCAT-GA
102739 AT
63 AT
*
102741 GTGCATCGATGCATGAAATGCATTCGATGTT
1 GTGCATCGATGCATCAAATGCATTCGATGTT
102772 CAATTTAATT
Statistics
Matches: 80, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
63 1 0.01
64 24 0.30
65 48 0.60
66 7 0.09
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGAAT
Found at i:104663 original size:66 final size:66
Alignment explanation
Indices: 104463--104667 Score: 295
Period size: 66 Copynumber: 3.1 Consensus size: 66
104453 GATCGCATTA
* * * * *
104463 GTGCAACTAATGAAAATTATCAATCTATTTTAATTAATGTATAATGGTGCATTATCGGCATAAAA
1 GTGCCACTAATGAAAATTATCGATCGATTTTGATTAATGCATAATGGTGCATTATCGGCATAAAA
104528 G
66 G
* * *
104529 GTGCCTCTAATGAAAATTATTGATTGA-TTTGATTAATGCATAATGGTGCATTATCGGCATAAAA
1 GTGCCACTAATGAAAATTATCGATCGATTTTGATTAATGCATAATGGTGCATTATCGGCATAAAA
104593 G
66 G
* * * *
104594 GTGCCACTAATGAAAATTATCGATCGATTTTGTTTAATGCATAATGGTGCATAATCGACATAAAC
1 GTGCCACTAATGAAAATTATCGATCGATTTTGATTAATGCATAATGGTGCATTATCGGCATAAAA
104659 G
66 G
104660 GTGCCACT
1 GTGCCACT
104668 CATGGTATTA
Statistics
Matches: 123, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
65 60 0.49
66 63 0.51
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Consensus pattern (66 bp):
GTGCCACTAATGAAAATTATCGATCGATTTTGATTAATGCATAATGGTGCATTATCGGCATAAAA
G
Found at i:109273 original size:16 final size:17
Alignment explanation
Indices: 109254--109285 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
109244 TTTGGAGAAT
109254 TAAATTA-AATAAATGA
1 TAAATTATAATAAATGA
109270 TAAATTATAATAAATG
1 TAAATTATAATAAATG
109286 GTTTAGAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.34
Consensus pattern (17 bp):
TAAATTATAATAAATGA
Found at i:110723 original size:66 final size:66
Alignment explanation
Indices: 110619--110969 Score: 438
Period size: 66 Copynumber: 5.3 Consensus size: 66
110609 GGTGATACTA
110619 GCATAAAAGGTGCCACTAAT-AAAATTATCGAT-AGATTTTGATTAATGCATAACGGTGCATTAT
1 GCATAAAAGGTGCCACTAATGAAAATTATCGATCA-ATTTTGATTAATGCATAACGGTGCATTAT
110682 TG
65 TG
* * * * *
110684 GCATAAAATGTGCTACTAATGAAAATTATCGATCAATTTTGATTAGTACATAACGGTGCATTATC
1 GCATAAAAGGTGCCACTAATGAAAATTATCGATCAATTTTGATTAATGCATAACGGTGCATTATT
110749 G
66 G
* * * * * * *
110750 ACATAAAAGGTACCACTAATGAAAATTATCAATCGATTTTGATTAATTCATAATGGTACATTATT
1 GCATAAAAGGTGCCACTAATGAAAATTATCGATCAATTTTGATTAATGCATAACGGTGCATTATT
110815 G
66 G
*
110816 GCATAAAAGGTTCCACTAATGAAAATTATCGATCAATTTTGATTAATGCATAACGGTGCATT-TT
1 GCATAAAAGGTGCCACTAATGAAAATTATCGATCAATTTTGATTAATGCATAACGGTGCATTATT
110880 CG
66 -G
* * * * * * * * ** *
110882 ACGTAAAATGTGCCACTAATGAAAATTATCGACCGATTTTGTTTAATGCATGACAGTTTATTATC
1 GCATAAAAGGTGCCACTAATGAAAATTATCGATCAATTTTGATTAATGCATAACGGTGCATTATT
110947 G
66 G
*
110948 GCATAAAAAGTGCCACTAATGA
1 GCATAAAAGGTGCCACTAATGA
110970 TATTCATAAA
Statistics
Matches: 244, Mismatches: 38, Indels: 7
0.84 0.13 0.02
Matches are distributed among these distances:
65 20 0.08
66 222 0.91
67 2 0.01
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (66 bp):
GCATAAAAGGTGCCACTAATGAAAATTATCGATCAATTTTGATTAATGCATAACGGTGCATTATT
G
Found at i:110876 original size:132 final size:132
Alignment explanation
Indices: 110620--110969 Score: 495
Period size: 132 Copynumber: 2.7 Consensus size: 132
110610 GTGATACTAG
* *
110620 CATAAAAGGTGCCACTAAT-AAAATTATCGATAGATTTTGATTAATGCATAACGGTGCATTATTG
1 CATAAAAGGTGCCACTAATGAAAATTATCGATCGATTTTGATTAATGCATAACGGTACATTATTG
* * *
110684 GCATAAAATGTGCTACTAATGAAAATTATCGATCAATTTTGATTAGTACATAACGGTGCATTATC
66 GCATAAAAAGTGCCACTAATGAAAATTATCGATCAATTTTGATTAATACATAACGGTGCATTATC
110749 GA
131 GA
* * * *
110751 CATAAAAGGTACCACTAATGAAAATTATCAATCGATTTTGATTAATTCATAATGGTACATTATTG
1 CATAAAAGGTGCCACTAATGAAAATTATCGATCGATTTTGATTAATGCATAACGGTACATTATTG
* * * *
110816 GCATAAAAGGTTCCACTAATGAAAATTATCGATCAATTTTGATTAATGCATAACGGTGCATTTTC
66 GCATAAAAAGTGCCACTAATGAAAATTATCGATCAATTTTGATTAATACATAACGGTGCATTATC
110881 GA
131 GA
* * * * * * ** *
110883 CGTAAAATGTGCCACTAATGAAAATTATCGACCGATTTTGTTTAATGCATGACAGTTTATTATCG
1 CATAAAAGGTGCCACTAATGAAAATTATCGATCGATTTTGATTAATGCATAACGGTACATTATTG
110948 GCATAAAAAGTGCCACTAATGA
66 GCATAAAAAGTGCCACTAATGA
110970 TATTCATAAA
Statistics
Matches: 191, Mismatches: 27, Indels: 1
0.87 0.12 0.00
Matches are distributed among these distances:
131 18 0.09
132 173 0.91
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (132 bp):
CATAAAAGGTGCCACTAATGAAAATTATCGATCGATTTTGATTAATGCATAACGGTACATTATTG
GCATAAAAAGTGCCACTAATGAAAATTATCGATCAATTTTGATTAATACATAACGGTGCATTATC
GA
Found at i:115819 original size:24 final size:24
Alignment explanation
Indices: 115792--115856 Score: 112
Period size: 24 Copynumber: 2.7 Consensus size: 24
115782 TACTAGGACT
*
115792 TGTTGGAGGTGGACTTGTTGGAGG
1 TGTTAGAGGTGGACTTGTTGGAGG
115816 TGTTAGAGGTGGACTTGTTGGAGG
1 TGTTAGAGGTGGACTTGTTGGAGG
*
115840 TGTTAGAGGTGCACTTG
1 TGTTAGAGGTGGACTTG
115857 CTACAAGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.15, C:0.06, G:0.45, T:0.34
Consensus pattern (24 bp):
TGTTAGAGGTGGACTTGTTGGAGG
Found at i:115841 original size:15 final size:15
Alignment explanation
Indices: 115787--115817 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
115777 TGGCCTACTA
115787 GGACTTGTTGGAGGT
1 GGACTTGTTGGAGGT
115802 GGACTTGTTGGAGGT
1 GGACTTGTTGGAGGT
115817 G
1 G
115818 TTAGAGGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.06, G:0.48, T:0.32
Consensus pattern (15 bp):
GGACTTGTTGGAGGT
Found at i:119468 original size:21 final size:21
Alignment explanation
Indices: 119444--119523 Score: 90
Period size: 21 Copynumber: 3.7 Consensus size: 21
119434 TTTTCGTAAA
119444 AGTACTTTGTGTACTTGGAGT
1 AGTACTTTGTGTACTTGGAGT
*
119465 AGTAATTTGTGTACTATGGCAAG-
1 AGTACTTTGTGTACT-TGG--AGT
* **
119488 AGTACTTTCTGTACTTATAGT
1 AGTACTTTGTGTACTTGGAGT
119509 AGTACTTTGTGTACT
1 AGTACTTTGTGTACT
