Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold289
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: 700734
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:139292 original size:21 final size:21
Alignment explanation
Indices: 139263--139307 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
139253 AAGTTTTCAT
*
139263 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
139283 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
139305 TTT
1 TTT
139308 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:141533 original size:13 final size:13
Alignment explanation
Indices: 141515--141540 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
141505 CAATTTTTTG
141515 TGTATCGATACAT
1 TGTATCGATACAT
141528 TGTATCGATACAT
1 TGTATCGATACAT
141541 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:142614 original size:28 final size:28
Alignment explanation
Indices: 142582--143410 Score: 870
Period size: 28 Copynumber: 28.9 Consensus size: 28
142572 TGTTCATCTC
*
142582 TTCAAAGCCCACAAGTCAATGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * * *
142610 TTCAAAGCCCATAATTCAATGGCACCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
142638 TTCAAAGCCCACAAATCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
142666 TTCAAAGCCCACAAGTCAATGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
142694 TTCAAAGCCCACAAGTCAGCGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
* *
142723 TTCAAAGCCCATAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
* * * ***
142752 TTCACAGCCCATAAGTTAGTGGCATATT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * *
142780 TTCAAAGCCCACAAGTTAGTGGAATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * *
142808 TTTAAAGCCCACAAGTCATTGGCACCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
142836 TTCAAAGCCCACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
* * *
142865 TTCAAAGCTCGCAAGTCAGTGGCACTCGT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
** *
142894 TTCAAAGCCTGCAAGTCAGTGGCACTCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
142922 TTCAAAGCCCACAAGTCAGTGACACCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
142950 TTCAAAGCCCACGAAAAGTAAGAGGCACCCT
1 TTCAAAGCCCAC---AAGTCAGTGGCACCCT
**
142981 TTCAAAGCCCACAAGTCAGTGGCACTAT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
143009 TATCAAAGCCCACAAGTCAGTAGCATCCT
1 T-TCAAAGCCCACAAGTCAGTGGCACCCT
* * *
143038 TTCAAAGCCCACGAGTCGGTGGCAACTCTT
1 TTCAAAGCCCACAAGTCAGTGGC-AC-CCT
* * *
143068 TTCAAAGCTCACAAGTCAGTGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * *
143096 TTCAAAGCCCACGAGTCGGTGGCACTCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
143124 TTCAAAGCCCATAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
143152 TTCAAAGCCCACAAGTTAGTGGCACTCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
143180 ATCAAAGCCCATAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
143208 TTCAAAGCCCACGCAAGTCAGTGGCACCCT
1 TTCAAAGCCCA--CAAGTCAGTGGCACCCT
*
143238 TTCAAAGCCCACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
* *
143267 TTCAAAGCCCACAAGTCAGTGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
143295 TTCAAAGCCCACACGAGTC-GATGGTAACTCTT
1 TTCAAAGCCCACA--AGTCAG-TGG-CAC-CCT
* * *
143327 TTCAAAGCCCACAAATTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * *
143355 TTCAAAGCCCACGAGCCCA-TGACAACTCCT
1 TTCAAAGCCCACAAG-TCAGTGGC-AC-CCT
*
143385 TTCAAAGCCACACAAGTTAGTGGCAC
1 TTCAAAGCC-CACAAGTCAGTGGCAC
143411 TTTTTAAAAG
Statistics
Matches: 677, Mismatches: 102, Indels: 42
0.82 0.12 0.05
Matches are distributed among these distances:
28 392 0.58
29 159 0.23
30 76 0.11
31 34 0.05
32 16 0.02
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCACCCT
Found at i:142782 original size:142 final size:142
Alignment explanation
Indices: 142582--143410 Score: 904
Period size: 142 Copynumber: 5.8 Consensus size: 142
142572 TGTTCATCTC
* * * *
142582 TTCAAAGCCCACAAGTCAATGGCAC-CCTTTCAAAGCCCATAATTCAATGGCA-CCTTTTCAAAG
1 TTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCATCC-TTTCAAAG
*
142645 CCCACAAATCAGTGGCACCCTTTCAAAGCCCACAAGTCAATGGCACCCTTTCAAAGCCCACAAGT
65 CCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAATGGCACCCTTTCAAAGCCCACAAGT
*
142710 CAGCGGCACTCTT
130 CAGTGGCACTCTT
* * * * * **
142723 TTCAAAGCCCATAAGTCAGTGGCACTCTTTTCACAGCCCATAAGTTAGTGGCATATTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGC
* * * * * *
142788 CCACAAGTTAGTGGAATCCTTTTAAAGCCCACAAGTCATTGGCACCTTTTCAAAGCCCACAAGTC
66 CCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAATGGCACCCTTTCAAAGCCCACAAGTC
142853 AGTGGCACTCTT
131 AGTGGCACTCTT
* * * **
142865 TTCAAAGCTCGCAAGTCAGTGGCACTCGTTTCAAAGCCTGCAAGTCAGTGGCA-CTCTTTCAAAG
1 TTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCATC-CTTTCAAAG
* * *
142929 CCCACAAGTCAGTGACACCTTTTCAAAGCCCACGAAAAGT-AAGAGGCACCCTTTCAAAGCCCAC
65 CCCACAAGTCAGTGGCACCCTTTCAAAGCCCAC---AAGTCAA-TGGCACCCTTTCAAAGCCCAC
*
142993 AAGTCAGTGGCACTATT
126 AAGTCAGTGGCACTCTT
* * * * *
143010 ATCAAAGCCCACAAGTCAGTAGCA-TCCTTTCAAAGCCCACGAGTCGGTGGCAACTCTTTTCAAA
1 TTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGC-A-TCCTTTCAAA
* * * * ** * *
143074 GCTCACAAGTCAGTGGCATCTTTTCAAAGCCCACGAGTCGGTGGCACTCTTTCAAAGCCCATAAG
64 GCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAATGGCACCCTTTCAAAGCCCACAAG
*
143139 TCAGTGGCAC-CCT
129 TCAGTGGCACTCTT
* * * *
143152 TTCAAAGCCCACAAGTTAGTGGCACT-CTATCAAAGCCCATAAGTCAGTGGCACCCTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGC
* *
143216 CCACGCAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAA
66 CCA--CAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAATGGCAC-CCTTTCAAAGCCCACAA
143281 GTCAGTGGCA-TCTT
128 GTCAGTGGCACTCTT
* * * *
143295 TTCAAAGCCCACACGAGTC-GATGGTAACTCTTTTCAAAGCCCACAAATTAGTGGCATCCTTTCA
1 TTCAAAGCCCACA--AGTCAG-TGG-CACTCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCA
* * * * *
143359 AAGCCCACGAGCCCA-TGACAACTCCTTTCAAAGCCACACAAGTTAGTGGCAC
62 AAGCCCACAAG-TCAGTGGC-AC-CCTTTCAAAGCC-CACAAGTCAATGGCAC
143411 TTTTTAAAAG
Statistics
Matches: 574, Mismatches: 89, Indels: 43
0.81 0.13 0.06
Matches are distributed among these distances:
140 12 0.02
141 24 0.04
142 260 0.45
143 74 0.13
144 24 0.04
145 72 0.13
146 45 0.08
147 48 0.08
148 15 0.03
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (142 bp):
TTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGC
CCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAATGGCACCCTTTCAAAGCCCACAAGTC
AGTGGCACTCTT
Found at i:143546 original size:45 final size:46
Alignment explanation
Indices: 143476--143598 Score: 140
Period size: 49 Copynumber: 2.6 Consensus size: 46
143466 CTGGCTGACA
* * *
143476 TCGCTAGCATTGAATCAGCATATTGGCACCTTT-ATTAGCCCAATG
1 TCGCTGGCCTTGAATCAGCACATTGGCACCTTTCATTAGCCCAATG
* * *
143521 TCGCTGGCCTTGAATCAACACATTGGTCCACTTTTCCCTTAGCCCAATG
1 TCGCTGGCCTTGAATCAGCACATTGG--CACCTTT-CATTAGCCCAATG
**
143570 TCGCTGGCCTTGAATTGGCACATTGGCAC
1 TCGCTGGCCTTGAATCAGCACATTGGCAC
143599 TCCTCTCATC
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
45 22 0.34
47 9 0.14
49 34 0.52
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.30
Consensus pattern (46 bp):
TCGCTGGCCTTGAATCAGCACATTGGCACCTTTCATTAGCCCAATG
Found at i:151410 original size:16 final size:16
Alignment explanation
Indices: 151398--151430 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
151388 CCTGAACCTG
151398 AAAGAAATCGAACCCA
1 AAAGAAATCGAACCCA
*
151414 AAAGAACTCGAACCCA
1 AAAGAAATCGAACCCA
151430 A
1 A
151431 GAAAACCTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.27, G:0.12, T:0.06
Consensus pattern (16 bp):
AAAGAAATCGAACCCA
Found at i:151442 original size:16 final size:16
Alignment explanation
Indices: 151407--151464 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
151397 GAAAGAAATC
*
151407 GAACCC-AAAAGAACT
1 GAACCCAAAAAAAACT
* *
151422 CGAACCCAAGAAAACCT
1 -GAACCCAAAAAAAACT
**
151439 GAACATAAAAAAAACT
1 GAACCCAAAAAAAACT
151455 GAACCCAAAA
1 GAACCCAAAA
151465 CAGACCCGAA
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
16 26 0.81
17 6 0.19
ACGTcount: A:0.57, C:0.26, G:0.10, T:0.07
Consensus pattern (16 bp):
GAACCCAAAAAAAACT
Found at i:151630 original size:22 final size:22
Alignment explanation
Indices: 151615--151658 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
151605 AAATAGTAAT
151615 TTATCAAAAAGTAAATTATATC
1 TTATCAAAAAGTAAATTATATC
151637 TTATCAAAAAGTAAATTATATC
1 TTATCAAAAAGTAAATTATATC
151659 ATGAGCTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.09, G:0.05, T:0.36
Consensus pattern (22 bp):
TTATCAAAAAGTAAATTATATC
Found at i:152564 original size:18 final size:18
Alignment explanation
Indices: 152525--152564 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
152515 AATAAATATT
* *
152525 TAAAATTTAATTTTATAT
1 TAAAAATTAATTTTATAA
*
152543 TAAAAATTAATTTTGTAA
1 TAAAAATTAATTTTATAA
152561 TAAA
1 TAAA
152565 TATAGATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
TAAAAATTAATTTTATAA
Found at i:152592 original size:16 final size:15
Alignment explanation
Indices: 152558--152612 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 15
152548 ATTAATTTTG
152558 TAATAAATATAGAT-TT
1 TAATAAATA-A-ATATT
152574 TAATAAATAAATATAT
1 TAATAAATAAATAT-T
152590 TAA-AAATAACATATT
1 TAATAAATAA-ATATT
152605 ATAATAAA
1 -TAATAAA
152613 ATTTTACTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
14 2 0.06
15 9 0.26
16 20 0.59
17 3 0.09
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (15 bp):
TAATAAATAAATATT
Found at i:152790 original size:15 final size:16
Alignment explanation
Indices: 152750--152801 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 16
152740 AACTAGAACC
* *
152750 CAAACCTGAAAAAGCT
1 CAAACCAGAAAAGGCT
152766 CAAACCAGAAAAGGCT
1 CAAACCAGAAAAGGCT
* *
152782 CAAA-TAGAATAGGCT
1 CAAACCAGAAAAGGCT
152797 CAAAC
1 CAAAC
152802 TCGAAAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
15 13 0.42
16 18 0.58
ACGTcount: A:0.50, C:0.23, G:0.15, T:0.12
Consensus pattern (16 bp):
CAAACCAGAAAAGGCT
Found at i:154024 original size:10 final size:10
Alignment explanation
Indices: 154009--154040 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
153999 TATCGATAAA
154009 ATCACTGTTC
1 ATCACTGTTC
*
154019 ATCACTATTC
1 ATCACTGTTC
154029 ATCACTGTTC
1 ATCACTGTTC
154039 AT
1 AT
154041 ATATCGATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.25, C:0.28, G:0.06, T:0.41
Consensus pattern (10 bp):
ATCACTGTTC
Found at i:160048 original size:101 final size:100
Alignment explanation
Indices: 159764--160110 Score: 328
Period size: 101 Copynumber: 3.6 Consensus size: 100
159754 TGAGTAAAAG
* ** * * * *
159764 CAGGGCTGGAGTATCCTTTTGGAATAATAGAGATAGAGTTTCCCCAAAGATATAAATATTTAAGA
1 CAGGGTTGGAGTATCCCCTCGGAATAGTAGGGATAGAGTTTCCCTAAAGATATAAATATTTAAGA
*
159829 GCAAAGAGAAAATTTAATTTTTATTTTTATGAAGAA
66 GCAAAGAGAAAATTTAA-TTTTATTTTTATGAACAA
* * * * * *
159865 CAGGGTTAGAATATCCCCTCGGAGTAGTGGGGATAGAGTTTCCCTGAAG--ATAAA-A-TT-ATA
1 CAGGGTTGGAGTATCCCCTCGGAATAGTAGGGATAGAGTTTCCCTAAAGATATAAATATTTAAGA
159925 -CAAA-AGAAAATTTAA----ATTTTTAT-AACAA
66 GCAAAGAGAAAATTTAATTTTATTTTTATGAACAA
** * *
159953 TGGGGTTGGAGTATCCCCTCGGAATAGTAGGGATAGAGTTTTCTTAAAGATATAAATATTTAAGA
1 CAGGGTTGGAGTATCCCCTCGGAATAGTAGGGATAGAGTTTCCCTAAAGATATAAATATTTAAGA
* *
160018 GCAAAGAGAAAATTTAATTTTCATTTTTTATTAAGAA
66 GCAAAGAGAAAATTTAATTTT-A-TTTTTATGAACAA
* * * *
160055 CAGGGTTGGAGCA-CCCGTTC-GAAGTAGTGGGGATGGAGTTTCCCTAAAGATA-AAAT