119524 ATGGCACTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
20 2 0.04
21 28 0.57
22 4 0.08
23 13 0.27
24 2 0.04
ACGTcount: A:0.24, C:0.11, G:0.23, T:0.42
Consensus pattern (21 bp):
AGTACTTTGTGTACTTGGAGT
Found at i:119510 original size:44 final size:44
Alignment explanation
Indices: 119444--119529 Score: 136
Period size: 44 Copynumber: 2.0 Consensus size: 44
119434 TTTTCGTAAA
* *
119444 AGTACTTTGTGTACTTGGAGTAGTAATTTGTGTACTATGGCAAG
1 AGTACTTTCTGTACTTAGAGTAGTAATTTGTGTACTATGGCAAG
* *
119488 AGTACTTTCTGTACTTATAGTAGTACTTTGTGTACTATGGCA
1 AGTACTTTCTGTACTTAGAGTAGTAATTTGTGTACTATGGCA
119530 CTTTGTGTGC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.24, C:0.12, G:0.23, T:0.41
Consensus pattern (44 bp):
AGTACTTTCTGTACTTAGAGTAGTAATTTGTGTACTATGGCAAG
Found at i:119975 original size:23 final size:21
Alignment explanation
Indices: 119926--120001 Score: 116
Period size: 21 Copynumber: 3.5 Consensus size: 21
119916 TTTCTTATGG
119926 GTACTTTGTGTACTTGGAGTA
1 GTACTTTGTGTACTTGGAGTA
*
119947 GTACTTTGTGTACTATGGCAATA
1 GTACTTTGTGTACT-TGG-AGTA
*
119970 GTACTTTGTGTACTTGTAGTA
1 GTACTTTGTGTACTTGGAGTA
119991 GTACTTTGTGT
1 GTACTTTGTGT
120002 GCAAGGATGG
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
21 28 0.56
22 5 0.10
23 17 0.34
ACGTcount: A:0.20, C:0.11, G:0.25, T:0.45
Consensus pattern (21 bp):
GTACTTTGTGTACTTGGAGTA
Found at i:128420 original size:9 final size:10
Alignment explanation
Indices: 128401--128444 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
128391 TTTGGACCAG
128401 AAAAATAAAA
1 AAAAATAAAA
128411 AAAAATAAAAA
1 AAAAAT-AAAA
* *
128422 AAAAATACAT
1 AAAAATAAAA
*
128432 AGAAATAAAA
1 AAAAATAAAA
128442 AAA
1 AAA
128445 TATGTATACT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
10 17 0.63
11 10 0.37
ACGTcount: A:0.84, C:0.02, G:0.02, T:0.11
Consensus pattern (10 bp):
AAAAATAAAA
Found at i:128426 original size:21 final size:21
Alignment explanation
Indices: 128401--128444 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
128391 TTTGGACCAG
128401 AAAAATAAAAAAAAATAAAAA
1 AAAAATAAAAAAAAATAAAAA
* * *
128422 AAAAATACATAGAAATAAAAA
1 AAAAATAAAAAAAAATAAAAA
128443 AA
1 AA
128445 TATGTATACT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.84, C:0.02, G:0.02, T:0.11
Consensus pattern (21 bp):
AAAAATAAAAAAAAATAAAAA
Found at i:128717 original size:38 final size:37
Alignment explanation
Indices: 128474--128759 Score: 236
Period size: 38 Copynumber: 7.8 Consensus size: 37
128464 ATATTTCGAA
*
128474 AAAAATTG-TTTCTAAA--ATATATTATATATATTTTC
1 AAAAATTGTTTTCAAAACTATATATTATATAT-TTTTC
* *
128509 TAAAAA-TGTTTT--AAACTATATATTATACATAATTTC
1 -AAAAATTGTTTTCAAAACTATATATTATATAT-TTTTC
* *
128545 ATAAAA-TGTTTTCAAAATTATATATTATATTTTTTTTTTC
1 A-AAAATTGTTTTCAAAACTATATATTATA---TATTTTTC
* * *
128585 AAAAATGTTTTTTTAAAACCATATATTATATATTTTT-
1 AAAAAT-TGTTTTCAAAACTATATATTATATATTTTTC
* * *
128622 -AAAA-TGTTTTCAAAATTCTATA-T-TATATTTTTA
1 AAAAATTGTTTTCAAAACTATATATTATATATTTTTC
** * * *
128655 AAAAAACGTTTACAAATCTTATATATTATGTATGTTTTC
1 AAAAATTGTTTTCAAAAC-TATATATTATATAT-TTTTC
*
128694 AAAAATTGTTTTCAAAACGATATATTATATATTTTTTC
1 AAAAATTGTTTTCAAAACTATATATTATATA-TTTTTC
128732 AAAAATTGTTTTCAAAACTATATATTAT
1 AAAAATTGTTTTCAAAACTATATATTAT
128760 GTATATATTA
Statistics
Matches: 201, Mismatches: 30, Indels: 36
0.75 0.11 0.13
Matches are distributed among these distances:
32 9 0.04
33 1 0.00
34 20 0.10
35 11 0.05
36 44 0.22
37 1 0.00
38 67 0.33
39 23 0.11
40 5 0.02
41 20 0.10
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.49
Consensus pattern (37 bp):
AAAAATTGTTTTCAAAACTATATATTATATATTTTTC
Found at i:128718 original size:74 final size:72
Alignment explanation
Indices: 128546--128763 Score: 181
Period size: 75 Copynumber: 3.0 Consensus size: 72
128536 CATAATTTCA
** * ** * ** *
128546 TAAAATGTTTTCAAAATTATATATTATATTTTTTTTTTCAAAAATGTTTTTTTAAAACCATATAT
1 TAAAATGTTTTCAAAACGATATATTATA-TATTTTTTAAAAAAACG--TTTACAAAACTATATAT
*
128611 TATATATTTT
63 TATGTATTTT
*** *
128621 TAAAATGTTTTCAAAATTCTATA-T-TATA-TTTTTAAAAAAACGTTTACAAATCTTATATATTA
1 TAAAATGTTTTCAAAACGATATATTATATATTTTTTAAAAAAACGTTTACAAAAC-TATATATTA
128683 TGTATGTTT
65 TGTAT-TTT
* ** *
128692 TCAAAAATTGTTTTCAAAACGATATATTATATATTTTTTCAAAAATTGTTTTCAAAACTATATAT
1 T--AAAA-TGTTTTCAAAACGATATATTATATATTTTTTAAAAAAACGTTTACAAAACTATATAT
128757 TATGTAT
63 TATGTAT
128764 ATATTAAATA
Statistics
Matches: 117, Mismatches: 18, Indels: 15
0.78 0.12 0.10
Matches are distributed among these distances:
69 7 0.06
70 12 0.10
71 15 0.13
72 1 0.01
73 6 0.05
74 16 0.14
75 23 0.20
76 18 0.15
77 19 0.16
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.50
Consensus pattern (72 bp):
TAAAATGTTTTCAAAACGATATATTATATATTTTTTAAAAAAACGTTTACAAAACTATATATTAT
GTATTTT
Found at i:129530 original size:23 final size:23
Alignment explanation
Indices: 129472--129530 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 23
129462 ACCTTATTTA
* *
129472 GCACTTCGGTGTATTTCTACGCG
1 GCACTTCGGTGCAATTCTACGCG
* *
129495 GCACTAT-GATGCAATTCTACGTG
1 GCACT-TCGGTGCAATTCTACGCG
*
129518 TCACTTCGGTGCA
1 GCACTTCGGTGCA
129531 TTTATACGAG
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
22 1 0.04
23 26 0.93
24 1 0.04
ACGTcount: A:0.19, C:0.25, G:0.24, T:0.32
Consensus pattern (23 bp):
GCACTTCGGTGCAATTCTACGCG
Found at i:129800 original size:16 final size:17
Alignment explanation
Indices: 129779--129812 Score: 52
Period size: 16 Copynumber: 2.0 Consensus size: 17
129769 TTTGTTATAA
129779 GTAAGAGA-ATATGAAT
1 GTAAGAGACATATGAAT
129795 GTAAGAGATCATATGAAT
1 GTAAGAGA-CATATGAAT
129813 AAGAAATAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
18 8 0.50
ACGTcount: A:0.47, C:0.03, G:0.24, T:0.26
Consensus pattern (17 bp):
GTAAGAGACATATGAAT
Found at i:133104 original size:20 final size:20