1 CAGGGTTGGAGTATCCC-CTCGGAA-TAGTAGGGATAGAGTTTCCCTAAAGATATAAAT
160111 GATACGAGAA
Statistics
Matches: 197, Mismatches: 33, Indels: 32
0.75 0.13 0.12
Matches are distributed among these distances:
88 44 0.22
89 8 0.04
90 5 0.03
91 1 0.01
92 2 0.01
93 2 0.01
94 15 0.08
95 15 0.08
96 2 0.01
97 2 0.01
98 1 0.01
99 5 0.03
100 1 0.01
101 54 0.27
102 40 0.20
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.31
Consensus pattern (100 bp):
CAGGGTTGGAGTATCCCCTCGGAATAGTAGGGATAGAGTTTCCCTAAAGATATAAATATTTAAGA
GCAAAGAGAAAATTTAATTTTATTTTTATGAACAA
Found at i:160126 original size:189 final size:187
Alignment explanation
Indices: 159770--160187 Score: 518
Period size: 189 Copynumber: 2.2 Consensus size: 187
159760 AAAGCAGGGC
** * * * *
159770 TGGAGTATCCTTTTGGAATAATAGAGATAGAGTTTCCCCAAAGATATAAATATTTAAGAGCAAAG
1 TGGAGTATCCCCTCGGAATAGTAGGGATAGAGTTTTCCCAAAGATATAAATATTTAAGAGCAAAG
* * *
159835 AGAAAATTTAATTTTTATTTTTATGAAGAACAGGGTTAGAATATCCCCTCGGAGTAGTGGGGATA
66 AGAAAATTTAATTTTCATTTTTATGAAGAACAGGGTTAGAACATCCCCTCGAAGTAGTGGGGATA
* * * *
159900 GAGTTTCCCTGAAGATAAAATTATACAAAAGAAAATTTAAATTTTT-ATAACAATGGGGT
131 GAGTTTCCCTAAAGATAAAATGATACAAAAGAAAATTT-AATTTTTGA-AA-AATGAGGA
**
159959 TGGAGTATCCCCTCGGAATAGTAGGGATAGAGTTTTCTTAAAGATATAAATATTTAAGAGCAAAG
1 TGGAGTATCCCCTCGGAATAGTAGGGATAGAGTTTTCCCAAAGATATAAATATTTAAGAGCAAAG
* * * *
160024 AGAAAATTTAATTTTCATTTTTTATTAAGAACAGGGTTGGAGCA-CCCGTTCGAAGTAGTGGGGA
66 AGAAAATTTAATTTTCA-TTTTTATGAAGAACAGGGTTAGAACATCCC-CTCGAAGTAGTGGGGA
* * * * *
160088 TGGAGTTTCCCTAAAGATAAAATGATACGAGA-AAAATTTGATTTTTGAAAACTGAGGA
129 TAGAGTTTCCCTAAAGATAAAATGATACAAAAGAAAATTTAATTTTTGAAAAATGAGGA
* * * *
160146 TGGAGTGTCCCCTCGGAATAGTGGGGATGGAGTTTTTCCAAA
1 TGGAGTATCCCCTCGGAATAGTAGGGATAGAGTTTTCCCAAA
160188 AATTATATGA
Statistics
Matches: 196, Mismatches: 30, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
187 41 0.21
188 8 0.04
189 84 0.43
190 63 0.32
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (187 bp):
TGGAGTATCCCCTCGGAATAGTAGGGATAGAGTTTTCCCAAAGATATAAATATTTAAGAGCAAAG
AGAAAATTTAATTTTCATTTTTATGAAGAACAGGGTTAGAACATCCCCTCGAAGTAGTGGGGATA
GAGTTTCCCTAAAGATAAAATGATACAAAAGAAAATTTAATTTTTGAAAAATGAGGA
Found at i:164367 original size:22 final size:23
Alignment explanation
Indices: 164331--164377 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
164321 TGGAAAATGT
164331 GATAATCATATAATGA-ACTGATG
1 GATAATCATATAATGAGA-TGATG
*
164354 GATAA-CATTTAATGAGATGATG
1 GATAATCATATAATGAGATGATG
164376 GA
1 GA
164378 CATATTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.43, C:0.06, G:0.21, T:0.30
Consensus pattern (23 bp):
GATAATCATATAATGAGATGATG
Found at i:165349 original size:20 final size:20
Alignment explanation
Indices: 165324--165397 Score: 87
Period size: 20 Copynumber: 3.7 Consensus size: 20
165314 GTAAAAAGAC
*
165324 AGAATGTATCAATACATTGA
1 AGAATGTATCGATACATTGA
*
165344 AGAATGTATCGATACATTCA
1 AGAATGTATCGATACATTGA
*
165364 TA-CATGTATCGATACATTGA
1 -AGAATGTATCGATACATTGA
* *
165384 AAAATGTATTGATA
1 AGAATGTATCGATA
165398 TATCTGGGTA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
19 1 0.02
20 44 0.96
21 1 0.02
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.32
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:165844 original size:48 final size:48
Alignment explanation
Indices: 165787--165991 Score: 315
Period size: 48 Copynumber: 4.3 Consensus size: 48
165777 CAATATGTTA
*
165787 ATTCAAGGCCAACGACATTGAGCTAAGGGAAAAGTGGACAATGTGCTG
1 ATTCAAGGCCAGCGACATTGAGCTAAGGGAAAAGTGGACAATGTGCTG
* *
165835 ATTCAAGGCCAGTGACATTGAGCTAAGGGAAAAGTAGACAATGTGCTG
1 ATTCAAGGCCAGCGACATTGAGCTAAGGGAAAAGTGGACAATGTGCTG
* * *
165883 ATTCAAGGCCAGCGACGTTGAGCAAAGGGAAAAGTGGATAATGTGCTG
1 ATTCAAGGCCAGCGACATTGAGCTAAGGGAAAAGTGGACAATGTGCTG
* * *
165931 ATTCAAGGCCAGCAACATTGAGCTAA--TAAAGGTGGACAATGTGCTG
1 ATTCAAGGCCAGCGACATTGAGCTAAGGGAAAAGTGGACAATGTGCTG
165977 ATTCAAGGCCAGCGA
1 ATTCAAGGCCAGCGA
165992 TATCAGACTT
Statistics
Matches: 142, Mismatches: 15, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
46 31 0.22
48 111 0.78
ACGTcount: A:0.35, C:0.17, G:0.29, T:0.20
Consensus pattern (48 bp):
ATTCAAGGCCAGCGACATTGAGCTAAGGGAAAAGTGGACAATGTGCTG
Found at i:166203 original size:28 final size:28
Alignment explanation
Indices: 166066--167072 Score: 739
Period size: 32 Copynumber: 33.8 Consensus size: 28
166056 TTTTTTAAAA
*
166066 AAAGG-TGCCACTAACTTATGTGGGCTTTG
1 AAAGGATGCCACTGAC-T-TGTGGGCTTTG
* *
166095 AAAAGAGTTGCCACTGACTCGTGTGAGCTTTG
1 -AAAG-GATGCCACTGACT--TGTGGGCTTTG
* * *
166127 AAAAGAGTGCCACTGGCTTATGGGCTTTG
1 AAAGGA-TGCCACTGACTTGTGGGCTTTG
*
166156 AAAAGAGTGCCACTGACTTGTGGGCTTTG
1 AAAGGA-TGCCACTGACTTGTGGGCTTTG
**
166185 AAAAAATGCCACTGACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* *
166213 AAAAGAGTGCCACTAACTTGTGGGCTTTG
1 AAAGGA-TGCCACTGACTTGTGGGCTTTG
*
166242 AAAGGGTGCCACTGACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
166270 AAAGGATGCCACTGACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* *
166298 AAATGGGTTGCCACCGACTTGTGTGGGCTTTG
1 AAA--GGATGCCACTGAC-T-TGTGGGCTTTG
* * ** * *
166330 AAATGGGTTACCACCAAATTGTGTGAGCTTTC
1 AAA--GGATGCCACTGACTTGTG-G-GCTTTG
* *
166362 AAATGGGTTGCCACCGACTTGTGTGGGCTTTG
1 AAA--GGATGCCACTGAC-T-TGTGGGCTTTG
*
166394 AGAAGGATGCCACTGACTTGTGGGCTTTA
1 A-AAGGATGCCACTGACTTGTGGGCTTTG
*
166423 AAAGGATGCCACTAACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* * *
166451 ATATGGGTTGCCA-TCGACTTGTGTGGGCTTTC
1 A-A-AGGATGCCACT-GAC-T-TGTGGGCTTTG
* *
166483 AAATGAGTTGCCACCGACTTGTGTGGGCTTTG
1 AAA-G-GATGCCACTGAC-T-TGTGGGCTTTG
**
166515 AAATAATGCCACTGACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* * *
166543 AAGTAGGTTTCCACCGACTTGTGTGGGCTTTG
1 AA--AGGATGCCACTGAC-T-TGTGGGCTTTG
*
166575 -AAGTAATGCCACTGACTTGTGGGCTTTG
1 AAAG-GATGCCACTGACTTGTGGGCTTTG
* * *
166603 -AAGTAATGCCATTGACTAGTGGGCTTTG
1 AAAG-GATGCCACTGACTTGTGGGCTTTG
166631 AGAAGGATGCCACTGACTTGTGGGCTTTG
1 A-AAGGATGCCACTGACTTGTGGGCTTTG
166660 AGAAGGATGCCACTGACTTGTGGGCTTTG
1 A-AAGGATGCCACTGACTTGTGGGCTTTG
* *
166689 AGAAGGATGCCACTAACTTGTGGGCTTTA
1 A-AAGGATGCCACTGACTTGTGGGCTTTG
*
166718 AAAGGATGCCACTGACCTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
*
166746 AAATGGGTTGCCACTGACTTGTGTGGCTTTG
1 AAA--GGATGCCACTGACTTGTG-GGCTTTG
* *
166777 AAAGGATGCCACTAACTTGTGTGGGCTTTC
1 AAAGGATGCCACTGAC-T-TGTGGGCTTTG
* * *
166807 AAATGGGTTGCCACCGACTTGTGTGGGCATTG
1 AAA--GGATGCCACTGAC-T-TGTGGGCTTTG
* *
166839 AAATAGGTTGCCA-TCGACTTGTGTGGGCTTTC
1 -AA-AGGATGCCACT-GAC-T-TGTGGGCTTTG
* *
166871 AAATGAGTTGCCACCGACTTGTGTGGGCTTTG
1 AAA-G-GATGCCACTGAC-T-TGTGGGCTTTG
* *
166903 AAATGGGTTGCCACTGACTTATGTGGGCTTTC
1 AAA--GGATGCCACTGAC-T-TGTGGGCTTTG
* * **
166935 AAATGAGTTGCCATTGACTCGTGTGGGCTTAA
1 AAA-G-GATGCCACTGACT--TGTGGGCTTTG
* *
166967 AAAGGGGTGCCACTGACTTGTAGGCTTTG
1 AAA-GGATGCCACTGACTTGTGGGCTTTG
* * * **
166996 GAAGGGTGCCACTGACTTGTGGACTTAA
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* * *
167024 AAAGGATGCCACGGAGTTGTGGAC-TTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* *
167051 AAACGGATGCCACAGAGTTGTG
1 AAA-GGATGCCACTGACTTGTG
167073 AACTTAAAAG
Statistics
Matches: 827, Mismatches: 104, Indels: 94
0.81 0.10 0.09
Matches are distributed among these distances:
27 4 0.00
28 239 0.29
29 182 0.22
30 86 0.10
31 64 0.08
32 240 0.29
33 7 0.01
34 5 0.01
ACGTcount: A:0.22, C:0.18, G:0.30, T:0.30
Consensus pattern (28 bp):
AAAGGATGCCACTGACTTGTGGGCTTTG
Found at i:167077 original size:28 final size:27
Alignment explanation
Indices: 166997--167090 Score: 107
Period size: 28 Copynumber: 3.4 Consensus size: 27
166987 TAGGCTTTGG
* * *
166997 AAGGGTGCCACTGACTTGTGGACTTAAA
1 AAGGATGCCACAGAGTTGTGGACTT-AA
*
167025 AAGGATGCCACGGAGTTGTGGACTTGAA
1 AAGGATGCCACAGAGTTGTGGACTT-AA
* *
167053 ACGGATGCCACAGAGTTGTGAACTTAA
1 AAGGATGCCACAGAGTTGTGGACTTAA
*
167080 AAGGGTGCCAC
1 AAGGATGCCAC
167091 GGAATGGTGG
Statistics
Matches: 57, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
27 11 0.19
28 46 0.81
ACGTcount: A:0.30, C:0.18, G:0.31, T:0.21
Consensus pattern (27 bp):
AAGGATGCCACAGAGTTGTGGACTTAA
Found at i:171942 original size:61 final size:61
Alignment explanation
Indices: 171855--171997 Score: 241
Period size: 61 Copynumber: 2.3 Consensus size: 61
171845 CCCTATGCAA
171855 ATGCGGAGGGTTACTCACGAAAGAATAGGTAATTTACATCCTGGAAGTTAGTGCTATGCCT
1 ATGCGGAGGGTTACTCACGAAAGAATAGGTAATTTACATCCTGGAAGTTAGTGCTATGCCT
* * * * *
171916 ATGTGGAGGGTTACTCATGAGAGAATAGGTAATTTACATCTTGGAAGTTATTGCTATGCCT
1 ATGCGGAGGGTTACTCACGAAAGAATAGGTAATTTACATCCTGGAAGTTAGTGCTATGCCT
171977 ATGCGGAGGGTTACTCACGAA
1 ATGCGGAGGGTTACTCACGAA
171998 GGCAAATAGC
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
61 74 1.00
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (61 bp):
ATGCGGAGGGTTACTCACGAAAGAATAGGTAATTTACATCCTGGAAGTTAGTGCTATGCCT
Found at i:172950 original size:21 final size:21
Alignment explanation
Indices: 172908--172950 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
172898 TTTTACCCAG
* **
172908 ATGTATCGATACATTTTTTTA
1 ATGTATCGATACATATAGTTA
172929 ATGTATCGATACATATAGTTA
1 ATGTATCGATACATATAGTTA
172950 A
1 A
172951 AATTAAGCAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (21 bp):
ATGTATCGATACATATAGTTA
Found at i:176911 original size:46 final size:46
Alignment explanation
Indices: 176825--176913 Score: 124
Period size: 46 Copynumber: 1.9 Consensus size: 46
176815 TTCATCTAAA
* * *
176825 TAGGTGGAAGATCAATGATGTTTTTATTTTCTAAGTTTCATTTTGT
1 TAGGTAGAAGATCAATGAAGTTTTTATTTTCTAAGCTTCATTTTGT
* * *
176871 TAGGTAGAAGATCAATGAAGTTTTTCTTTTGTTAGCTTCATTT
1 TAGGTAGAAGATCAATGAAGTTTTTATTTTCTAAGCTTCATTT
176914 GATTAAGTGG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 37 1.00
ACGTcount: A:0.25, C:0.08, G:0.19, T:0.48
Consensus pattern (46 bp):
TAGGTAGAAGATCAATGAAGTTTTTATTTTCTAAGCTTCATTTTGT
Found at i:177200 original size:60 final size:60
Alignment explanation
Indices: 177112--177258 Score: 165
Period size: 60 Copynumber: 2.5 Consensus size: 60
177102 GAAAACCAGT
* * * *
177112 TTTGTTTTATCTGGTTTGG-AACAAAACTAGTAAAATTGATAGT-TTTTAAGTTTTTTTTTG
1 TTTGCTTTATTTGGTTTGGCAA-AAAACTAGTAAAATTGAT-GTCTTTTAAGTTTTCTTTCG
* * * *
177172 TTTGCTTTATTTGGTTAGGCAAAAAACTAGTAAAGTTGGTTTCTTTTAAGTTTTCTTTCG
1 TTTGCTTTATTTGGTTTGGCAAAAAACTAGTAAAATTGATGTCTTTTAAGTTTTCTTTCG
*
177232 TCCT-CTTTATTTGGTTTGGCAAAAAAC
1 T-TTGCTTTATTTGGTTTGGCAAAAAAC
177259 CAATATAGTT
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
59 1 0.01
60 70 0.95
61 3 0.04
ACGTcount: A:0.25, C:0.10, G:0.17, T:0.48
Consensus pattern (60 bp):
TTTGCTTTATTTGGTTTGGCAAAAAACTAGTAAAATTGATGTCTTTTAAGTTTTCTTTCG
Found at i:182498 original size:13 final size:13
Alignment explanation
Indices: 182480--182504 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
182470 ACAAAAGATC
182480 AATGTATCGATAT
1 AATGTATCGATAT
182493 AATGTATCGATA
1 AATGTATCGATA
182505 CATTTGAGTA
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:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (13 bp):
AATGTATCGATAT
Found at i:182583 original size:19 final size:19
Alignment explanation
Indices: 182559--182659 Score: 142
Period size: 19 Copynumber: 5.6 Consensus size: 19
182549 AGCGATACAT
182559 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
182578 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
*
182597 TGCATCGATACAACACTTA
1 TGTATCGATACAACACTTA
182616 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
*
182629 TGTATCGATACAACATTTA
1 TGTATCGATACAACACTTA
182648 TGTATCGATACA
1 TGTATCGATACA
182660 GTTACTGTTT
Statistics
Matches: 74, Mismatches: 2, Indels: 12
0.84 0.02 0.14
Matches are distributed among these distances:
13 9 0.12
14 1 0.01
16 6 0.08
18 1 0.01
19 57 0.77
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.33
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:182634 original size:13 final size:13
Alignment explanation
Indices: 182616--182640 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
182606 ACAACACTTA
182616 TGTATCGATACAT
1 TGTATCGATACAT
182629 TGTATCGATACA
1 TGTATCGATACA
182641 ACATTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:182641 original size:32 final size:32
Alignment explanation
Indices: 182546--182659 Score: 147
Period size: 32 Copynumber: 3.4 Consensus size: 32
182536 GCAGTAGCTT
*
182546 TGTAGCGATACATTGTATCGATACAACACTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
*
182578 TGTATCGATACAACACTTATGCATCGATACAACACTTA
1 TGTATCGAT---ACA--T-TGTATCGATACAACACTTA
*
182616 TGTATCGATACATTGTATCGATACAACATTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
182648 TGTATCGATACA
1 TGTATCGATACA
182660 GTTACTGTTT
Statistics
Matches: 72, Mismatches: 4, Indels: 12
0.82 0.05 0.14
Matches are distributed among these distances:
32 37 0.51
33 1 0.01
35 6 0.08
37 1 0.01
38 27 0.38
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.32
Consensus pattern (32 bp):
TGTATCGATACATTGTATCGATACAACACTTA
Found at i:183573 original size:49 final size:49
Alignment explanation
Indices: 183408--183720 Score: 260
Period size: 49 Copynumber: 6.6 Consensus size: 49
183398 GAAGAATGAA
* * * * *
183408 AATGTGCTGATTCATGGCCAGCGACATTAGACTTGAAGAAG-A-ATGCC
1 AATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGAAGATGCC
* ** * * *
183455 AATATGCTGAGACAAGGCCAACGACATTGGGCTTAGGAATGTTAAAGATGCC
1 AATGTGCTGATTCAAGGCCAACGACATTGGACTTA--AA-GATGAAGATGCC
* * * *
183507 AATATGCTGATTCAAGGCCAACGATATCGGACTTAAAGATGAAGATACC
1 AATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGAAGATGCC
* ** *
183556 AATGTGCTGATTTAAGGCCGGCAACATTGGACTT-AA-A-G--G-TGCC
1 AATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGAAGATGCC
* *
183599 AA-GATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATGCC
1 AATG-TGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGAAGATGCC
**
183648 AATGTGCTGATTCAAGGCTGACGACATTGGACTT--A-A--AAG-TGCC
1 AATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGAAGATGCC
* *
183691 AATATGCTGATTCAAGGCCAGCGACATTGG
1 AATGTGCTGATTCAAGGCCAACGACATTGG
183721 TTTAAAGGTG
Statistics
Matches: 214, Mismatches: 39, Indels: 30
0.76 0.14 0.11
Matches are distributed among these distances:
42 1 0.00
43 61 0.29
44 6 0.03
45 1 0.00
46 3 0.01
47 29 0.14
48 3 0.01
49 70 0.33
50 4 0.02
51 1 0.00
52 35 0.16
ACGTcount: A:0.33, C:0.18, G:0.26, T:0.23
Consensus pattern (49 bp):
AATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGAAGATGCC
Found at i:183628 original size:43 final size:43
Alignment explanation
Indices: 183496--183814 Score: 320
Period size: 42 Copynumber: 7.2 Consensus size: 43
183486 CTTAGGAATG
* * *
183496 TTAAAGATGCCAATATGCTGATTCAAGGCCAACGATATCGGAC
1 TTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
* * * * * *
183539 TTAAAGATGAAGATACCAATGTGCTGATTTAAGGCCGGCAACATTGGAC
1 TT-AA-A-G--G-TGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
*
183588 TTAAAGGTGCCAAGATGCTGATTCAAGGCCAGCGATATTGGAC
1 TTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
* * *
183631 TTAAAGATGAAGATGCCAATGTGCTGATTCAAGG-CTGACGACATTGGAC
1 TT-AA-A-G--G-TGCCAATATGCTGATTCAAGGCCAG-CGATATTGGAC
* * *
183680 TTAAAAGTGCCAATATGCTGATTCAAGGCCAGCGACATTGG-T
1 TTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
* *
183722 TTAAAGGTGCTAATATGCTGATTCAAGGCCAGCGATATTGG-T
1 TTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
*
183764 TTAAAGGTGCCAATATGCTGATTCAAGGCCAGTGATATTGGAC
1 TTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
183807 TTAGAAGG
1 TTA-AAGG
183815 AGATGCCACC
Statistics
Matches: 230, Mismatches: 30, Indels: 31
0.79 0.10 0.11
Matches are distributed among these distances:
42 78 0.34
43 65 0.28
44 12 0.05
45 2 0.01
46 3 0.01
47 2 0.01
48 7 0.03
49 61 0.27
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (43 bp):
TTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
Found at i:183653 original size:92 final size:92
Alignment explanation
Indices: 183496--183809 Score: 410
Period size: 92 Copynumber: 3.5 Consensus size: 92
183486 CTTAGGAATG
* * * *
183496 TTAAAGATGCCAATATGCTGATTCAAGGCCAACGATATCGGACTTAAAGATGAAGATACCAATGT
1 TTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGT
* *
183561 GCTGATTTAAGGCCGGCAACATTGGAC
66 GCTGATTCAAGGCCGGCGACATTGGAC
*
183588 TTAAAGGTGCCAAGATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGT
1 TTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGT
* *
183653 GCTGATTCAAGGCTGACGACATTGGAC
66 GCTGATTCAAGGCCGGCGACATTGGAC
* * * * *
183680 TTAAAAGTGCCAATATGCTGATTCAAGGCCAGCGACATTGG--TTTAA-A-G--G-TGCTAATAT
1 TTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGT
* * *
183738 GCTGATTCAAGGCCAGCGATATTGG-T
66 GCTGATTCAAGGCCGGCGACATTGGAC
*
183764 TTAAAGGTGCCAATATGCTGATTCAAGGCCAGTGATATTGGACTTA
1 TTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTA
183810 GAAGGAGATG
Statistics
Matches: 196, Mismatches: 24, Indels: 10
0.85 0.10 0.04
Matches are distributed among these distances:
84 38 0.19
85 28 0.14
86 3 0.02
88 1 0.01
89 1 0.01
90 4 0.02
92 121 0.62
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (92 bp):
TTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGT
GCTGATTCAAGGCCGGCGACATTGGAC
Found at i:183917 original size:29 final size:29
Alignment explanation
Indices: 183879--184077 Score: 253
Period size: 29 Copynumber: 6.9 Consensus size: 29
183869 TTGAAGGTTA
*
183879 CCACTGACTTATGGGCTTTGGAAAAGATG
1 CCACTGACTTGTGGGCTTTGGAAAAGATG
*
183908 CCAC-GAACTTGTGGGCTTTGGAAAAGGGTG
1 CCACTG-ACTTGTGGGCTTTGGAAAA-GATG
* * * *
183938 CCACTAACTTGTGGGCTTT-TAAAGGTTG
1 CCACTGACTTGTGGGCTTTGGAAAAGATG
183966 CCACTGACTTGTGGGCTTTGGAAAAGATG
1 CCACTGACTTGTGGGCTTTGGAAAAGATG
* * * *
183995 CCACGGACTTGTGGG-TTTATG-AAGGTTG
1 CCACTGACTTGTGGGCTTT-GGAAAAGATG
184023 CCACTGACTTGTGGGCTTTGGAAAAGATG
1 CCACTGACTTGTGGGCTTTGGAAAAGATG
184052 CCACTGACTTGTGGGCTTTGGAAAAG
1 CCACTGACTTGTGGGCTTTGGAAAAG
184078 GTGAGGAATG
Statistics
Matches: 145, Mismatches: 18, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
28 45 0.31
29 80 0.55
30 20 0.14
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.29
Consensus pattern (29 bp):
CCACTGACTTGTGGGCTTTGGAAAAGATG
Found at i:184024 original size:57 final size:57
Alignment explanation
Indices: 183879--184070 Score: 262
Period size: 57 Copynumber: 3.3 Consensus size: 57
183869 TTGAAGGTTA
* * * * *
183879 CCACTGACTTATGGGCTTTGGAAAAGATGCCAC-GAACTTGTGGGCTTTGGAAAAGGGTG
1 CCACTGACTTGTGGGCTTT-TAAAGGTTGCCACTG-ACTTGTGGGCTTTGGAAAA-GATG
*
183938 CCACTAACTTGTGGGCTTTTAAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGATG
1 CCACTGACTTGTGGGCTTTTAAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGATG
* *
183995 CCACGGACTTGTGGG-TTTATGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGATG
1 CCACTGACTTGTGGGCTTT-TAAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGATG
184052 CCACTGACTTGTGGGCTTT
1 CCACTGACTTGTGGGCTTT
184071 GGAAAAGGTG
Statistics
Matches: 120, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
56 3 0.03
57 67 0.56
58 32 0.27
59 18 0.15
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.30
Consensus pattern (57 bp):
CCACTGACTTGTGGGCTTTTAAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGATG
Found at i:185520 original size:10 final size:10
Alignment explanation
Indices: 185511--185549 Score: 69
Period size: 10 Copynumber: 3.8 Consensus size: 10
185501 GTTGTTGTTT
185511 TTTTTTGTTTG
1 TTTTTT-TTTG
185522 TTTTTTTTTG
1 TTTTTTTTTG
185532 TTTTTTTTTG
1 TTTTTTTTTG
185542 TTTTTTTT
1 TTTTTTTT
185550 GCGAAGGACG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
10 22 0.79
11 6 0.21
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:185522 original size:14 final size:14
Alignment explanation
Indices: 185505--185540 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
185495 TTTGTTGTTG
185505 TTGTTTTTTTTTGT
1 TTGTTTTTTTTTGT
185519 TTGTTTTTTTTTGT
1 TTGTTTTTTTTTGT
185533 TT-TTTTTT
1 TTGTTTTTT
185541 GTTTTTTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 6 0.27
14 16 0.73
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (14 bp):
TTGTTTTTTTTTGT
Found at i:185522 original size:20 final size:19
Alignment explanation
Indices: 185493--185549 Score: 68
Period size: 18 Copynumber: 3.1 Consensus size: 19
185483 ATCCGAACCC
185493 TTTTTG-TTGTTGTTGTTTT
1 TTTTTGTTTGTTGTT-TTTT
185512 TTTTTGTTTGTT-TTTTTT
1 TTTTTGTTTGTTGTTTTTT
185530 TGTTTT-TTT-TTGTTTTTT
1 T-TTTTGTTTGTTGTTTTTT
185548 TT
1 TT
185550 GCGAAGGACG
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
17 3 0.09
18 15 0.43
19 12 0.34
20 5 0.14
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (19 bp):
TTTTTGTTTGTTGTTTTTT
Found at i:185534 original size:24 final size:23
Alignment explanation
Indices: 185505--185549 Score: 81
Period size: 24 Copynumber: 1.9 Consensus size: 23
185495 TTTGTTGTTG
185505 TTGTTTTTTTTTGTTTGTTTTTTT
1 TTGTTTTTTTTTGTTT-TTTTTTT
185529 TTGTTTTTTTTTGTTTTTTTT
1 TTGTTTTTTTTTGTTTTTTTT
185550 GCGAAGGACG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (23 bp):
TTGTTTTTTTTTGTTTTTTTTTT
Found at i:195983 original size:13 final size:13
Alignment explanation
Indices: 195965--195992 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
195955 TACAAAAGAT
195965 CAATGTATCGATA
1 CAATGTATCGATA
195978 CAATGTATCGATA
1 CAATGTATCGATA
195991 CA
1 CA
195993 TTTGAGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:196069 original size:19 final size:20
Alignment explanation
Indices: 196045--196097 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 20
196035 AGCGATACAT
196045 TGTATCGATACAACACT-TA
1 TGTATCGATACAACACTGTA
**
196064 TGTATCGATACAGTTACTGTA
1 TGTATCGATACA-ACACTGTA
196085 TGTATCGATACAA
1 TGTATCGATACAA
196098 ATTGTTGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 12 0.41
20 3 0.10
21 14 0.48
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (20 bp):
TGTATCGATACAACACTGTA
Found at i:196701 original size:17 final size:16
Alignment explanation
Indices: 196662--196702 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
196652 TTAGTTTATG
196662 TAGATTTG-GCTAAGC
1 TAGATTTGTGCTAAGC
*
196677 TA-ATTTGTGCTTAGAC
1 TAGATTTGTGCTAAG-C
196693 TAGATTTGTG
1 TAGATTTGTG
196703 GTTGATTAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 5 0.23
15 7 0.32
16 3 0.14
17 7 0.32
ACGTcount: A:0.24, C:0.10, G:0.24, T:0.41
Consensus pattern (16 bp):
TAGATTTGTGCTAAGC
Found at i:198720 original size:2 final size:2
Alignment explanation
Indices: 198713--198739 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
198703 AGAAAAACTA
198713 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 A
198740 GGGCATTCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:199383 original size:19 final size:20
Alignment explanation
Indices: 199359--199399 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
199349 AACTATTATG
199359 ATAAATATTAAT-AATAAAA
1 ATAAATATTAATGAATAAAA
*
199378 ATAAATATTAATGATTAAAA
1 ATAAATATTAATGAATAAAA
199398 AT
1 AT
199400 TTTAAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (20 bp):
ATAAATATTAATGAATAAAA