Alignment explanation
Indices: 133079--133136 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
133069 CACATGTTAA
*
133079 AGAATGCATCGATGCACTGT
1 AGAATGCATCGATGCACTAT
133099 AGAATGCATCGATGCACTAT
1 AGAATGCATCGATGCACTAT
133119 AGAATGCATCGATGCACT
1 AGAATGCATCGATGCACT
133137 TCAAGGGGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.24
Consensus pattern (20 bp):
AGAATGCATCGATGCACTAT
Found at i:134919 original size:23 final size:23
Alignment explanation
Indices: 134886--134953 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
134876 AACCTTATAT
134886 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * *
134909 GGCACTACGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
*
134932 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
134954 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.29
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:136779 original size:16 final size:16
Alignment explanation
Indices: 136760--136806 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
136750 AGAATAAAAC
*
136760 AAATGAAAAATAAATT
1 AAATAAAAAATAAATT
* *
136776 AAATTAAATATAAATT
1 AAATAAAAAATAAATT
136792 AAACTAAAAAATAAA
1 AAA-TAAAAAATAAA
136807 ATAACATTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
16 17 0.65
17 9 0.35
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (16 bp):
AAATAAAAAATAAATT
Found at i:137591 original size:21 final size:22
Alignment explanation
Indices: 137544--137592 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
137534 TAAGCCCCCA
* * *
137544 TCGGGGTCGTTCCCGATTGCTT
1 TCGGGGTCATTCCCGAGTGATT
137566 T-GGGGTCATTCCCG-GTGATT
1 TCGGGGTCATTCCCGAGTGATT
137586 TCGGGGT
1 TCGGGGT
137593 TTTTTGCCCT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 5 0.22
21 17 0.74
22 1 0.04
ACGTcount: A:0.06, C:0.22, G:0.37, T:0.35
Consensus pattern (22 bp):
TCGGGGTCATTCCCGAGTGATT
Found at i:137956 original size:2 final size:2
Alignment explanation
Indices: 137951--137982 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
137941 GTATACTACA
137951 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
137983 TTTGAAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:138074 original size:37 final size:38
Alignment explanation
Indices: 138022--138100 Score: 106
Period size: 37 Copynumber: 2.1 Consensus size: 38
138012 TTTTTCTAAA
* * *
138022 ATATATTATATATAATTTCCAAAAACGTTTT-AAAACT
1 ATATACTATACATAATTTCAAAAAACGTTTTCAAAACT
* *
138059 ATATACTATACATAATTTCAAAAAATGTTTTCAAAATT
1 ATATACTATACATAATTTCAAAAAACGTTTTCAAAACT
138097 ATAT
1 ATAT
138101 GTTGTATATA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
37 27 0.75
38 9 0.25
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.41
Consensus pattern (38 bp):
ATATACTATACATAATTTCAAAAAACGTTTTCAAAACT
Found at i:138171 original size:144 final size:143
Alignment explanation
Indices: 138013--138278 Score: 324
Period size: 144 Copynumber: 1.9 Consensus size: 143
138003 ACCCAACATT
* *
138013 TTTTCTAAAATATATTATATATAATTTCCAAAAACGTTTT-AAAAC-TATATACTATACAT-AAT
1 TTTTCTAAAATATA-TAT-TATAATTTCAAAAAACATTTTAAAAACTTATATACTATACATGAAT
* * * *
138075 TTCAAAAAATGTTTTCAAAATTATATGTTGTATATATTTTTTTAAAAATGCTTTTTAAAACCATA
64 TTCAAAAAATGTTTTCAAAACTATATATTATATATA-TTTTTTAAAAATG-TTTTCAAAACCATA
138140 AATATATTTTTAAAATA
127 AATATATTTTTAAAATA
* * * * **
138157 TTTTC-AAAATTATATATTATATTTTTAAAAAACATTTTAAAAACTTATATATTATATATGTTTT
1 TTTTCTAAAA-TATATATTATAATTTCAAAAAACATTTTAAAAACTTATATACTATACATGAATT
** *
138221 TTGAAAAATGTTTTCAAAACTATATATTATATATATTTTTTAAAATTGTTTTCAAAAC
65 TCAAAAAATGTTTTCAAAACTATATATTATATATATTTTTTAAAAATGTTTTCAAAAC
138279 TATATATTAT
Statistics
Matches: 103, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
142 17 0.17
143 21 0.20
144 33 0.32
145 32 0.31
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (143 bp):
TTTTCTAAAATATATATTATAATTTCAAAAAACATTTTAAAAACTTATATACTATACATGAATTT
CAAAAAATGTTTTCAAAACTATATATTATATATATTTTTTAAAAATGTTTTCAAAACCATAAATA
TATTTTTAAAATA
Found at i:138212 original size:35 final size:32
Alignment explanation
Indices: 138142--138213 Score: 99
Period size: 34 Copynumber: 2.2 Consensus size: 32
138132 AAACCATAAA
* *
138142 TATATTTTTAAAATATTTTCAAAATTATATAT
1 TATATTTTTAAAACATTTTAAAAATTATATAT
138174 TATATTTTTAAAAAACATTTTAAAAACTTATATAT
1 TATATTTTT--AAAACATTTTAAAAA-TTATATAT
138209 TATAT
1 TATAT
138214 ATGTTTTTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
32 9 0.26
34 13 0.37
35 13 0.37
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (32 bp):
TATATTTTTAAAACATTTTAAAAATTATATAT
Found at i:138271 original size:38 final size:38
Alignment explanation
Indices: 138022--138292 Score: 233
Period size: 38 Copynumber: 7.3 Consensus size: 38
138012 TTTTTCTAAA
* ** *
138022 ATATATTATATATAATTTCCAAAAACGTTTT-AAAACT
1 ATATATTATATATATTTTTTAAAAATGTTTTCAAAACT
* * * ** *
138059 ATATACTATACATAATTTCAAAAAATGTTTTCAAAATT
1 ATATATTATATATATTTTTTAAAAATGTTTTCAAAACT
* * *
138097 ATATGTTGTATATATTTTTTTAAAAATGCTTTTTAAAAC-
1 ATATATTATATATA-TTTTTTAAAAATG-TTTTCAAAACT
* *
138136 -CATA--A-ATATA-TTTTT-AAAATATTTTCAAAA-T
1 ATATATTATATATATTTTTTAAAAATGTTTTCAAAACT
* ** *
138167 -TATA-TAT-TATATTTTTAAAAAACATTTTAAAAACTT
1 ATATATTATATATATTTTTTAAAAATGTTTTCAAAAC-T
*
138203 ATATATTATATATGTTTTTTGAAAAATGTTTTCAAAACT
1 ATATATTATATATATTTTTT-AAAAATGTTTTCAAAACT
*
138242 ATATATTATATATATTTTTTAAAATTGTTTTCAAAACT
1 ATATATTATATATATTTTTTAAAAATGTTTTCAAAACT
138280 ATATATTATATAT
1 ATATATTATATAT
138293 TATGTATATA
Statistics
Matches: 190, Mismatches: 30, Indels: 27
0.77 0.12 0.11
Matches are distributed among these distances:
31 11 0.06
32 10 0.05
33 9 0.05
34 13 0.07
35 5 0.03
36 1 0.01
37 31 0.16
38 50 0.26
39 38 0.20
40 22 0.12
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (38 bp):
ATATATTATATATATTTTTTAAAAATGTTTTCAAAACT