Found at i:200790 original size:4 final size:4
Alignment explanation
Indices: 200781--200808 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
200771 ATTAAATATT
200781 AATA AATA AATA AATA AATA AATA AATA
1 AATA AATA AATA AATA AATA AATA AATA
200809 TAATTAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AATA
Found at i:209158 original size:16 final size:16
Alignment explanation
Indices: 209137--209194 Score: 64
Period size: 16 Copynumber: 3.6 Consensus size: 16
209127 AACTAAAACC
209137 TAAACTCGAAAATACT
1 TAAACTCGAAAATACT
209153 TAAACTCG-AAATGACT
1 TAAACTCGAAAAT-ACT
* **
209169 TAAACCCGAAAAGGCT
1 TAAACTCGAAAATACT
*
209185 CAAACTCGAA
1 TAAACTCGAA
209195 TAGGCTCGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
15 4 0.11
16 28 0.80
17 3 0.09
ACGTcount: A:0.47, C:0.22, G:0.12, T:0.19
Consensus pattern (16 bp):
TAAACTCGAAAATACT
Found at i:209199 original size:16 final size:16
Alignment explanation
Indices: 209170--209211 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
209160 GAAATGACTT
209170 AAACCCGAAAAGGCTC
1 AAACCCGAAAAGGCTC
* *
209186 AAACTCGAATAGGCTC
1 AAACCCGAAAAGGCTC
*
209202 GAACCC-AAAA
1 AAACCCGAAAA
209212 AAGACCAAAA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
15 3 0.14
16 18 0.86
ACGTcount: A:0.45, C:0.29, G:0.17, T:0.10
Consensus pattern (16 bp):
AAACCCGAAAAGGCTC
Found at i:209207 original size:32 final size:31
Alignment explanation
Indices: 209171--209244 Score: 76
Period size: 32 Copynumber: 2.3 Consensus size: 31
209161 AAATGACTTA
* * *
209171 AACCCGAAAAGGCTCAAACTCGAATAGGCTCG
1 AACCCGAAAAGAC-CAAAATCGAATAAGCTCG
* *
209203 AACCCAAAAAAGACCAAAATCGAATAAGCTTG
1 AACCC-GAAAAGACCAAAATCGAATAAGCTCG
*
209235 AACTCGAAAA
1 AACCCGAAAA
209245 ATATCAAACT
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
31 4 0.12
32 24 0.71
33 6 0.18
ACGTcount: A:0.47, C:0.24, G:0.16, T:0.12
Consensus pattern (31 bp):
AACCCGAAAAGACCAAAATCGAATAAGCTCG
Found at i:214165 original size:191 final size:189
Alignment explanation
Indices: 213778--214191 Score: 523
Period size: 191 Copynumber: 2.2 Consensus size: 189
213768 AGCAGGGCTG
** *
213778 GAGTATCCTTTTGGAATAGTAGGGATGGAGTTT-TTCCAAAGTTATAAATATTTAAGAGCAAAGA
1 GAGTATCCCCTTGGAATAGTAGGGATGGAGTTTCTT-CAAAGATATAAATATTTAAGAGCAAAGA
** **
213842 GAAAATTTAATTTTTATTTTTATGAAGAATGGGATTAGAGTATTCCCTCAGAGTAGTGGGGATGG
65 GAAAATTTAATTTTTATTTTTATGAAGAATGGGATTAGACCACCCCCTCAGAGTAGTGGGGATGG
* * * * *
213907 AGTTTCCCTAAGGATAAAATTATATGAAAGAAAATTTAAATTTTTTTCACAACGGGGTTA
130 AGTTTCCCTAAAGATAAAATTATATCAAAGAAAATTTAAATATTTATCACAACGGGATTA
* * * *
213967 AAGTATCCCCTTGGAATAGTAGGGATGGAGTTTCCTT-GAAGATATAAATATTTAAGAGTAATGA
1 GAGTATCCCCTTGGAATAGTAGGGATGGAGTTT-CTTCAAAGATATAAATATTTAAGAGCAAAGA
* *
214031 GAAAATTTAATTTTTATTTTTTTATGAAGAATAGGGTTTA-ACCACCCCCTCGGAGTAGTGGGGA
65 GAAAATTTAATTTTTA--TTTTTATGAAGAAT-GGGATTAGACCACCCCCTCAGAGTAGTGGGGA
* *
214095 TGGAGTTTTTCC-AAAGATAAAATTATA-CAAAGAAAAATTTAAATATTTATCAGAACGGGATTA
127 TGGAG-TTTCCCTAAAGATAAAATTATATCAAAG-AAAATTTAAATATTTATCACAACGGGATTA
* * *
214158 GAGTATCCCCTTGGAACAGTGGGGATAGAGTTTC
1 GAGTATCCCCTTGGAATAGTAGGGATGGAGTTTC
214192 GCTAAGAATA
Statistics
Matches: 194, Mismatches: 24, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
189 69 0.36
190 5 0.03
191 109 0.56
192 11 0.06
ACGTcount: A:0.35, C:0.10, G:0.22, T:0.33
Consensus pattern (189 bp):
GAGTATCCCCTTGGAATAGTAGGGATGGAGTTTCTTCAAAGATATAAATATTTAAGAGCAAAGAG
AAAATTTAATTTTTATTTTTATGAAGAATGGGATTAGACCACCCCCTCAGAGTAGTGGGGATGGA
GTTTCCCTAAAGATAAAATTATATCAAAGAAAATTTAAATATTTATCACAACGGGATTA
Found at i:218360 original size:31 final size:31
Alignment explanation
Indices: 218318--218477 Score: 234
Period size: 31 Copynumber: 5.2 Consensus size: 31
218308 GTTTGGGTTC
* * *
218318 GAAAAGGTGCCACGGAGTTGTGGACTTTGAA
1 GAAAAGATGCCACTGAGTCGTGGACTTTGAA
218349 GAAAAGATGCCACTGAGTCGTGGACTTTGAA
1 GAAAAGATGCCACTGAGTCGTGGACTTTGAA
*
218380 GAAAAGATGCCACTGAGTCATGGACTTTGAA
1 GAAAAGATGCCACTGAGTCGTGGACTTTGAA
*
218411 GAAAAGATGCCACTGAGCCGTGGACTTTTG--
1 GAAAAGATGCCACTGAGTCGTGGAC-TTTGAA
*
218441 GAAGAGATTGCCACTGAGTCGTGGACTTTGAA
1 GAAAAGA-TGCCACTGAGTCGTGGACTTTGAA
218473 GAAAA
1 GAAAA
218478 AAGATTTGAA
Statistics
Matches: 116, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
30 10 0.09
31 98 0.84
32 8 0.07
ACGTcount: A:0.32, C:0.16, G:0.30, T:0.23
Consensus pattern (31 bp):
GAAAAGATGCCACTGAGTCGTGGACTTTGAA
Found at i:219491 original size:9 final size:9
Alignment explanation
Indices: 219472--219531 Score: 61
Period size: 9 Copynumber: 6.9 Consensus size: 9
219462 AGATTTTCTG
219472 TTTTGTTTT
1 TTTTGTTTT
*
219481 TTGT-TTTT
1 TTTTGTTTT
219489 TTTTGTTTT
1 TTTTGTTTT
*
219498 TTTTCTTTT
1 TTTTGTTTT
*
219507 TTTT-CTTT
1 TTTTGTTTT
**
219515 TTTCCTTTT
1 TTTTGTTTT
219524 TTTTGTTT
1 TTTTGTTT
219532 GGAAAAGAAC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
8 13 0.32
9 28 0.68
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.87
Consensus pattern (9 bp):
TTTTGTTTT
Found at i:219492 original size:10 final size:10
Alignment explanation
Indices: 219477--219510 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
219467 TTCTGTTTTG
219477 TTTTTTGTTT
1 TTTTTTGTTT
219487 TTTTTTGTTT
1 TTTTTTGTTT
219497 TTTTTCT-TTT
1 TTTTT-TGTTT
219507 TTTT
1 TTTT
219511 CTTTTTTCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 22 0.96
11 1 0.04
ACGTcount: A:0.00, C:0.03, G:0.06, T:0.91
Consensus pattern (10 bp):
TTTTTTGTTT
Found at i:219494 original size:17 final size:17
Alignment explanation
Indices: 219472--219531 Score: 75
Period size: 17 Copynumber: 3.5 Consensus size: 17
219462 AGATTTTCTG
*
219472 TTTTGTTTTTTGTTTTT
1 TTTTGTTTTTTCTTTTT
*
219489 TTTTGTTTTTTTTCTTTT
1 TTTTGTTTTTTCT-TTTT
* *
219507 TTTTCTTTTTTCCTTTT
1 TTTTGTTTTTTCTTTTT
219524 TTTTGTTT
1 TTTTGTTT
219532 GGAAAAGAAC
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
17 23 0.62
18 14 0.38
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.87
Consensus pattern (17 bp):
TTTTGTTTTTTCTTTTT
Found at i:219783 original size:8 final size:8
Alignment explanation
Indices: 219770--219799 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
219760 GCCTTTGCAC
219770 TTTTTTTG
1 TTTTTTTG
219778 TTTTTTTG
1 TTTTTTTG
219786 -TTTTTTG
1 TTTTTTTG
219793 TTTTTTT
1 TTTTTTT
219800 TTATGTTTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (8 bp):
TTTTTTTG
Found at i:219789 original size:15 final size:15
Alignment explanation
Indices: 219771--219799 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
219761 CCTTTGCACT
219771 TTTTTTGTTTTTTTG
1 TTTTTTGTTTTTTTG
219786 TTTTTTGTTTTTTT
1 TTTTTTGTTTTTTT
219800 TTATGTTTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (15 bp):
TTTTTTGTTTTTTTG
Found at i:220405 original size:19 final size:18
Alignment explanation
Indices: 220381--220448 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
220371 CAGTAGCTAA
220381 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
220400 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
220415 -T-TGTATCGATACAACAC
1 TTATGTATCGATACAA-AC
220432 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
220449 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 2 0.05
19 27 0.63
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:220421 original size:13 final size:13
Alignment explanation
Indices: 220403--220427 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
220393 ACAATACTTA
220403 TGTATCGATACAT
1 TGTATCGATACAT
220416 TGTATCGATACA
1 TGTATCGATACA
220428 ACACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:220425 original size:32 final size:32
Alignment explanation
Indices: 220384--220446 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
220374 TAGCTAATTA
*
220384 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAACACTTATGTATCGATACAT
220416 TGTATCGATACAACACTTATGTATCGATACA
1 TGTATCGATACAACACTTATGTATCGATACA
220447 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAACACTTATGTATCGATACAT
Found at i:224669 original size:20 final size:20
Alignment explanation
Indices: 224644--224720 Score: 102
Period size: 20 Copynumber: 3.9 Consensus size: 20
224634 GTAAAAAGAT
224644 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
*
224664 AGAATGTATCGATACATTCA
1 AGAATGTATCGATACATTGA
* *
224684 TA-CATGTATCGATGCATTGA
1 -AGAATGTATCGATACATTGA
*
224704 AAAATGTATCGATACAT
1 AGAATGTATCGATACAT
224721 CTAGGTAAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
19 1 0.02
20 47 0.96
21 1 0.02
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:224762 original size:50 final size:50
Alignment explanation
Indices: 224687--224781 Score: 156
Period size: 50 Copynumber: 1.9 Consensus size: 50
224677 ACATTCATAC
* *
224687 ATGTATCGATGCATTGAAAAATGTATCGATACATCTA-GGTAAAAGACAAA
1 ATGTATCAATACATTGAAAAATGTATCGATACATC-AGGGTAAAAGACAAA
224737 ATGTATCAATACATTGAAAAATGTATCGATACATCAGGGTAAAAG
1 ATGTATCAATACATTGAAAAATGTATCGATACATCAGGGTAAAAG
224782 TGACTTTTCC
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
49 1 0.02
50 41 0.98
ACGTcount: A:0.44, C:0.12, G:0.18, T:0.26
Consensus pattern (50 bp):
ATGTATCAATACATTGAAAAATGTATCGATACATCAGGGTAAAAGACAAA
Found at i:225847 original size:48 final size:49
Alignment explanation
Indices: 225754--225887 Score: 200
Period size: 48 Copynumber: 2.8 Consensus size: 49
225744 TGAGAGGAGT
** * *
225754 GCCAATGTGCCAATTCAAGGCCAGCAACATTGGGTTAATGGAAAAG-TG
1 GCCAATGTGCTGATTCAAGGCCAGCAACATTGGGCTAATGGAAAAGAAG
*
225802 GACCAATGTGCTGATTCAAGGCC-GCTACATTGGGCTAATGGAAAAGAAG
1 G-CCAATGTGCTGATTCAAGGCCAGCAACATTGGGCTAATGGAAAAGAAG
225851 GCCAATGTGCTGATTCAAGGCCAGCAACATTGGGCTA
1 GCCAATGTGCTGATTCAAGGCCAGCAACATTGGGCTA
225888 CTAAAGGTGC
Statistics
Matches: 77, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
48 43 0.56
49 34 0.44
ACGTcount: A:0.31, C:0.20, G:0.28, T:0.21
Consensus pattern (49 bp):
GCCAATGTGCTGATTCAAGGCCAGCAACATTGGGCTAATGGAAAAGAAG
Found at i:226009 original size:32 final size:33
Alignment explanation
Indices: 225957--226051 Score: 113
Period size: 32 Copynumber: 2.9 Consensus size: 33
225947 TGGTAATTTG
*
225957 AAAAGGGTTGCCACTGACTTGTGTGGGCTTTAA
1 AAAAAGGTTGCCACTGACTTGTGTGGGCTTTAA
* * *
225990 AAAAAGGTT-CCACTAACTTGTGTAGGCTTTGA
1 AAAAAGGTTGCCACTGACTTGTGTGGGCTTTAA
* * *
226022 AAAGA-GTTGCCATTGACTTGCGTGGGCTTT
1 AAAAAGGTTGCCACTGACTTGTGTGGGCTTT
226052 GAAAGGGTGC
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
31 3 0.06
32 41 0.79
33 8 0.15
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.32
Consensus pattern (33 bp):
AAAAAGGTTGCCACTGACTTGTGTGGGCTTTAA
Found at i:226075 original size:28 final size:28
Alignment explanation
Indices: 225953--226766 Score: 889
Period size: 28 Copynumber: 28.4 Consensus size: 28
225943 AAAGTGGTAA
225953 TTTGAAAAGGGTTGCCACTGACTTGTGTGGGC
1 TTTG-AAAGGG-TGCCACTGAC-T-TGTGGGC
* * * *
225985 TTTAAAAAAAGGTTCCACTAACTTGTGTAGGC
1 TTT--GAAAGGGTGCCACTGACTTGTG--GGC
* *
226017 TTTGAAAAGAGTTGCCATTGACTTGCGTGGGC
1 TTTG-AAAG-GGTGCCACTGACTT--GTGGGC
*
226049 TTTGAAAGGGTGCCACTGAGTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
* * * *
226077 ATTGAAATGGTGCCACTAACTTATGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
* *
226105 TTTGAAATGATGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
* *
226133 TTTAAAATGAG-GCCACT-ATCTTGTAGGG-
1 TTTGAAA-GGGTGCCACTGA-CTTGT-GGGC
* *
226161 TTTAAAAGGGTGCCACCGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
* *
226189 TTTAAAAGGGTATGCCACTGTCTTGTGGGC
1 TTTGAAAGGG--TGCCACTGACTTGTGGGC
*
226219 TTTGAAAAGGGTGCCATTGACTTGTGGGC
1 TTTG-AAAGGGTGCCACTGACTTGTGGGC
*
226248 TTTGAAAGGGTGCCACTGATTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
* *
226276 TTTGAAAGGATGCCACTGACTTATGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
*
226304 TTTGAAAGGGTGTCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
* * ** *
226332 TTTGAAATGATGCCACCAACTTGTGCGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
*
226360 TTTGAAAGGATGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
226388 TTTGAAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
* *
226416 TTTGAAAGGATGCCACCGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
* ** *
226444 TTTGAAAGGATGCCACCAACTTATGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
226472 TTTGAAAGGGTATGCCACT-ATCTTGTGGGC
1 TTTGAAAGGG--TGCCACTGA-CTTGTGGGC
*
226502 TTTGAAAAGGTGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
*
226530 TTTGAAAGTGTGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
*
226558 TTTGAAAGGGCGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
* *
226586 TTTGAAAGGATGCCGCTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
* *
226614 TTTGAAAGGATGCCAGTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
* * *
226642 TTTGAAAAGATGCCAGTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
* * * *
226670 TTTGAAAAGATGCTAGTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
* *
226698 TTTGAAAAGATGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
* * * *
226726 ATTGAGAAGGATGTCACTGACTTGTGGGA
1 TTTGA-AAGGGTGCCACTGACTTGTGGGC
226755 TTTGAAAAGGGT
1 TTTG-AAAGGGT
226767 CGTATTGATG
Statistics
Matches: 680, Mismatches: 79, Indels: 49
0.84 0.10 0.06
Matches are distributed among these distances:
27 6 0.01
28 506 0.74
29 54 0.08
30 58 0.09
31 14 0.02
32 34 0.05
33 5 0.01
34 3 0.00
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.30
Consensus pattern (28 bp):
TTTGAAAGGGTGCCACTGACTTGTGGGC
Found at i:237667 original size:15 final size:15
Alignment explanation
Indices: 237628--237672 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
237618 GTTTATCGAC
*
237628 GATTTTGTGGTGGGT
1 GATTTTGTGGTGGAT
**
237643 GATTAGGTGGTGGAT
1 GATTTTGTGGTGGAT
237658 GATTTTGTGGTGGAT
1 GATTTTGTGGTGGAT
237673 TTAGCGGAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.13, C:0.00, G:0.44, T:0.42
Consensus pattern (15 bp):
GATTTTGTGGTGGAT
Found at i:245195 original size:20 final size:19
Alignment explanation
Indices: 245165--245238 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 19
245155 AAAAGACAGG
*
245165 ATGTATTGATACATTGAAGA
1 ATGTATCGATACATTGAA-A
* * *
245185 ATGTGTCGATACATTCATAC
1 ATGTATCGATACATTGA-AA
*
245205 ATGTATCAATACATTGAAAA
1 ATGTATCGATACATTG-AAA
245225 ATGTATCGATACAT
1 ATGTATCGATACAT
245239 CTGGGTAAAA
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
20 41 0.95
21 2 0.05
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (19 bp):
ATGTATCGATACATTGAAA
Found at i:245298 original size:24 final size:24
Alignment explanation
Indices: 245221--245303 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 24
245211 CAATACATTG
*
245221 AAAAATGTATCGATACATCTGGGT
1 AAAAATGTATCGATACATCTAGGT
*
245245 AAAAGATATAATGTATTGATACAT-TA---
1 ---A-A-A-AATGTATCGATACATCTAGGT
245271 AAAAATGTATCGATACATCTAGGT
1 AAAAATGTATCGATACATCTAGGT
245295 AAAAATGTA
1 AAAAATGTA
245304 ACTTTTTCAT
Statistics
Matches: 46, Mismatches: 3, Indels: 17
0.70 0.05 0.26
Matches are distributed among these distances:
20 14 0.30
21 3 0.07
22 1 0.02
23 1 0.02
24 9 0.20
27 1 0.02
28 1 0.02
29 2 0.04
30 14 0.30
ACGTcount: A:0.46, C:0.08, G:0.16, T:0.30
Consensus pattern (24 bp):
AAAAATGTATCGATACATCTAGGT
Found at i:246412 original size:60 final size:59
Alignment explanation
Indices: 246312--246514 Score: 221
Period size: 60 Copynumber: 3.4 Consensus size: 59
246302 TCACTCTATC
* *
246312 TGGTTAGG-AACAAAACTAGTAAAATTGGTAGT-TTTTAAGTTTTCTTTTATCTACTTTATT
1 TGGTTAGGCAA-AAGACTAATAAAATTGGTA-TCTTTTAAGTTTTCTTTTATCT-CTTTATT
* * * * * *
246372 TGGTTAGGCAAAAGACCAATAAAGTTGGTATCTTTAAAGTTTTCTTTCATCTGTTTTATC
1 TGGTTAGGCAAAAGACTAATAAAATTGGTATCTTTTAAGTTTTCTTTTATCT-CTTTATT
* * *
246432 TGGTTAGGCAAAAGACTAGTAAAATTGGTACCTTTTAAGTTTTCTTTTGTCCTCTTTATT
1 TGGTTAGGCAAAAGACTAATAAAATTGGTATCTTTTAAGTTTTCTTTTAT-CTCTTTATT
* * *
246492 TAGTAAGGCAAAAAACTAATAAA
1 TGGTTAGGCAAAAGACTAATAAA
246515 GCATTCTTTT
Statistics
Matches: 118, Mismatches: 22, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
59 1 0.01
60 113 0.96
61 4 0.03
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (59 bp):
TGGTTAGGCAAAAGACTAATAAAATTGGTATCTTTTAAGTTTTCTTTTATCTCTTTATT
Found at i:248401 original size:13 final size:13
Alignment explanation
Indices: 248383--248407 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
248373 CATAAAATGT
248383 TGTATCGATACAA
1 TGTATCGATACAA
248396 TGTATCGATACA
1 TGTATCGATACA
248408 TTTTTTTTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:248489 original size:13 final size:13
Alignment explanation
Indices: 248471--248495 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
248461 ATTACTCACA
248471 TGTATCGATACAT
1 TGTATCGATACAT
248484 TGTATCGATACA
1 TGTATCGATACA
248496 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:248560 original size:52 final size:52
Alignment explanation
Indices: 248504--248628 Score: 214
Period size: 52 Copynumber: 2.4 Consensus size: 52
248494 CACTGATCTT
*
248504 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
248556 TGTATCGATACAAGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
248608 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
248629 CTTTTCATAT
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 68 1.00
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:253409 original size:52 final size:52
Alignment explanation
Indices: 253348--253487 Score: 192
Period size: 52 Copynumber: 2.7 Consensus size: 52
253338 TCTAGAATGA
* *
253348 AAATGTATCGATACATTTTTCATTGTATCGATACATTCT-GAATTTTTGAGCC
1 AAATGTATCGATACATTATTCATTGTATCGATACATTCTCG-ATTTTTGACCC
* * *
253400 AAATGTATCGATACATTCTTCATTGTATCGATATATTCTCGATTTTTTACCC
1 AAATGTATCGATACATTATTCATTGTATCGATACATTCTCGATTTTTGACCC
* **
253452 AAATATATCGATACATTATTCAACGTATCGATACAT
1 AAATGTATCGATACATTATTCATTGTATCGATACAT
253488 GCAAGCAATT
Statistics
Matches: 78, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
52 77 0.99
53 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.41
Consensus pattern (52 bp):
AAATGTATCGATACATTATTCATTGTATCGATACATTCTCGATTTTTGACCC
Found at i:255842 original size:26 final size:26
Alignment explanation
Indices: 255804--255861 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 26
255794 ATTTACCAAA
*
255804 ATTTTATCGGGGA-TACT-TCAACCCC
1 ATTTTTTCGGGGATTACTCT-AACCCC
255829 ATTTTTTCGAGGGATTACTCTAACCCC
1 ATTTTTTCG-GGGATTACTCTAACCCC
255856 ATTTTT
1 ATTTTT
255862 AAAATTGTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 8 0.28
26 4 0.14
27 16 0.55
28 1 0.03
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.40
Consensus pattern (26 bp):
ATTTTTTCGGGGATTACTCTAACCCC
Found at i:256021 original size:102 final size:96
Alignment explanation
Indices: 255813--256060 Score: 237
Period size: 102 Copynumber: 2.5 Consensus size: 96
255803 AATTTTATCG
* * * * * *
255813 GGGATACTTCAACCCCATTTTTTCGAGGGATTACTCTAACCCCATTTTTAAAATTGTCAAAATTT
1 GGGATACTCCAACCCCATTCTTCCAAGGGAATACTCTAACCCCATTTTTAAAATAGTCAAAATTT
*
255878 AAATCTTATTTTCATCTGAGTCATAATCATT
66 AAATCTTATTTTCATCTGAGTCATAATCATC
* **
255909 GGGAACACTCCAACCCCATTCTTCCAAGGGAATACTCTAACCTTATTTTTAAAAAAAACTAGTCA
1 GGG-ATACTCCAACCCCATTCTTCCAAGGGAATACTCTAACCCCATTTTT----AAAA-TAGTCA
* ** *
255974 AGATTTAAATCTTATTTTCATCTG-GATTGTCATCATC
60 AAATTTAAATCTTATTTTCATCTGAG-TCATAATCATC
* * ** * *
256011 GAGGATACTCCAACTCCATTCCTCTGAGGGGATACTCCAACCCCATTTTT
1 G-GGATACTCCAACCCCATTCTTCCAAGGGAATACTCTAACCCCATTTTT
256061 CAACCAAAAT
Statistics
Matches: 121, Mismatches: 23, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
96 3 0.02
97 38 0.31
101 5 0.04
102 73 0.60
103 2 0.02
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.35
Consensus pattern (96 bp):
GGGATACTCCAACCCCATTCTTCCAAGGGAATACTCTAACCCCATTTTTAAAATAGTCAAAATTT
AAATCTTATTTTCATCTGAGTCATAATCATC
Found at i:257162 original size:33 final size:33
Alignment explanation
Indices: 257125--257191 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
257115 TTCAACGATT
257125 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
257158 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
257191 T
1 T
257192 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:257163 original size:13 final size:13
Alignment explanation
Indices: 257145--257169 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
257135 CATAAAATGT
257145 TGTATCGATACAA
1 TGTATCGATACAA
257158 TGTATCGATACA
1 TGTATCGATACA
257170 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:257250 original size:13 final size:13
Alignment explanation
Indices: 257232--257256 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
257222 ATTACTCAAA
257232 TGTATCGATACAT
1 TGTATCGATACAT
257245 TGTATCGATACA
1 TGTATCGATACA
257257 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:257358 original size:52 final size:52
Alignment explanation
Indices: 257265--257392 Score: 249
Period size: 52 Copynumber: 2.5 Consensus size: 52
257255 CACTGATCTT
257265 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACATTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATTAAA
257316 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATTAAA
257368 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
257393 TCATATTTCG
Statistics
Matches: 76, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
51 19 0.25
52 57 0.75
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATTAAA
Found at i:265626 original size:30 final size:30
Alignment explanation
Indices: 265590--265646 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
265580 AAATACCTTT
265590 TCAAAGTCCACGACTCAGTGGCATTTTGTC
1 TCAAAGTCCACGACTCAGTGGCATTTTGTC
265620 TCAAAGTCCACGACTCAGTGGCATTTT
1 TCAAAGTCCACGACTCAGTGGCATTTT
265647 TTCTTTAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (30 bp):
TCAAAGTCCACGACTCAGTGGCATTTTGTC
Found at i:265681 original size:33 final size:34
Alignment explanation
Indices: 265622--265981 Score: 338
Period size: 33 Copynumber: 10.8 Consensus size: 34
265612 ATTTTGTCTC
* * *
265622 AAAGTCCACGACTCAGTGGCA-T-TTTTTC-TTT
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCTTTT
** *
265653 AAAGCCCACAACTCTATGGCACACTTTTTCTTTTT
1 AAAGCCCACAACTCCGTGGCACTCTTTTTC-TTTT
**
265688 AAAGCCCACAACTTTGTGGCACTCTTTTTCCCTTTT
1 AAAGCCCACAACTCCGTGGCACTCTTTTT--CTTTT
265724 CAAAGCCCACAACTCCGTGGCAC-CTTTTTCTTTTT
1 -AAAGCCCACAACTCCGTGGCACTCTTTTTC-TTTT
* *
265759 ACAGCCCATAACTCCGTGGCAC-C-----CTTTT
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCTTTT
* * * *
265787 -AAGTCCACGACTACGTGGCACTC-TTTTCCTTT
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCTTTT
* *
265819 AAAGCCCACAACTCCGTGGCACTCTTTTCCTTCT
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCTTTT
*
265853 -AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT
1 AAAGCCCACAACTCCGTGGCACTCTTTTT-CTTTT
265887 -AAGCCCACAACTCCGTGGCACTCTTTTTTCCCTTTT
1 AAAGCCCACAACTCCGTGGCACTC-TTTTT--CTTTT
*
265923 AAAGCCCACAACTCCGTGGCAC-CTTGTTCTTTT
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCTTTT
* * *
265956 TAAGTCCACAACTTCGTGGCA-TCTTT
1 AAAGCCCACAACTCCGTGGCACTCTTT