Found at i:138625 original size:23 final size:22
Alignment explanation
Indices: 138570--138630 Score: 72
Period size: 23 Copynumber: 2.8 Consensus size: 22
138560 TTTCGTAAGG
138570 GTACTTTGTGTACT-TGGAGTA
1 GTACTTTGTGTACTATGGAGTA
**
138591 GTTGTTTGTGTACTATGGCTAG-A
1 GTACTTTGTGTACTATGG--AGTA
138614 GTACTTTGTGTACTATG
1 GTACTTTGTGTACTATG
138631 TCACTTTGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 12 0.36
22 3 0.09
23 16 0.48
24 2 0.06
ACGTcount: A:0.18, C:0.10, G:0.28, T:0.44
Consensus pattern (22 bp):
GTACTTTGTGTACTATGGAGTA
Found at i:138827 original size:21 final size:23
Alignment explanation
Indices: 138800--138846 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 23
138790 ATTGTTTCGC
138800 TTATGATTTGGAATAAATGTTTA
1 TTATGATTTGGAATAAATGTTTA
138823 TTGATGATTTGGAATAAATGTTTA
1 TT-ATGATTTGGAATAAATGTTTA
138847 ACCTGTGGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 2 0.09
24 21 0.91
ACGTcount: A:0.34, C:0.00, G:0.19, T:0.47
Consensus pattern (23 bp):
TTATGATTTGGAATAAATGTTTA
Found at i:146256 original size:21 final size:22
Alignment explanation
Indices: 146232--146293 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 22
146222 TTTTCGTAAA
*
146232 AGTAATTTGTGTACT-TGG-AG
1 AGTACTTTGTGTACTATGGAAG
*
146252 TAGTACTTTTTGTACTATGGCAAG
1 -AGTACTTTGTGTACTATGG-AAG
146276 AGTACTTTGTGTACTATG
1 AGTACTTTGTGTACTATG
146294 ACACTTTGTG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 13 0.37
22 3 0.09
23 17 0.49
24 2 0.06
ACGTcount: A:0.24, C:0.10, G:0.24, T:0.42
Consensus pattern (22 bp):
AGTACTTTGTGTACTATGGAAG
Found at i:148589 original size:21 final size:21
Alignment explanation
Indices: 148564--148603 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
148554 AAGACTTTAT
148564 TTTCAAAA-TACAAAAATGATA
1 TTTCAAAATTA-AAAAATGATA
148585 TTTCAAAATTAAAAAATGA
1 TTTCAAAATTAAAAAATGA
148604 AAATAGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.57, C:0.07, G:0.05, T:0.30
Consensus pattern (21 bp):
TTTCAAAATTAAAAAATGATA
Found at i:149773 original size:12 final size:12
Alignment explanation
Indices: 149758--149789 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
149748 TTCTCTTATA
149758 TTTTCTTCTCAT
1 TTTTCTTCTCAT
149770 TTTTCTTCTCAT
1 TTTTCTTCTCAT
149782 TTTTCTTC
1 TTTTCTTC
149790 AAAATCAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.06, C:0.25, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTTCTTCTCAT
Found at i:159300 original size:24 final size:24
Alignment explanation
Indices: 159263--159314 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
159253 CTTGGGACTC
* *
159263 CAAATCAACAAAAGAAAAGATTGT
1 CAAATCAACAAAAGAAAAAATTGA
159287 CAAATCAAGC-AAAGAAAAAATTGA
1 CAAATCAA-CAAAAGAAAAAATTGA
159311 CAAA
1 CAAA
159315 AGCACTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 24 0.96
25 1 0.04
ACGTcount: A:0.62, C:0.13, G:0.12, T:0.13
Consensus pattern (24 bp):
CAAATCAACAAAAGAAAAAATTGA
Found at i:159562 original size:317 final size:317
Alignment explanation
Indices: 158987--159600 Score: 1097
Period size: 317 Copynumber: 1.9 Consensus size: 317
158977 TTATGTTTTT
* * * *
158987 AAATTGATAAAATCACTTTATGGTTTAAAACAAGCTCTAAGAGCTTTGTATGAAACATTGTCAAA
1 AAATTGACAAAAGCACTTTATGGTTTAAAACAAGCTCCAAGAGCTTGGTATGAAACATTGTCAAA
* *
159052 CTTTTTAATTAAAAAAGATTTTTCAAAAGGGAAGGTTGACACTACATTGTTTTTAAATCATAAAG
66 CTTTTTAATTAAAAAAGATTTTTCAAAAGGGAAGGTTGAAACTACATTGTTTTTAAAGCATAAAG
159117 GTAAAGATTTATTAGTAGTTCAAATTTATGTCGATGATATAATATTTGGTTCTACTAATGATGCT
131 GTAAAGATTTATTAGTAGTTCAAATTTATGTCGATGATATAATATTTGGTTCTACTAATGATGCT
*
159182 CTTTGCCAAGAATTTTCTAAGCTAATGCAAGGTGAATTCGAGATGAGCATGATGGTGGAGCTCTC
196 CTTTGCCAAGAATTTTCTAAGCTAACGCAAGGTGAATTCGAGATGAGCATGATGGTGGAGCTCTC
159247 ATTTTTCTTGGGACTCCAAATCAA-CAAAAGAAAAGATTGTCAAATCAAGCAAAGAAA
261 ATTTTTCTTGGGACTCCAAATCAAGC-AAAGAAAAGATTGTCAAATCAAGCAAAGAAA
*
159304 AAATTGACAAAAGCACTTTATGGTTTAAAACAAGCTCCAAGAGCTTGGTATGAAAGATTGTCAAA
1 AAATTGACAAAAGCACTTTATGGTTTAAAACAAGCTCCAAGAGCTTGGTATGAAACATTGTCAAA
* *
159369 CTTTTTAATTGAAAAAGGTTTTTCAAAAGGGAAGGTTGAAACTACATTGTTTTTAAAGCATAAAG
66 CTTTTTAATTAAAAAAGATTTTTCAAAAGGGAAGGTTGAAACTACATTGTTTTTAAAGCATAAAG
159434 GTAAAGATTTATTAGTAGTTCAAATTTATGTCGATGATATAATATTTGGTTCTACTAATGATGCT
131 GTAAAGATTTATTAGTAGTTCAAATTTATGTCGATGATATAATATTTGGTTCTACTAATGATGCT
159499 CTTTGCCAAGAATTTTCTAAGCTAACGCAAGGTGAATTCGAGATGAGCATGATGAG-GGAGCTCT
196 CTTTGCCAAGAATTTTCTAAGCTAACGCAAGGTGAATTCGAGATGAGCATGATG-GTGGAGCTCT
*
159563 CATTTTTCTTGGGACTCCAAATCAAGCAAATAAAAGAT
260 CATTTTTCTTGGGACTCCAAATCAAGCAAAGAAAAGAT
159601 GGCATCTTCA
Statistics
Matches: 284, Mismatches: 11, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
317 282 0.99
318 2 0.01
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (317 bp):
AAATTGACAAAAGCACTTTATGGTTTAAAACAAGCTCCAAGAGCTTGGTATGAAACATTGTCAAA
CTTTTTAATTAAAAAAGATTTTTCAAAAGGGAAGGTTGAAACTACATTGTTTTTAAAGCATAAAG
GTAAAGATTTATTAGTAGTTCAAATTTATGTCGATGATATAATATTTGGTTCTACTAATGATGCT
CTTTGCCAAGAATTTTCTAAGCTAACGCAAGGTGAATTCGAGATGAGCATGATGGTGGAGCTCTC
ATTTTTCTTGGGACTCCAAATCAAGCAAAGAAAAGATTGTCAAATCAAGCAAAGAAA
Found at i:165224 original size:18 final size:17
Alignment explanation
Indices: 165170--165218 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
165160 TTGGATCCTT
* *
165170 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
165188 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
165206 AGTGCATTCGATG
1 AGTGCA-TCGATG
165219 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:165327 original size:64 final size:62
Alignment explanation
Indices: 165164--165328 Score: 154
Period size: 64 Copynumber: 2.6 Consensus size: 62
165154 TGACCGTTGG
* * *
165164 ATCCTTAGTGCATCGGTGCACT-AAGAGTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAAT
1 ATCCTCAGTGCATCGATGCA-TGAA-A-TGCATCGATGCATCAAATGCATTCGATGTTTCAAAAT