265982 CACCCTTTCT
Statistics
Matches: 278, Mismatches: 31, Indels: 38
0.80 0.09 0.11
Matches are distributed among these distances:
27 16 0.06
28 5 0.02
29 1 0.00
31 17 0.06
32 4 0.01
33 79 0.28
34 56 0.20
35 42 0.15
36 16 0.06
37 42 0.15
ACGTcount: A:0.21, C:0.33, G:0.13, T:0.34
Consensus pattern (34 bp):
AAAGCCCACAACTCCGTGGCACTCTTTTTCTTTT
Found at i:265859 original size:164 final size:164
Alignment explanation
Indices: 265623--265945 Score: 442
Period size: 164 Copynumber: 2.0 Consensus size: 164
265613 TTTTGTCTCA
* * * *
265623 AAGTCCACGACTCAGTGGCATTTTTTCTTTAAAGCCCACAACTCTATGGCACACTTTTTCTTTTT
1 AAGTCCACGACTCAGTGGCATTTTTCCTTTAAAGCCCACAACTCCATGGCACACTTTTTCCTTCT
**
265688 AAAGCCCACAACTTTGTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCAC-C-TTT
66 AAAGCCCACAACTCCGTGGCACTCTTTTT-CC--TTCAAAGCCCACAACTCCGTGGCACTCTTTT
* * *
265751 TT-CTTTTTACAGCCCATAACTCCGTGGCACCCTTTT
128 TTCCCTTTTAAAGCCCACAACTCCGTGGCACCCTTTT
* *
265787 AAGTCCACGACT-ACGTGGCACTCTTTTCCTTTAAAGCCCACAACTCCGTGGCACTC-TTTTCCT
1 AAGTCCACGACTCA-GTGGCA-T-TTTTCCTTTAAAGCCCACAACTCCATGGCACACTTTTTCCT
*
265850 TCT-AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGCCCACAACTCCGTGGCACTCTTTT
63 TCTAAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCAAAGCCCACAACTCCGTGGCACTCTTTT
265914 TTCCCTTTTAAAGCCCACAACTCCGTGGCACC
128 TTCCCTTTTAAAGCCCACAACTCCGTGGCACC
265946 TTGTTCTTTT
Statistics
Matches: 141, Mismatches: 12, Indels: 12
0.85 0.07 0.07
Matches are distributed among these distances:
161 24 0.17
162 1 0.01
163 8 0.06
164 70 0.50
165 9 0.06
166 29 0.21
ACGTcount: A:0.21, C:0.34, G:0.13, T:0.33
Consensus pattern (164 bp):
AAGTCCACGACTCAGTGGCATTTTTCCTTTAAAGCCCACAACTCCATGGCACACTTTTTCCTTCT
AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCAAAGCCCACAACTCCGTGGCACTCTTTTTTC
CCTTTTAAAGCCCACAACTCCGTGGCACCCTTTT
Found at i:266062 original size:34 final size:33
Alignment explanation
Indices: 265983--266221 Score: 349
Period size: 33 Copynumber: 7.2 Consensus size: 33
265973 GGCATCTTTC
*
265983 ACCCTT-TCTAAAGCCCACACAGGTCGGTGGCA
1 ACCCTTCTCTAAAGCCCACACAAGTCGGTGGCA
* *
266015 AACATTCTCTAAAGCCCACACAAGTCGGTGGCAA
1 ACCCTTCTCTAAAGCCCACACAAGTCGGTGGC-A
266049 ACCCTTCTCTAAAGCCCACACAAGTCGGTGGCA
1 ACCCTTCTCTAAAGCCCACACAAGTCGGTGGCA
266082 A-CCTTCCTCTAAAGCCCACACAAGTCGGTGGCAA
1 ACCCTT-CTCTAAAGCCCACACAAGTCGGTGGC-A
* * *
266116 ACCCTTCCCCAAAGCCCACACAAGTTGGTGGCA
1 ACCCTTCTCTAAAGCCCACACAAGTCGGTGGCA
* *
266149 ACCCTTC-CCAAAGCCCACACAAGTTGGTGGCA
1 ACCCTTCTCTAAAGCCCACACAAGTCGGTGGCA
*
266181 ACCATTCTCTAAAGCCCACACAAGTCGGTGGCA
1 ACCCTTCTCTAAAGCCCACACAAGTCGGTGGCA
266214 ACCCTTCT
1 ACCCTTCT
266222 AAGCCCAATA
Statistics
Matches: 189, Mismatches: 12, Indels: 11
0.89 0.06 0.05
Matches are distributed among these distances:
32 39 0.21
33 90 0.48
34 56 0.30
35 4 0.02
ACGTcount: A:0.28, C:0.36, G:0.18, T:0.18
Consensus pattern (33 bp):
ACCCTTCTCTAAAGCCCACACAAGTCGGTGGCA
Found at i:266076 original size:67 final size:67
Alignment explanation
Indices: 265983--266221 Score: 351
Period size: 67 Copynumber: 3.6 Consensus size: 67
265973 GGCATCTTTC
* *
265983 ACCCTT-TCTAAAGCCCACACAGGTCGGTGGCAAACATTCTCTAAAGCCCACACAAGTCGGTGGC
1 ACCCTTCTCTAAAGCCCACACAAGTCGGTGGCAAACCTTCTCTAAAGCCCACACAAGTCGGTGGC
266047 AA
66 AA
266049 ACCCTTCTCTAAAGCCCACACAAGTCGGTGGC-AACCTTCCTCTAAAGCCCACACAAGTCGGTGG
1 ACCCTTCTCTAAAGCCCACACAAGTCGGTGGCAAACCTT-CTCTAAAGCCCACACAAGTCGGTGG
266113 CAA
65 CAA
* * * * * *
266116 ACCCTTCCCCAAAGCCCACACAAGTTGGTGGCAACCCTTC-CCAAAGCCCACACAAGTTGGTGGC
1 ACCCTTCTCTAAAGCCCACACAAGTCGGTGGCAAACCTTCTCTAAAGCCCACACAAGTCGGTGGC
266180 -A
66 AA
* *
266181 ACCATTCTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCT
1 ACCCTTCTCTAAAGCCCACACAAGTCGGTGGCAAACCTTCT
266222 AAGCCCAATA
Statistics
Matches: 157, Mismatches: 12, Indels: 8
0.89 0.07 0.05
Matches are distributed among these distances:
65 37 0.24
66 33 0.21
67 82 0.52
68 5 0.03
ACGTcount: A:0.28, C:0.36, G:0.18, T:0.18
Consensus pattern (67 bp):
ACCCTTCTCTAAAGCCCACACAAGTCGGTGGCAAACCTTCTCTAAAGCCCACACAAGTCGGTGGC
AA
Found at i:266279 original size:49 final size:49
Alignment explanation
Indices: 266221--266981 Score: 975
Period size: 49 Copynumber: 15.7 Consensus size: 49
266211 GCAACCCTTC
* * *
266221 TAAGCCCAATATAGCTGGCCCTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
266270 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC-TCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
266318 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
266361 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC--TT-CATCTT
* * * * *
266413 TAAGTCCAATGTAGCTGGCCTTGACTCATCACATTGGCA-CTTGCACCAT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTT-CATCTT
* *
266462 TAAGTCC-ATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
266510 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC-TCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
266558 TAAATCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
266601 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
266650 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCA-CAAT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATC-TT
* * *
266699 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACTTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * * * *
266748 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTAGCA-CTTGCACCAT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTT-CATCTT
* *
266797 TAAGTCC-ATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
266845 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
266894 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC--TT-CATCTT
* *
266946 TAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTG
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTG
266982 ACATCCTTTT
Statistics
Matches: 619, Mismatches: 68, Indels: 47
0.84 0.09 0.06
Matches are distributed among these distances:
43 79 0.13
45 2 0.00
48 163 0.26
49 294 0.47
50 2 0.00
51 3 0.00
52 76 0.12
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.31
Consensus pattern (49 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
Found at i:266546 original size:97 final size:98
Alignment explanation
Indices: 266221--267040 Score: 1012
Period size: 97 Copynumber: 8.4 Consensus size: 98
266211 GCAACCCTTC
* * *
266221 TAAGCCCAATATAGCTGGCCCTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATAGCT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCT
*
266286 GGCCTTGAATCAGCACATTGGCACC-TCACCTT
66 GGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
266318 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATATAGCT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCT
*
266377 GGCCTTGAATCAGCATATTGGCACCTTTTCCATCTT
66 GGCCTTGAATCAGCACATTGGCACC--TT-CATCTT
* * * * * * *
266413 TAAGTCCAATGTAGCTGGCCTTGACTCATCACATTGGCA-CTTGCACCATTAAGTCC-ATATAGC
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTT-CATCTTTAAGTCCAATGTAGC
* *
266476 TGGCCTTGAATCAGCATATTGGCACCTTTATCTT
65 TGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
266510 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC-TCACCTTTAAATCCAATGTAGCT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCT
266574 GGCCTTGAATCAGCACATTGGCA----C--CTT
66 GGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
266601 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCT
* *
266666 GGCCTTGACTCAGCACATTGGCACCTTCA-CAAT
66 GGCCTTGAATCAGCACATTGGCACCTTCATC-TT
* *
266699 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACTTTTATCTTTAAGTCCAATGTAGCT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCT
* * * *
266764 GGCCTTGACTCAGCACATTAGCA-CTTGCACCAT
66 GGCCTTGAATCAGCACATTGGCACCTT-CATCTT
*
266797 TAAGTCC-ATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCT
*
266861 GGCCTTGACTCAGCACATTGGCACCTTCATCTT
66 GGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
266894 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTTTAAGTTCAATGTA
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC--TT-CATCTTTAAGTCCAATGTA
*
266959 GCTGGCCTTGAATCAGCACATTGACATCCTTTTTCATCATCTT
63 GCTGGCCTTGAATCAGCACATTGGCA-CC----T--TCATCTT
* * * * *
267002 TAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCA
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA
267041 TCTTTATCAC
Statistics
Matches: 649, Mismatches: 41, Indels: 55
0.87 0.06 0.07
Matches are distributed among these distances:
91 86 0.13
92 42 0.06
93 1 0.00
94 1 0.00
95 42 0.06
96 12 0.02
97 199 0.31
98 136 0.21
99 2 0.00
100 35 0.05
101 50 0.08
102 2 0.00
106 1 0.00
108 40 0.06
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.31
Consensus pattern (98 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCT
GGCCTTGAATCAGCACATTGGCACCTTCATCTT
Found at i:267021 original size:56 final size:53
Alignment explanation
Indices: 266598--267029 Score: 333
Period size: 49 Copynumber: 8.6 Consensus size: 53
266588 ACATTGGCAC
* * *
266598 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC--TT-T-AT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATCGACACCTTTTCTCAT
* * * * *
266647 CTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACC--TTCACA-
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATCGACACCTTTTCTCAT
* * * *
266697 -ATTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-C-TTT-T-AT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATCGACACCTTTTCTCAT
* * * * *
266745 CTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACAT-TAGCA-C--TT-GCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATCGA-CACCTTTTCTCAT
* * * *
266794 CATTAAGTCC-ATATAGCTGGCCTTGAATCAGCATATTGGCACC--TT-T-AT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATCGACACCTTTTCTCAT
* * * *
266842 CTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACC---T-TCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATCGACACCTTTTCTCAT
* *
266891 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATCGACACCTTTTCTCAT
* * *
266943 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCATCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATCGACA-CC-TTTTC-TCAT
* * * *
266999 CTTTAAGCCCAATATCGTTGGCCATGAATCA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCA
267030 ACATATTGGC
Statistics
Matches: 320, Mismatches: 44, Indels: 31
0.81 0.11 0.08
Matches are distributed among these distances:
47 1 0.00
48 40 0.12
49 202 0.63
51 1 0.00
52 41 0.13
53 2 0.01
54 5 0.02
56 28 0.09
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (53 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATCGACACCTTTTCTCAT
Found at i:267912 original size:20 final size:20
Alignment explanation
Indices: 267868--267925 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
267858 ATTTCAACGA
***
267868 TTTGTATCGATACATAAAAT
1 TTTGTATCGATACATATTTT
*
267888 GTTGTATCGATACATATTTT
1 TTTGTATCGATACATATTTT
267908 TTTGTATCGATACA-ATTT
1 TTTGTATCGATACATATTT
267926 AAGCTGCTGC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
19 4 0.12
20 29 0.88
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.47
Consensus pattern (20 bp):
TTTGTATCGATACATATTTT
Found at i:267982 original size:13 final size:13
Alignment explanation
Indices: 267964--267988 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
267954 ATTACTCAAA
267964 TGTATCGATACAT
1 TGTATCGATACAT
267977 TGTATCGATACA
1 TGTATCGATACA
267989 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:268090 original size:52 final size:52
Alignment explanation
Indices: 267997--268124 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
267987 CACTGATCTT
*
267997 TGTATCGATACTTGCAGGC-AATTTGCCCAGATATATCGATACATTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATATATCGATACATTATTAAA
*
268048 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATATATCGATACATTATTAAA
268100 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
268125 TCATATTTCG
Statistics
Matches: 74, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
51 18 0.24
52 56 0.76
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATATATCGATACATTATTAAA
Found at i:273260 original size:19 final size:20
Alignment explanation
Indices: 273236--273275 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
273226 AACTATTATG
273236 ATAAATATTAATAA-TAAAA
1 ATAAATATTAATAATTAAAA
273255 ATAAATATTAATAATTAAAA
1 ATAAATATTAATAATTAAAA
273275 A
1 A
273276 AATTAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAAATATTAATAATTAAAA
Found at i:273280 original size:16 final size:17
Alignment explanation
Indices: 273238--273292 Score: 60
Period size: 19 Copynumber: 3.2 Consensus size: 17
273228 CTATTATGAT
*
273238 AAATATTAATAATAAAAA
1 AAATATTAATAAT-TAAA
273256 TAAATATTAATAATTAAA
1 -AAATATTAATAATTAAA
*
273274 AAA-ATTAA-AATTATA
1 AAATATTAATAATTAAA
273289 AAAT
1 AAAT
273293 TATAAAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
15 9 0.27
16 5 0.15
17 3 0.09
18 3 0.09
19 13 0.39
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATATTAATAATTAAA
Found at i:273290 original size:8 final size:8
Alignment explanation
Indices: 273279--273310 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
273269 TTAAAAAAAT
273279 TAAAATTA
1 TAAAATTA
273287 TAAAATTA
1 TAAAATTA
273295 TAAAATTA
1 TAAAATTA
*
273303 TGAAATTA
1 TAAAATTA
273311 CCTTGTAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (8 bp):
TAAAATTA
Found at i:273293 original size:23 final size:22
Alignment explanation
Indices: 273236--273299 Score: 55
Period size: 19 Copynumber: 3.0 Consensus size: 22
273226 AACTATTATG
*
273236 ATAAATATTAATAA-T--AAAA
1 ATAAATATTAAAAATTAAAAAA
*
273255 ATAAATATTAATAATTAAAAAA
1 ATAAATATTAAAAATTAAAAAA
*
273277 ATTAAA-ATTATAAAATTATAAAA
1 A-TAAATATTA-AAAATTAAAAAA
273300 TTATGAAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
19 14 0.37
20 1 0.03
22 9 0.24
23 14 0.37
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (22 bp):
ATAAATATTAAAAATTAAAAAA
Found at i:274576 original size:2 final size:2
Alignment explanation
Indices: 274569--274594 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
274559 ACTGATCGGA
274569 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
274595 GTAAAATGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:278383 original size:14 final size:14
Alignment explanation
Indices: 278364--278393 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
278354 ACAGCCTATT
278364 TAAGATCTCAATGC
1 TAAGATCTCAATGC
278378 TAAGATCTCAATGC
1 TAAGATCTCAATGC
278392 TA
1 TA
278394 TCTCTGTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.30
Consensus pattern (14 bp):
TAAGATCTCAATGC
Found at i:279575 original size:20 final size:21
Alignment explanation
Indices: 279534--279585 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
279524 ACAACAAGGT
279534 AATGTATCGATACATAAGTG-
1 AATGTATCGATACATAAGTGA
***
279554 AATGTATCGATACATGTTTGA
1 AATGTATCGATACATAAGTGA
279575 AATGTATCGAT
1 AATGTATCGAT
279586 GCAAGACCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.37, C:0.10, G:0.19, T:0.35
Consensus pattern (21 bp):
AATGTATCGATACATAAGTGA
Found at i:279732 original size:52 final size:51
Alignment explanation
Indices: 279624--279762 Score: 163
Period size: 51 Copynumber: 2.7 Consensus size: 51
279614 TCCTGAAAGA
* * *
279624 AAATGTATAGATACATTTTTAATTATATTGATACAGTATGGGTTTTGACCC
1 AAATGTATAGATACATTTTTAATTATATCGATACATTATGGGTTTTAACCC
* * *
279675 AAATGTATCGATACATTTTTTATTATATCGATACATTCTGGGTTTTTAACCC
1 AAATGTATAGATACATTTTTAATTATATCGATACATTATGGG-TTTTAACCC
* * * *
279727 AAATGTATGGATATATTCTTCAA-TGTATCGATACAT
1 AAATGTATAGATACATT-TTTAATTATATCGATACAT
279763 GCAGTCTATT
Statistics
Matches: 75, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
51 37 0.49
52 35 0.47
53 3 0.04
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (51 bp):
AAATGTATAGATACATTTTTAATTATATCGATACATTATGGGTTTTAACCC
Found at i:287462 original size:13 final size:13
Alignment explanation
Indices: 287444--287470 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
287434 ACAACATTCC
287444 TTGTATCGATACA
1 TTGTATCGATACA
287457 TTGTATCGATACA
1 TTGTATCGATACA
287470 T
1 T
287471 GGGTTACTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:289368 original size:21 final size:22
Alignment explanation
Indices: 289344--289405 Score: 74
Period size: 21 Copynumber: 2.9 Consensus size: 22
289334 AATTTTTAGA
*
289344 TTTGACAAAGGGGGAGAAATT-
1 TTTGATAAAGGGGGAGAAATTC
289365 TTTGATTAAA-GGGGAGAAATTC
1 TTTGA-TAAAGGGGGAGAAATTC
* *
289387 TTTAATTAAGGGGGAGAAA
1 TTTGATAAAGGGGGAGAAA
289406 AATGAAAACT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
21 19 0.54
22 16 0.46
ACGTcount: A:0.39, C:0.03, G:0.31, T:0.27
Consensus pattern (22 bp):
TTTGATAAAGGGGGAGAAATTC
Found at i:289376 original size:22 final size:23
Alignment explanation
Indices: 289350--289405 Score: 82
Period size: 22 Copynumber: 2.6 Consensus size: 23
289340 TAGATTTGAC
*
289350 AAAGGGGGAGAAATT-TTTGATT
1 AAAGGGGGAGAAATTCTTTAATT
289372 AAA-GGGGAGAAATTCTTTAATT
1 AAAGGGGGAGAAATTCTTTAATT
289394 -AAGGGGGAGAAA
1 AAAGGGGGAGAAA
289406 AATGAAAACT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 13 0.42
22 18 0.58
ACGTcount: A:0.41, C:0.02, G:0.32, T:0.25
Consensus pattern (23 bp):
AAAGGGGGAGAAATTCTTTAATT
Found at i:289985 original size:19 final size:20
Alignment explanation
Indices: 289961--290012 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
289951 TGTATCAAGA
*
289961 CATTGTATCGATACAT-GTT
1 CATTGTATCGATACATGGAT
289980 CATTGTATCGATACATGGAT
1 CATTGTATCGATACATGGAT
*
290000 AATTGTATCGATA
1 CATTGTATCGATA
290013 TATGAGATTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.38
Consensus pattern (20 bp):
CATTGTATCGATACATGGAT
Found at i:290082 original size:13 final size:13
Alignment explanation
Indices: 290061--290113 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
290051 CGATACATGG
*
290061 TACAATGTATCGA
1 TACATTGTATCGA
290074 TACATTGTATCGA
1 TACATTGTATCGA
290087 TACA-TG-AT-G-
1 TACATTGTATCGA
290096 -A-ATTGTATCGA
1 TACATTGTATCGA
290107 TACATTG
1 TACATTG
290114 CTTGTAACGG
Statistics
Matches: 33, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
7 1 0.03
8 3 0.09
9 2 0.06
10 2 0.06
11 2 0.06
12 3 0.09
13 20 0.61
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:290087 original size:33 final size:33
Alignment explanation
Indices: 290045--290113 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
290035 CTACCACTGT
*
290045 TTGTATCGATACATGGT-ACAATGTATCGATACA
1 TTGTATCGATACATGATGA-AATGTATCGATACA
*
290078 TTGTATCGATACATGATGAATTGTATCGATACA
1 TTGTATCGATACATGATGAAATGTATCGATACA
290111 TTG
1 TTG
290114 CTTGTAACGG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 32 0.97
34 1 0.03
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (33 bp):
TTGTATCGATACATGATGAAATGTATCGATACA
Found at i:291344 original size:80 final size:81
Alignment explanation
Indices: 291211--291362 Score: 186
Period size: 81 Copynumber: 1.9 Consensus size: 81
291201 TAAATTTCTC
* * *
291211 CTTCTAAAACATTAAAATTTTCATCTTAGAGGGTACTCCGACCCCATCAATTT-CGAGGAGATAC
1 CTTCTAAAACATTAAAATTTTCATCTCAGAGGGTACTCCAACCCCAACAATTTCCGAGGAGATAC
291275 TCAAACCCCGTTTTTA
66 TCAAACCCCGTTTTTA
* * *
291291 CTTCTAAAACATT-GAATTTCCTCATCTCAG-GGGATACTCCAACCTCAAC-ATTTCCGAGGGGA
1 CTTCTAAAACATTAAAATTT--TCATCTCAGAGGG-TACTCCAACCCCAACAATTTCCGAGGAGA
*
291353 TACTCCAACC
63 TACTCAAACC
291363 TCACCATTTT
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
79 5 0.08
80 20 0.33
81 36 0.59
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.29
Consensus pattern (81 bp):
CTTCTAAAACATTAAAATTTTCATCTCAGAGGGTACTCCAACCCCAACAATTTCCGAGGAGATAC
TCAAACCCCGTTTTTA
Found at i:291359 original size:28 final size:28
Alignment explanation
Indices: 291319--291388 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
291309 TCCTCATCTC
291319 AGGGGATACTCCAACCTCAACATTTCCG
1 AGGGGATACTCCAACCTCAACATTTCCG
* *
291347 AGGGGATACTCCAACCTCACCATTTTCG
1 AGGGGATACTCCAACCTCAACATTTCCG
291375 AGGGGATACTCCAA
1 AGGGGATACTCCAA
291389 ACCAGTTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (28 bp):
AGGGGATACTCCAACCTCAACATTTCCG
Found at i:291469 original size:107 final size:108
Alignment explanation
Indices: 291261--291469 Score: 271
Period size: 107 Copynumber: 1.9 Consensus size: 108
291251 ACCCCATCAA
* * * *
291261 TTTCGAGGAGATACTCAAACCCCGTTTTTACTTCTAAAACATTGAATTTCCTCATCTCAGGGGAT
1 TTTCGAGGAGATACTCAAACCCAGTTTTTACTTCCAAAACATTAAATTT-CTCATCTCAGAGGAT
* *
291326 ACTCCAACCTCAACATTTCCGAGGGGATACTCCAACCTCACCAT
65 ACTCCAACCCCAACATTTCCGAGGGAATACTCCAACCTCACCAT
* *
291370 TTTCGAGGGGATACTCCAAA-CCAGTTTTTACTTCCAAAATATTAAAATTT-TCATCTC-GAGGA
1 TTTCGAGGAGATACT-CAAACCCAGTTTTTACTTCCAAAACATT-AAATTTCTCATCTCAGAGGA
* * *
291432 TACTCCAACCCCACCATTTCTGAGGGAATACTTCAACC
64 TACTCCAACCCCAACATTTCCGAGGGAATACTCCAACC
291470 CCATCTTTAC
Statistics
Matches: 87, Mismatches: 11, Indels: 6
0.84 0.11 0.06
Matches are distributed among these distances:
107 37 0.43
108 7 0.08
109 34 0.39
110 9 0.10
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.29
Consensus pattern (108 bp):
TTTCGAGGAGATACTCAAACCCAGTTTTTACTTCCAAAACATTAAATTTCTCATCTCAGAGGATA
CTCCAACCCCAACATTTCCGAGGGAATACTCCAACCTCACCAT
Found at i:291481 original size:79 final size:79
Alignment explanation
Indices: 291350--291521 Score: 206
Period size: 79 Copynumber: 2.2 Consensus size: 79
291340 ATTTCCGAGG
* * *
291350 GGATACTCCAACCTCACCATTTTCGAGGGGATACTCCAAACCAGTTTTTACTTCCAAAATATTAA
1 GGATACTCCAACCCCACCATTTTCGAGGGAATACTCCAAACCAGTCTTTACTTCCAAAATATTAA
291415 AATTTTCAT-CTCGA
66 AATTTTCATCCT-GA
* * **
291429 GGATACTCCAACCCCACCA-TTTCTGAGGGAATACTTCAACCCCA-TCTTTACTTTTAAAATATT
1 GGATACTCCAACCCCACCATTTTC-GAGGGAATACTCCAA-ACCAGTCTTTACTTCCAAAATATT
*
291492 AAATTTTTCATCCTGA
64 AAAATTTTCATCCTGA
* *
291508 AGATACTCTAACCC
1 GGATACTCCAACCC
291522 TATTATCTTT
Statistics
Matches: 80, Mismatches: 10, Indels: 6
0.83 0.10 0.06
Matches are distributed among these distances:
78 4 0.05
79 71 0.89
80 5 0.06
ACGTcount: A:0.31, C:0.27, G:0.10, T:0.32
Consensus pattern (79 bp):
GGATACTCCAACCCCACCATTTTCGAGGGAATACTCCAAACCAGTCTTTACTTCCAAAATATTAA
AATTTTCATCCTGA
Found at i:291535 original size:79 final size:79
Alignment explanation
Indices: 291351--291551 Score: 196
Period size: 79 Copynumber: 2.5 Consensus size: 79
291341 TTTCCGAGGG
* * * * *
291351 GATACTCCAACCTCACCATTT-TCGAGGGGATACTCCAA-ACCAGTTTTTACTTCCAAAATATTA
1 GATACTCCAACCCCACCATTTCT-GAGGGAATACTCTAACCCCA-TCTTTACTTCCAAAATATTA
*
291414 AAATTTTCATCTCGAG
64 AAATTTTCATCTCGAA
**
291430 GATACTCCAACCCCACCATTTCTGAGGGAATACT-TCAACCCCATCTTTACTTTTAAAATATTAA
1 GATACTCCAACCCCACCATTTCTGAGGGAATACTCT-AACCCCATCTTTACTTCCAAAATATTAA
*
291494 ATTTTTCATC-CTGAA
65 AATTTTCATCTC-GAA
* * ** *
291509 GATACTCTAACCCTATTATCTT-TGAGGGGATACTCTAACCCCA
1 GATACTCCAACCCCACCAT-TTCTGAGGGAATACTCTAACCCCA
291552 ATTTTCACCA
Statistics
Matches: 102, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
78 1 0.01
79 94 0.92
80 7 0.07