* ** * ***
165228 AGCCAGAGTGCATCAATGCATGGCTGGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA
1 ATCCTCAGTGCATCGATGCAT-G-AAATGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAA
165293 -
62 T
165293 ATCCTCAGTGCATCGATGCATGAAATGCATTCGATG
1 ATCCTCAGTGCATCGATGCATGAAATGCA-TCGATG
165329 TTCAATTTAT
Statistics
Matches: 79, Mismatches: 16, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
63 5 0.06
64 49 0.62
65 22 0.28
66 3 0.04
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.28
Consensus pattern (62 bp):
ATCCTCAGTGCATCGATGCATGAAATGCATCGATGCATCAAATGCATTCGATGTTTCAAAAT
Found at i:173168 original size:64 final size:63
Alignment explanation
Indices: 173100--173309 Score: 219
Period size: 65 Copynumber: 3.3 Consensus size: 63
173090 TGTACTAAGA
* *
173100 GTGCATCGATACATCAAGTGCATTCGATGTTTCAAAATATCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATATCCAGAGTGCATCGATGCATGG-TG
** * *
173164 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCGTCAATGCATGGTA
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATATCCAGAGTGCATCGATGCATGGT-
*
173228 T
63 G
* ** *
173229 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTATTTCATG-GTGCATCGATGCATGGAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATA-TCCA-GAGTGCATCGATGCATGG--
173292 TG
62 TG
*
173294 GTGAATCGATGCATCA
1 GTGCATCGATGCATCA
173310 CTCTGAAAAA
Statistics
Matches: 120, Mismatches: 18, Indels: 15
0.78 0.12 0.10
Matches are distributed among these distances:
62 1 0.01
63 5 0.04
64 44 0.37
65 66 0.55
66 4 0.03
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATATCCAGAGTGCATCGATGCATGGTG
Found at i:174608 original size:18 final size:18
Alignment explanation
Indices: 174585--174636 Score: 77
Period size: 18 Copynumber: 2.9 Consensus size: 18
174575 TAGGGTTATA
*
174585 GGTTGGTGATTGACTGAG
1 GGTTGGTGCTTGACTGAG
*
174603 GGTTGGTGCTTGACTAAG
1 GGTTGGTGCTTGACTGAG
*
174621 GGTTGTTGCTTGACTG
1 GGTTGGTGCTTGACTG
174637 TTGTAATCCC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.13, C:0.10, G:0.40, T:0.37
Consensus pattern (18 bp):
GGTTGGTGCTTGACTGAG
Found at i:174899 original size:18 final size:19
Alignment explanation
Indices: 174864--174910 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
174854 GCCTCTGCTG
174864 AAAAATAAA-AACAAAAAT
1 AAAAATAAATAACAAAAAT
*
174882 AAAAATAAATAA-ATAAAT
1 AAAAATAAATAACAAAAAT
174900 AGAAAA-AAATA
1 A-AAAATAAATA
174911 TGTATACTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 20 0.77
19 6 0.23
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.15
Consensus pattern (19 bp):
AAAAATAAATAACAAAAAT
Found at i:175141 original size:139 final size:139
Alignment explanation
Indices: 174956--175225 Score: 336
Period size: 139 Copynumber: 1.9 Consensus size: 139
174946 AAAACCCAAC
*
174956 ATGTTTTCTAAAATATATTATATATTTTTTGAAAAACGTTTTAAAAC-TATATATTATACATAAT
1 ATGTTTTCTAAAATATATTATATATTTTTTAAAAAACGTTTTAAAACTTATATATTATACATAAT
* * * *
175020 TTCAAAAAATTGTTTTCAAAA-T-TATATTATATATTTTTTTCAAAAATGTTTTTTTAAAACCAT
66 TTCAAAAAA-TGTTTTCAAAACTATATACTATATA-TATTTTCAAAAAT-TATTTTCAAAACCAT
175083 ATATATTTTTAA
128 ATATATTTTTAA
* **
175095 ATGTTTTC-AAAAT-TA-TATATTATATTTTTAAAAAATGTTTTCAAAACTTATATATTATGTAT
1 ATGTTTTCTAAAATATATTATA-TAT-TTTTTAAAAAACGTTTT-AAAACTTATATATTATACAT
** * *
175157 GTTTTCGAAAAATGTTTTCAAAACTATATACTATATATATTTTCAAAAATTATTTTCAAAACTAT
63 AATTTCAAAAAATGTTTTCAAAACTATATACTATATATATTTTCAAAAATTATTTTCAAAACCAT
175222 ATAT
128 ATAT
175226 TATATATTTT
Statistics
Matches: 113, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
136 4 0.04
137 5 0.04
138 20 0.18
139 40 0.35
140 34 0.30
141 10 0.09
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.48
Consensus pattern (139 bp):
ATGTTTTCTAAAATATATTATATATTTTTTAAAAAACGTTTTAAAACTTATATATTATACATAAT
TTCAAAAAATGTTTTCAAAACTATATACTATATATATTTTCAAAAATTATTTTCAAAACCATATA
TATTTTTAA
Found at i:175200 original size:38 final size:36
Alignment explanation
Indices: 174956--175235 Score: 221
Period size: 38 Copynumber: 7.9 Consensus size: 36
174946 AAAACCCAAC
* *
174956 ATGTTTTCTAAAA-TATAT-TATATATTTTTTGAAAA
1 ATGTTTTC-AAAACTATATATATATATATTTTCAAAA
* * *
174991 ACGTTTT-AAAACTATATATTATACATAATTTCAAAAA
1 ATGTTTTCAAAACTATATA-TATATATATTTTC-AAAA
* *
175028 ATTGTTTTCAAAATTATAT-TATATATTTTTTTCAAAA
1 A-TGTTTTCAAAACTATATATATATA-TATTTTCAAAA
* *
175065 ATGTTTTTTTAAAAC----CATATATAT-TTTT---AA
1 ATG--TTTTCAAAACTATATATATATATATTTTCAAAA
* *
175095 ATGTTTTCAAAATTATATAT-TATAT-TTTTAAAAA
1 ATGTTTTCAAAACTATATATATATATATTTTCAAAA
* *
175129 ATGTTTTCAAAACTTATATATTATGTATGTTTTCGAAAA
1 ATGTTTTCAAAAC-TATATA-TATATATATTTTC-AAAA
175168 ATGTTTTCAAAACTATATACTATATATATTTTCAAAA
1 ATGTTTTCAAAACTATATA-TATATATATTTTCAAAA
*
175205 ATTATTTTCAAAACTATATAT-TATATATTTT
1 A-TGTTTTCAAAACTATATATATATATATTTT
175236 GTATATATCA
Statistics
Matches: 199, Mismatches: 23, Indels: 45
0.75 0.09 0.17
Matches are distributed among these distances:
28 8 0.04
30 5 0.03
31 9 0.05
32 2 0.01
33 8 0.04
34 20 0.10
35 18 0.09
36 22 0.11
37 25 0.13
38 56 0.28
39 26 0.13
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.49
Consensus pattern (36 bp):
ATGTTTTCAAAACTATATATATATATATTTTCAAAA
Found at i:187335 original size:5 final size:5
Alignment explanation
Indices: 187325--187363 Score: 60
Period size: 5 Copynumber: 7.6 Consensus size: 5
187315 AAACAAATAA
*
187325 AAATT AAATT AAGTAT AAATT AAATT AAATT AAATT AAA
1 AAATT AAATT AAAT-T AAATT AAATT AAATT AAATT AAA
187364 AAATAAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
5 27 0.87
6 4 0.13
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (5 bp):
AAATT
Found at i:187344 original size:16 final size:15
Alignment explanation
Indices: 187325--187363 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
187315 AAACAAATAA
*
187325 AAATTAAATTAAGTAT
1 AAATTAAATTAAAT-T
187341 AAATTAAATTAAATT
1 AAATTAAATTAAATT
187356 AAATTAAA
1 AAATTAAA
187364 AAATAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (15 bp):
AAATTAAATTAAATT
Found at i:188582 original size:38 final size:38
Alignment explanation
Indices: 188529--188800 Score: 276
Period size: 38 Copynumber: 7.3 Consensus size: 38
188519 GTTTTATAAA
188529 ATATATTATATATAATTTCCAAAAATGTTTT-AAAACT
1 ATATATTATATATAATTTCCAAAAATGTTTTCAAAACT
* *** *
188566 ATAATATTATACATAATTT-CAAAAA-AAATTCAAAATT
1 AT-ATATTATATATAATTTCCAAAAATGTTTTCAAAACT
* * * *
188603 ATATATTATATATATTTTTCAAAAATGTTTTTTAAAACC
1 ATATATTATATATAATTTCCAAAAATG-TTTTCAAAACT
** *
188642 ATATATTATATAT--TTT-TTAAAATGTTTTCAAAATT
1 ATATATTATATATAATTTCCAAAAATGTTTTCAAAACT
*
188677 ATATATTATAT-T--TTT-AAAAAATGTTTTCAAAACTT
1 ATATATTATATATAATTTCCAAAAATGTTTTCAAAAC-T
** *
188712 ATATATTATATATGTTTTCAAAAAATGTTTTCAAAACT
1 ATATATTATATATAATTTCCAAAAATGTTTTCAAAACT
* * *
188750 ATATATTATATATATTTTCTAAAATTGTTTTCAAAACT
1 ATATATTATATATAATTTCCAAAAATGTTTTCAAAACT
188788 ATATATTATATAT
1 ATATATTATATAT
188801 TATGGATATA
Statistics
Matches: 201, Mismatches: 24, Indels: 19
0.82 0.10 0.08
Matches are distributed among these distances:
34 19 0.09
35 31 0.15
36 23 0.11
37 24 0.12
38 67 0.33
39 37 0.18
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.47
Consensus pattern (38 bp):
ATATATTATATATAATTTCCAAAAATGTTTTCAAAACT
Found at i:188629 original size:74 final size:72
Alignment explanation
Indices: 188529--188801 Score: 304
Period size: 74 Copynumber: 3.7 Consensus size: 72
188519 GTTTTATAAA
* * * * *
188529 ATATATTATATATAATTTCCAAAAATGTTTT-AAAACTATAATATTATACATAATTTCAAAAAAA
1 ATATATTATATATATTTTTCAAAAATGTTTTCAAAACTAT-ATATTATATAT-TTTTCAAAAAAT
*
188593 ATTCAAAATT
64 TTTCAAAA-T
* * * **
188603 ATATATTATATATATTTTTCAAAAATGTTTTTTAAAACCATATATTATATATTTTTTAAAATGTT
1 ATATATTATATATATTTTTCAAAAATG-TTTTCAAAACTATATATTATATATTTTTCAAAAAATT
188668 TTCAAAAT
65 TTCAAAAT
*
188676 -TATA-TAT-TATATTTTTAAAAAATGTTTTCAAAACTTATATATTATATATGTTTTCAAAAAAT
1 ATATATTATATATATTTTTCAAAAATGTTTTCAAAAC-TATATATTATATAT-TTTTCAAAAAA-
188738 GTTTTCAAAACT
63 -TTTTCAAAA-T
*
188750 ATATATTATATATA-TTTTCTAAAATTGTTTTCAAAACTATATATTATATATT
1 ATATATTATATATATTTTTC-AAAAATGTTTTCAAAACTATATATTATATATT
188802 ATGGATATAT
Statistics
Matches: 170, Mismatches: 18, Indels: 21
0.81 0.09 0.10
Matches are distributed among these distances:
69 9 0.05
70 29 0.17
71 11 0.06
72 4 0.02
73 10 0.06
74 40 0.24
75 19 0.11
76 28 0.16
77 20 0.12
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.47
Consensus pattern (72 bp):
ATATATTATATATATTTTTCAAAAATGTTTTCAAAACTATATATTATATATTTTTCAAAAAATTT
TCAAAAT
Found at i:188741 original size:13 final size:13
Alignment explanation
Indices: 188723--188747 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
188713 TATATTATAT
188723 ATGTTTTCAAAAA
1 ATGTTTTCAAAAA
188736 ATGTTTTCAAAA
1 ATGTTTTCAAAA
188748 CTATATATTA
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:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (13 bp):
ATGTTTTCAAAAA
Found at i:188880 original size:24 final size:25
Alignment explanation
Indices: 188848--188907 Score: 88
Period size: 24 Copynumber: 2.4 Consensus size: 25
188838 TGACTACACC
*
188848 TGTGATTTGGAATAAATGTTT-A-T
1 TGTGGTTTGGAATAAATGTTTAACT
188871 TGATGGTTTGGAATAAATGTTTAACT
1 TG-TGGTTTGGAATAAATGTTTAACT
188897 TGTGGTTTGGA
1 TGTGGTTTGGA
188908 TTTTAAAGCC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
23 2 0.06
24 18 0.55
25 10 0.30
26 3 0.09
ACGTcount: A:0.27, C:0.02, G:0.27, T:0.45
Consensus pattern (25 bp):
TGTGGTTTGGAATAAATGTTTAACT
Found at i:189082 original size:21 final size:21
Alignment explanation
Indices: 189056--189131 Score: 64
Period size: 21 Copynumber: 3.5 Consensus size: 21
189046 TTTTCAAAGG
189056 GTACTTTGTGTACTTGGAGTA
1 GTACTTTGTGTACTTGGAGTA
* *
189077 GTACTTTTTGTATTATGGACAG-A
1 GTACTTTGTGTACT-TGG--AGTA
* * * *
189100 GTAATTTGTGTGCTTGTAATA
1 GTACTTTGTGTACTTGGAGTA
189121 GTACTTTGTGT
1 GTACTTTGTGT
189132 GCAAGGATGG
Statistics
Matches: 42, Mismatches: 9, Indels: 8
0.71 0.15 0.14
Matches are distributed among these distances:
20 1 0.02
21 23 0.55
22 5 0.12
23 11 0.26
24 2 0.05
ACGTcount: A:0.21, C:0.08, G:0.25, T:0.46
Consensus pattern (21 bp):
GTACTTTGTGTACTTGGAGTA
Found at i:189544 original size:21 final size:22
Alignment explanation
Indices: 189520--189573 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
189510 TTTCGTAATT
189520 GTACTTTGTGCACT-TGG-AGTA
1 GTACTTTGTGCACTATGGAAG-A
*
189541 GTACTTTGTGTACTATGGCAAGA
1 GTACTTTGTGCACTATGG-AAGA
189564 GTACTTTGTG
1 GTACTTTGTG
189574 TACCTATAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 13 0.45
22 3 0.10
23 11 0.38
24 2 0.07
ACGTcount: A:0.20, C:0.13, G:0.28, T:0.39
Consensus pattern (22 bp):
GTACTTTGTGCACTATGGAAGA
Found at i:189570 original size:23 final size:21
Alignment explanation
Indices: 189520--189595 Score: 79
Period size: 18 Copynumber: 3.7 Consensus size: 21
189510 TTTCGTAATT
*
189520 GTACTTTGTGCACTTGGAGTA
1 GTACTTTGTGTACTTGGAGTA
189541 GTACTTTGTGTACTATGGCAAG-A
1 GTACTTTGTGTACT-TGG--AGTA
*
189564 GTACTTTGTGTACCT--A-TA
1 GTACTTTGTGTACTTGGAGTA
189582 GTACTTTGTGTACT
1 GTACTTTGTGTACT
189596 ATGGCACTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
18 15 0.31
21 13 0.27
22 4 0.08
23 14 0.29
24 2 0.04
ACGTcount: A:0.21, C:0.14, G:0.24, T:0.41
Consensus pattern (21 bp):
GTACTTTGTGTACTTGGAGTA
Found at i:189586 original size:18 final size:17
Alignment explanation
Indices: 189563--189609 Score: 67
Period size: 17 Copynumber: 2.7 Consensus size: 17
189553 CTATGGCAAG
189563 AGTACTTTGTGTACCTAT
1 AGTACTTTGTGTA-CTAT
189581 AGTACTTTGTGTACTAT
1 AGTACTTTGTGTACTAT
* *
189598 GGCACTTTGTGT
1 AGTACTTTGTGT
189610 GCAAGGATGG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 14 0.52
18 13 0.48
ACGTcount: A:0.19, C:0.15, G:0.21, T:0.45
Consensus pattern (17 bp):
AGTACTTTGTGTACTAT
Found at i:208749 original size:22 final size:24
Alignment explanation
Indices: 208724--208768 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
208714 GCAATAAATA
*
208724 TAAGAAA-GAAT-TATAATGGAAT
1 TAAGAAATGAATATATAAAGGAAT
208746 TAAGAAATGAATATATAAAGGAA
1 TAAGAAATGAATATATAAAGGAA
208769 ATGAAATAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 7 0.35
23 4 0.20
24 9 0.45
ACGTcount: A:0.58, C:0.00, G:0.18, T:0.24
Consensus pattern (24 bp):
TAAGAAATGAATATATAAAGGAAT
Found at i:210178 original size:30 final size:31
Alignment explanation
Indices: 210139--210198 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
210129 ACATGATGCC
**
210139 ATGATATCTAAATTAAATGCAAACATAATAA
1 ATGATATCTAAAACAAATGCAAACATAATAA
* *
210170 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACAAATGCAAACATAATA
210199 TAAAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.55, C:0.10, G:0.07, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACAAATGCAAACATAATAA
Found at i:212839 original size:13 final size:13
Alignment explanation
Indices: 212821--212845 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
212811 ATAGTTGAAC
212821 AGTCTTCATATGT
1 AGTCTTCATATGT
212834 AGTCTTCATATG
1 AGTCTTCATATG
212846 CGCGTCTGTA
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:0.24, C:0.16, G:0.16, T:0.44
Consensus pattern (13 bp):
AGTCTTCATATGT
Found at i:215980 original size:19 final size:20
Alignment explanation
Indices: 215956--216001 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
215946 CAAAATGGCC
*
215956 CAATTTC-ACATTCTAACAT
1 CAATTTCAACACTCTAACAT
215975 CAATTTCAACACTCTAACAT
1 CAATTTCAACACTCTAACAT
*
215995 TAATTTC
1 CAATTTC
216002 TAGTATAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.37, C:0.26, G:0.00, T:0.37
Consensus pattern (20 bp):
CAATTTCAACACTCTAACAT
Found at i:217450 original size:9 final size:9
Alignment explanation
Indices: 217438--217472 Score: 52
Period size: 9 Copynumber: 3.7 Consensus size: 9
217428 ACCTTATTGT
217438 AATTATTAA
1 AATTATTAA
217447 AATTATTGAA
1 AATTATT-AA
217457 ACATTATTAA
1 A-ATTATTAA
217467 AATTAT
1 AATTAT
217473 ATTTACCTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 12 0.50
10 6 0.25
11 6 0.25
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (9 bp):
AATTATTAA
Found at i:221648 original size:36 final size:36
Alignment explanation
Indices: 221594--221696 Score: 127
Period size: 36 Copynumber: 2.9 Consensus size: 36
221584 GGGATTGTCC
* * *
221594 AATACACATGCAATTACACAGCAACTCAATATGACA
1 AATAAACATGCAATTACACAACAACTCAATATGAAA
* *
221630 AATAAACATGTAACTACACATA-AACTCAATATGAAA
1 AATAAACATGCAATTACACA-ACAACTCAATATGAAA
**
221666 AATGGACATGCAATTACACAACAACTCAATA
1 AATAAACATGCAATTACACAACAACTCAATA
221697 AAACAATAAC
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
35 1 0.02
36 55 0.98
ACGTcount: A:0.50, C:0.21, G:0.08, T:0.20
Consensus pattern (36 bp):
AATAAACATGCAATTACACAACAACTCAATATGAAA
Found at i:224682 original size:14 final size:14
Alignment explanation
Indices: 224663--224689 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
224653 AACAGACTAT
224663 TCTGTTTTCTACAG
1 TCTGTTTTCTACAG
224677 TCTGTTTTCTACA
1 TCTGTTTTCTACA
224690 TGGTATCAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.22, G:0.11, T:0.52
Consensus pattern (14 bp):
TCTGTTTTCTACAG
Found at i:230470 original size:49 final size:49
Alignment explanation
Indices: 230417--230515 Score: 189
Period size: 49 Copynumber: 2.0 Consensus size: 49
230407 ATTTTATGTG
*
230417 CTTATTTTATTTTGTAGTCTAGGGTGCACAATCATAACTTTCATGTCAT
1 CTTATTTTATTTTGTAGTCTAGGGTGCACAATCATAACTTTCATGGCAT
230466 CTTATTTTATTTTGTAGTCTAGGGTGCACAATCATAACTTTCATGGCAT
1 CTTATTTTATTTTGTAGTCTAGGGTGCACAATCATAACTTTCATGGCAT
230515 C
1 C
230516 CTATGAGAAT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.24, C:0.17, G:0.15, T:0.43
Consensus pattern (49 bp):
CTTATTTTATTTTGTAGTCTAGGGTGCACAATCATAACTTTCATGGCAT
Found at i:232268 original size:537 final size:540
Alignment explanation
Indices: 231252--232320 Score: 2036
Period size: 537 Copynumber: 2.0 Consensus size: 540
231242 TTAGTATCAC
231252 AGTACAACTTCATTGGACCGTCCCATTTTATTTTCAAATCTTTCAAAATAATCTTCAGCCACAAT
1 AGTACAACTTCATTGGACCGTCCCATTTTATTTTCAAATCTTTCAAAATAATCTTCAGCCACAAT
* *
231317 AATTCACAAATTCGAAATGCCATCGCCCTAAATTCAACTTCTGCACTGGATCTAGCCACAACATT
66 AATTCACAAATTCGAAATGCCATCACCCTAAATTCAACTTCTGCACTGAATCTAGCCACAACATT
231382 ATGCTTTTTGCTCCTCCAAGTCACTAGGTTTCCTCCCAGAAAGGTACATTACCCCGAGGTTGATC
131 ATGCTTTTTGCTCCTCCAAGTCACTAGGTTTCCTCCCAGAAAGGTACATTACCCCGAGGTTGATC
*
231447 TTCTATCAATTGTGGACCCTGCATGGTCTGCATCTGTATATGCTTCCAAAGTCAAACTTTCTCCC
196 TTCTATCAACTGTGGACCCTGCATGGTCTGCATCTGTATATGCTTCCAAAGTCAAACTTTCTCCC
231512 TTTTTAAATAAAATTCTTATGCCTGGTGTACCCTTTAAATACTGTAAAATTTGAGTCACAACCCT
261 TTTTTAAATAAAATTCTTATGCCTGGTGTACCCTTTAAATACTGTAAAATTTGAGTCACAACCCT
*
231577 TAGGTGTGATTCTTTAGGATTGTGCCTGAATTGACACAACTCCAACTGCATAAGCAATGTCTGGT
326 TAGGTGTGATTCTTTAGGATTGTGCATGAATTGACACAACTCCAACTGCATAAGCAATGTCTGGT
231642 CTGGTGTGTAACAAGTAAATGAGTCCTCCCACAAGCCTTTGATATGAGCTTTTATCGACTGCTAC
391 CTGGTGTGTAACAAGTAAATGAGTCCTCCCACAAGCCTTTGATATGAGCTTTTATCGACTGCTAC
231707 ATCTTTTGTTAAATCTCAAGGCGTGTGATTAACTTCTATTGGTGTTTCTATTGGTTTGCACCTCA
456 ATCTTTTGTTAAATCTCAAGGCGTGTGATTAACTTCTATTGGTGTTTCTATTGGTTTGCACCTCA
231772 GTTTTCCAGTTTATTTTCAT
521 GTTTTCCAGTTTATTTTCAT
231792 AGTACAACTTCATTGGACCGTCCCATTTTATTTTCAAATCTTTCAAAATAATCTTCAGCCACAAT
1 AGTACAACTTCATTGGACCGTCCCATTTTATTTTCAAATCTTTCAAAATAATCTTCAGCCACAAT
*
231857 AATTCACAAATTCGAAATG-CATCACCCTAAATTCAGCTTCTGCACTGAATCTAGCCACAACATT
66 AATTCACAAATTCGAAATGCCATCACCCTAAATTCAACTTCTGCACTGAATCTAGCCACAACATT
*
231921 GTGCTTTTTGCTCCTCCAAGTCACTAGGTTTCCTCCCAGAAAGGTACATTACCCCGAGGTTGATC
131 ATGCTTTTTGCTCCTCCAAGTCACTAGGTTTCCTCCCAGAAAGGTACATTACCCCGAGGTTGATC
231986 TTCTATCAACTGTGGACCCTGCATGGTCTGCATCTGTATATGCTTCCAAA-TCAAACTTTCTCCC
196 TTCTATCAACTGTGGACCCTGCATGGTCTGCATCTGTATATGCTTCCAAAGTCAAACTTTCTCCC
232050 TTTTTAAATAAAATTC-TATGCCTGGTGTACCCTTTAAATACTGTAAAATTTGAGTCACAACCCT
261 TTTTTAAATAAAATTCTTATGCCTGGTGTACCCTTTAAATACTGTAAAATTTGAGTCACAACCCT
232114 TAGGTGTGATTCTTTAGGATTGTGCATGAATTGACACAACTCCAACTGCATAAGCAATGTCTGGT
326 TAGGTGTGATTCTTTAGGATTGTGCATGAATTGACACAACTCCAACTGCATAAGCAATGTCTGGT
*
232179 CTGGTGTGTAACAAGTAAATGAGTCTTCCCACAAGCCTTTGATATGAGCTTTTATCGACTGCTAC
391 CTGGTGTGTAACAAGTAAATGAGTCCTCCCACAAGCCTTTGATATGAGCTTTTATCGACTGCTAC
*
232244 ATCTTTTGTTAAATCTCAAGGCGTGTGATTAACTTCTATTGGTGTTTCTGTTGGTTTGCACCTCA
456 ATCTTTTGTTAAATCTCAAGGCGTGTGATTAACTTCTATTGGTGTTTCTATTGGTTTGCACCTCA
*
232309 GTTTTCTAGTTT
521 GTTTTCCAGTTT
232321 CTGTCAACAA
Statistics
Matches: 520, Mismatches: 9, Indels: 3
0.98 0.02 0.01
Matches are distributed among these distances:
537 251 0.48
538 30 0.06
539 155 0.30
540 84 0.16
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (540 bp):
AGTACAACTTCATTGGACCGTCCCATTTTATTTTCAAATCTTTCAAAATAATCTTCAGCCACAAT
AATTCACAAATTCGAAATGCCATCACCCTAAATTCAACTTCTGCACTGAATCTAGCCACAACATT
ATGCTTTTTGCTCCTCCAAGTCACTAGGTTTCCTCCCAGAAAGGTACATTACCCCGAGGTTGATC
TTCTATCAACTGTGGACCCTGCATGGTCTGCATCTGTATATGCTTCCAAAGTCAAACTTTCTCCC
TTTTTAAATAAAATTCTTATGCCTGGTGTACCCTTTAAATACTGTAAAATTTGAGTCACAACCCT
TAGGTGTGATTCTTTAGGATTGTGCATGAATTGACACAACTCCAACTGCATAAGCAATGTCTGGT
CTGGTGTGTAACAAGTAAATGAGTCCTCCCACAAGCCTTTGATATGAGCTTTTATCGACTGCTAC
ATCTTTTGTTAAATCTCAAGGCGTGTGATTAACTTCTATTGGTGTTTCTATTGGTTTGCACCTCA
GTTTTCCAGTTTATTTTCAT
Found at i:233786 original size:29 final size:30
Alignment explanation
Indices: 233727--233798 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 30
233717 TATCCCTATA
* *
233727 TTTGTTTCTTTGTTTTTGTTGAGATGAG-T
1 TTTGTTTCTTTGTTTCTGCTGAGATGAGTT
* *
233756 TTTGTTTCCTTTGTTTCTGCTGTGA-GGGTT
1 TTTGTTT-CTTTGTTTCTGCTGAGATGAGTT
233786 TTTGTTTTCTTTG
1 TTTG-TTTCTTTG
233799 GTTTGTTGTG
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
29 9 0.25
30 24 0.67
31 3 0.08
ACGTcount: A:0.06, C:0.08, G:0.24, T:0.62
Consensus pattern (30 bp):
TTTGTTTCTTTGTTTCTGCTGAGATGAGTT
Found at i:241741 original size:36 final size:36
Alignment explanation
Indices: 241692--241775 Score: 116
Period size: 36 Copynumber: 2.3 Consensus size: 36
241682 GGTAGGTTCC
*
241692 GGTTCCGGATCCCAATTCTTAGGAACCGGTTG-AACA
1 GGTTCCGGTTCCCAATTCTTAGGAACCGG-TGCAACA
* *
241728 GGTTCCGGTTCCCATTTTTTAGGAACCGGTGCAACA
1 GGTTCCGGTTCCCAATTCTTAGGAACCGGTGCAACA
*
241764 GGTTCCGATTCC
1 GGTTCCGGTTCC
241776 GGTTCACAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
35 2 0.05
36 41 0.95
ACGTcount: A:0.20, C:0.26, G:0.25, T:0.29
Consensus pattern (36 bp):
GGTTCCGGTTCCCAATTCTTAGGAACCGGTGCAACA
Found at i:244457 original size:12 final size:12
Alignment explanation
Indices: 244442--244487 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
244432 CGGTTTTTTT
*
244442 ACCGGATAAAAA
1 ACCGGTTAAAAA
244454 ACCGGTTTGAAAAAA
1 ACCGG-TT--AAAAA
244469 ACCGGTTAAAAA
1 ACCGGTTAAAAA
244481 ACCGGTT
1 ACCGGTT
244488 TTTATCCGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 17 0.57
13 1 0.03
14 2 0.07
15 10 0.33
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (12 bp):
ACCGGTTAAAAA
Found at i:244469 original size:15 final size:13
Alignment explanation
Indices: 244448--244488 Score: 57
Period size: 12 Copynumber: 3.1 Consensus size: 13
244438 TTTTACCGGA
244448 TAAAAAACCGGTT
1 TAAAAAACCGGTT
244461 TGAAAAAAACCGG-T
1 T--AAAAAACCGGTT
244475 TAAAAAACCGGTT
1 TAAAAAACCGGTT
244488 T
1 T
244489 TTATCCGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 10 0.40
13 3 0.12
14 2 0.08
15 10 0.40
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (13 bp):
TAAAAAACCGGTT
Found at i:246800 original size:21 final size:21
Alignment explanation
Indices: 246776--246815 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
246766 TTTATTTTAT
246776 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
246797 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
246816 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:246863 original size:33 final size:33
Alignment explanation
Indices: 246810--246908 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
246800 TTTGTTTCAA
246810 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
246842 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
246875 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
246908 T
1 T
246909 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:246937 original size:13 final size:13
Alignment explanation
Indices: 246894--246948 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
246884 TTGGAAGTAT
246894 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
246907 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
246921 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
246934 TTAAGTATTTGAA
1 TTAAGTATTTCAA
246947 TT
1 TT
246949 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:247369 original size:15 final size:15
Alignment explanation
Indices: 247344--247399 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
247334 ATCTGGAATA
*
247344 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
247359 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
*
247374 TAAAAAAACCGGTTTTT
1 T--TAAAACCGGTTTTT
247391 TTAAAACCG
1 TTAAAACCG
247400 AAACCGGTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 21 0.62
17 13 0.38
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.43
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Done.