ACGTcount: A:0.31, C:0.26, G:0.10, T:0.32
Consensus pattern (79 bp):
GATACTCCAACCCCACCATTTCTGAGGGAATACTCTAACCCCATCTTTACTTCCAAAATATTAAA
ATTTTCATCTCGAA
Found at i:293264 original size:234 final size:234
Alignment explanation
Indices: 292855--293325 Score: 924
Period size: 234 Copynumber: 2.0 Consensus size: 234
292845 TATCATCAAT
292855 TTATCATATTTTCTTTAATTTAATTAGTTAAACTCATCAAATATTGAGAGCTTATATATTTTAGT
1 TTATCATATTTTCTTTAATTTAATTAGTTAAACTCATCAAATATTGAGAGCTTATATATTTTAGT
292920 GAAATTTTAAGTGCTTATTTGAATATTATTTTTATAGTATTATTATTATTATTTCAAGTAATGAT
66 GAAATTTTAAGTGCTTATTTGAATATTATTTTTATAGTATTATTATTATTATTTCAAGTAATGAT
*
292985 AATTAGAGTCTCGTACTAGTATAACAAAGTAATAAAGTAAATTAAAAAAAATGAAAACCATAATA
131 AATTAGAGTCTCGTAATAGTATAACAAAGTAATAAAGTAAATTAAAAAAAATGAAAACCATAATA
293050 GATAATAAATATAAAAAATAAAAAAATCATATATTAGAC
196 GATAATAAATATAAAAAATAAAAAAATCATATATTAGAC
293089 TTATCATATTTTCTTTAATTTAATTAGTTAAACTCATCAAATATTGAGAGCTTATATATTTTAGT
1 TTATCATATTTTCTTTAATTTAATTAGTTAAACTCATCAAATATTGAGAGCTTATATATTTTAGT
293154 GAAATTTTAAGTGCTTATTTGAATATTATTTTTATAGTATTATTATTATTATTTCAAGTAATGAT
66 GAAATTTTAAGTGCTTATTTGAATATTATTTTTATAGTATTATTATTATTATTTCAAGTAATGAT
*
293219 AATTAGAGTCTCGTAATAGTATAACAAAGTAATAAAGTAAATTAAAAAATATGAAAACCATAATA
131 AATTAGAGTCTCGTAATAGTATAACAAAGTAATAAAGTAAATTAAAAAAAATGAAAACCATAATA
293284 GATAATAAATATAAAAAATAAAAAAATCATATATTAGAC
196 GATAATAAATATAAAAAATAAAAAAATCATATATTAGAC
293323 TTA
1 TTA
293326 GACTAGCAAC
Statistics
Matches: 235, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
234 235 1.00
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.40
Consensus pattern (234 bp):
TTATCATATTTTCTTTAATTTAATTAGTTAAACTCATCAAATATTGAGAGCTTATATATTTTAGT
GAAATTTTAAGTGCTTATTTGAATATTATTTTTATAGTATTATTATTATTATTTCAAGTAATGAT
AATTAGAGTCTCGTAATAGTATAACAAAGTAATAAAGTAAATTAAAAAAAATGAAAACCATAATA
GATAATAAATATAAAAAATAAAAAAATCATATATTAGAC
Found at i:293507 original size:19 final size:19
Alignment explanation
Indices: 293483--293520 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
293473 CATTCAATAG
293483 CATTTTAATGGACAATCTC
1 CATTTTAATGGACAATCTC
*
293502 CATTTTAATGGATAATCTC
1 CATTTTAATGGACAATCTC
293521 TCCTCCAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (19 bp):
CATTTTAATGGACAATCTC
Found at i:294235 original size:16 final size:15
Alignment explanation
Indices: 294217--294258 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
294207 CCCGAACCGA
294217 AAAAAGCTCGAACTC
1 AAAAAGCTCGAACTC
* *
294232 AAAAGGTTCGAACTC
1 AAAAAGCTCGAACTC
294247 GAAAAAGCTCGA
1 -AAAAAGCTCGA
294259 TCTCGAATAG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.45, C:0.21, G:0.19, T:0.14
Consensus pattern (15 bp):
AAAAAGCTCGAACTC
Found at i:294263 original size:16 final size:16
Alignment explanation
Indices: 294217--294265 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
294207 CCCGAACCGA
294217 AAAAAGCTCGAACTC-
1 AAAAAGCTCGAACTCG
* *
294232 AAAAGGTTCGAACTCG
1 AAAAAGCTCGAACTCG
*
294248 AAAAAGCTCGATCTCG
1 AAAAAGCTCGAACTCG
294264 AA
1 AA
294266 TAGGCTTGAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
15 13 0.46
16 15 0.54
ACGTcount: A:0.43, C:0.22, G:0.18, T:0.16
Consensus pattern (16 bp):
AAAAAGCTCGAACTCG
Found at i:294282 original size:32 final size:31
Alignment explanation
Indices: 294209--294282 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
294199 AACTCGAACC
294209 CGAA-CCGAAAAAAGCTCGAACTCAAAAGGTT
1 CGAACCCG-AAAAAGCTCGAACTCAAAAGGTT
* * *
294240 CGAACTCGAAAAAGCTCGATCTCGAATAGGCTT
1 CGAACCCGAAAAAGCTCGAACTC-AAAAGG-TT
294273 -GAACCCGAAA
1 CGAACCCGAAA
294283 GAAACCTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
31 18 0.50
32 16 0.44
33 2 0.06
ACGTcount: A:0.41, C:0.24, G:0.20, T:0.15
Consensus pattern (31 bp):
CGAACCCGAAAAAGCTCGAACTCAAAAGGTT
Found at i:294309 original size:32 final size:33
Alignment explanation
Indices: 294264--294345 Score: 89
Period size: 32 Copynumber: 2.5 Consensus size: 33
294254 CTCGATCTCG
* * * *
294264 AATAGGCTTGAACCCGAAAGAA-ACCTAAACCA
1 AATAAGCTAGAACCCGAAAAAAGACCAAAACCA
*
294296 AATAAGCTAGAA-CCTAAAAAAGACCAAAACCA
1 AATAAGCTAGAACCCGAAAAAAGACCAAAACCA
294328 AATAAGCCTA-AACCCGAA
1 AATAAG-CTAGAACCCGAA
294346 TAGGTTAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
31 7 0.17
32 27 0.66
33 7 0.17
ACGTcount: A:0.52, C:0.24, G:0.12, T:0.11
Consensus pattern (33 bp):
AATAAGCTAGAACCCGAAAAAAGACCAAAACCA
Found at i:302196 original size:132 final size:131
Alignment explanation
Indices: 302030--302270 Score: 315
Period size: 132 Copynumber: 1.8 Consensus size: 131
302020 GAAAATTTGA
* * * * * *
302030 TTTTTGGAGAAAATCAGGGTTGAAGTATCCCCTCATAAATGGTGGGGTTGGAATATCCCCGTAGG
1 TTTTTGGAAAAAATCAGGGTTGAAGTATCCCCTCAGAAATGATAGGGTTGGAATAT-CCCGAAGA
*
302095 TGGGAAATTTAATATTTTT-AAAAGTAAAAATAGGGTTAGAGTATCTTCGAAAATGGAAAACTCG
65 TGGAAAATTTAATATTTTTGAAAA-TAAAAATAGGGTTAGAGTATCTTCGAAAATGGAAAACTCG
302159 ATG
129 ATG
* *
302162 TTTTTGGAAAAAAATGA-GGTTGGAGTATCCCCTCAGAAATGATAGGGTTGGAATATCCCGAAGA
1 TTTTTGG-AAAAAATCAGGGTTGAAGTATCCCCTCAGAAATGATAGGGTTGGAATATCCCGAAGA
* * * * *
302226 TGGAAAATTTGATGTTTTTGGAAATAAAGATGGGGTTAGAGTATC
65 TGGAAAATTTAATATTTTTGAAAATAAAAATAGGGTTAGAGTATC
302271 CTGTCAGAAA
Statistics
Matches: 93, Mismatches: 14, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
131 41 0.44
132 45 0.48
133 7 0.08
ACGTcount: A:0.34, C:0.10, G:0.26, T:0.30
Consensus pattern (131 bp):
TTTTTGGAAAAAATCAGGGTTGAAGTATCCCCTCAGAAATGATAGGGTTGGAATATCCCGAAGAT
GGAAAATTTAATATTTTTGAAAATAAAAATAGGGTTAGAGTATCTTCGAAAATGGAAAACTCGAT
G
Found at i:302363 original size:81 final size:80
Alignment explanation
Indices: 302127--302521 Score: 350
Period size: 81 Copynumber: 4.9 Consensus size: 80
302117 AGTAAAAATA
** * * * * * *
302127 GGGTTAGAGTATCTTCGAAAATGGAAAACTCGATGTTTTTGG-AA-AAAAATGAGGTTGGAGTAT
1 GGGTTAGAGTATCCCCGAAGATGAAAAATTTGATGTTTTTGGAAATAAAAATGGGGTTAGAGTAT
* * *
302190 CCCCTCAGAAATGATA
66 CCTCTCA-AAATGGTG
* * * *
302206 GGGTTGGAATAT-CCCGAAGATGGAAAATTTGATGTTTTTGGAAATAAAGATGGGGTTAGAGTAT
1 GGGTTAGAGTATCCCCGAAGATGAAAAATTTGATGTTTTTGGAAATAAAAATGGGGTTAGAGTAT
*
302270 CCTGTCAGAAATGGTG
66 CCTCTCA-AAATGGTG
* * * * * * * *
302286 GGGTTAGAGTATCCCCGAATATGAAAATTTTGATGTTTTTGGAAGTAAAAATAGGGTCAAAATGT
1 GGGTTAGAGTATCCCCGAAGATGAAAAATTTGATGTTTTTGGAAATAAAAATGGGGTTAGAGTAT
* *
302351 CCTCTCGAAAATGATA
66 CCTCTC-AAAATGGTG
* * * * * * * *
302367 GGGTTAAAATATCCTCGAAGATAAAAAATTTGATATTTTTAGAAGTAAAATTGGGGTTAGAGTAT
1 GGGTTAGAGTATCCCCGAAGATGAAAAATTTGATGTTTTTGGAAATAAAAATGGGGTTAGAGTAT
302432 CC-CTTCAAAAATGGTG
66 CCTC-TC-AAAATGGTG
* * * *
302448 GGGTTAGAGTATCTCAGAAAATGAAAAATTTGATGTTTTTGGAAATAAAGAA-GGGATTAGAGTA
1 GGGTTAGAGTATCCCCGAAGATGAAAAATTTGATGTTTTTGGAAATAAA-AATGGGGTTAGAGTA
*
302512 TCCCCTCAAA
65 TCCTCTCAAA
302522 GATAACGAGA
Statistics
Matches: 251, Mismatches: 58, Indels: 13
0.78 0.18 0.04
Matches are distributed among these distances:
78 24 0.10
79 12 0.05
80 42 0.17
81 170 0.68
82 3 0.01
ACGTcount: A:0.36, C:0.10, G:0.25, T:0.30
Consensus pattern (80 bp):
GGGTTAGAGTATCCCCGAAGATGAAAAATTTGATGTTTTTGGAAATAAAAATGGGGTTAGAGTAT
CCTCTCAAAATGGTG
Found at i:302426 original size:162 final size:161
Alignment explanation
Indices: 302198--302496 Score: 440
Period size: 162 Copynumber: 1.9 Consensus size: 161
302188 ATCCCCTCAG
** ** * *
302198 AAATGATAGGGTTGGAATATCCCGAAGATGGAAAATTTGATGTTTTTGGAAATAAAGATGGGGTT
1 AAATGATAGGGTTAAAATATCCCGAAGATAAAAAATTTGATATTTTTAGAAATAAAGATGGGGTT
* * * *
302263 AGAGTAT-CCTGTCAGAAATGGTGGGGTTAGAGTATCCCCGAATATGAAAATTTTGATGTTTTTG
66 AGAGTATCCCT-TCAAAAATGGTGGGGTTAGAGTATCCCAGAAAATGAAAAATTTGATGTTTTTG
*
302327 GAAGTAAAAATAGGGTCAAAATGTCCTCTCGA
130 GAAATAAAAATAGGGTCAAAATGTCCTCTCGA
*
302359 AAATGATAGGGTTAAAATATCCTCGAAGATAAAAAATTTGATATTTTTAGAAGTAAA-ATTGGGG
1 AAATGATAGGGTTAAAATATCC-CGAAGATAAAAAATTTGATATTTTTAGAAATAAAGA-TGGGG
*
302423 TTAGAGTATCCCTTCAAAAATGGTGGGGTTAGAGTATCTCAGAAAATGAAAAATTTGATGTTTTT
64 TTAGAGTATCCCTTCAAAAATGGTGGGGTTAGAGTATCCCAGAAAATGAAAAATTTGATGTTTTT
302488 GGAAATAAA
129 GGAAATAAA
302497 GAAGGGATTA
Statistics
Matches: 122, Mismatches: 13, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
161 21 0.17
162 98 0.80
163 3 0.02
ACGTcount: A:0.37, C:0.08, G:0.24, T:0.31
Consensus pattern (161 bp):
AAATGATAGGGTTAAAATATCCCGAAGATAAAAAATTTGATATTTTTAGAAATAAAGATGGGGTT
AGAGTATCCCTTCAAAAATGGTGGGGTTAGAGTATCCCAGAAAATGAAAAATTTGATGTTTTTGG
AAATAAAAATAGGGTCAAAATGTCCTCTCGA
Found at i:303555 original size:44 final size:44
Alignment explanation
Indices: 303493--303592 Score: 130
Period size: 44 Copynumber: 2.2 Consensus size: 44
303483 CTTTGAGGAC
*
303493 AAAAGGAATAAAAAGTGCCACCAACTTATGTTGGCTTTGAAAAAG
1 AAAAGGAA-AAAAAGTGCCACCAACTTATGTGGGCTTTGAAAAAG
* *
303538 AAAA-GAAAAAAAGGTGCCACCAATTTGTGTGGGCTTTGAAAAAG
1 AAAAGGAAAAAAA-GTGCCACCAACTTATGTGGGCTTTGAAAAAG
*
303582 AGAAATGAAAA
1 A-AAAGGAAAA
303593 GTATCTTGCT
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
43 5 0.10
44 32 0.65
45 7 0.14
46 5 0.10
ACGTcount: A:0.47, C:0.11, G:0.22, T:0.20
Consensus pattern (44 bp):
AAAAGGAAAAAAAGTGCCACCAACTTATGTGGGCTTTGAAAAAG
Found at i:303626 original size:120 final size:116
Alignment explanation
Indices: 303481--303780 Score: 354
Period size: 120 Copynumber: 2.5 Consensus size: 116
303471 AAAAGCCCTA
* * *
303481 CTCTTTGAGGAC-AAAAGGAATAAAAAGTGCCACCAACTTATGTTGGCTTTGAAAA-AGAAAAGA
1 CTCTTTAAGGACTAAAAGG-ATAAAAAGTGCCACCAACTTGTGTGGGCTTT-AAAAGA-AAAAG-
* * ** *
303544 AAAAAAGGTGCCACCAATTTGTGTGGGCTTTGAAAAAGAGAAATGAAAAGTATCTTG
62 AAAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAA-A-AAAAGAAAAACATCCTG
*
303601 CTCTTTAAGGACTAAAAGGATAAAAAGTATGCCACCAACTTGTGTGGGCTTTAGAAGAAAAAGAA
1 CTCTTTAAGGACTAAAAGGATAAAAAG--TGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGAA
* *
303666 AAAGGGTGCCACCAACTTGTGTGGGCTTTGAAAAAAAAAAGAAAAACGTCCTG
64 AAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAAAAAAAGAAAAACATCCTG
* *
303719 CTCTTTGAA-GATTAAAAGGATAAAAAGATGTGCCACCAACTTGTGTGGGCTTTAGAAGAAAA
1 CTCTTT-AAGGACTAAAAGGAT-AAAA-A-GTGCCACCAACTTGTGTGGGCTTTAAAAGAAAA
303781 GGGATATGCT
Statistics
Matches: 160, Mismatches: 12, Indels: 17
0.85 0.06 0.09
Matches are distributed among these distances:
118 29 0.18
119 39 0.24
120 55 0.34
121 15 0.09
122 22 0.14
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.23
Consensus pattern (116 bp):
CTCTTTAAGGACTAAAAGGATAAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGAAAA
AAGGTGCCACCAACTTGTGTGGGCTTTGAAAAAAAAAAGAAAAACATCCTG
Found at i:303676 original size:42 final size:43
Alignment explanation
Indices: 303630--303711 Score: 139
Period size: 42 Copynumber: 1.9 Consensus size: 43
303620 ATAAAAAGTA
* *
303630 TGCCACCAACTTGTGTGGGCTTT-AGAAGAAAAAGAAAAAGGG
1 TGCCACCAACTTGTGTGGGCTTTGAAAAAAAAAAGAAAAAGGG
303672 TGCCACCAACTTGTGTGGGCTTTGAAAAAAAAAAGAAAAA
1 TGCCACCAACTTGTGTGGGCTTTGAAAAAAAAAAGAAAAA
303712 CGTCCTGCTC
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
42 23 0.62
43 14 0.38
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.20
Consensus pattern (43 bp):
TGCCACCAACTTGTGTGGGCTTTGAAAAAAAAAAGAAAAAGGG
Found at i:303791 original size:70 final size:65
Alignment explanation
Indices: 303746--303912 Score: 176
Period size: 65 Copynumber: 2.5 Consensus size: 65
303736 GGATAAAAAG
*
303746 ATGTGCCACCAACTTGTGTGGGCTTTAGAAGAAAAGGGATATGCTCTTTAAGGACTAAACATAAA
1 ATGTGCCACCAACTTGTATGGGCTTTAGAAGAAAAGGGATATGCTCTTTAAGGACTAAACATAAA
* * ** * * *
303811 ATGTGCTACCAACTTGTATTGGCTTTAGAAGAAAAAACG-TCCTGCTCTTTGAGGACTAAAAAAG
1 ATGTGCCACCAACTTGTATGGGCTTTAGAAG-AAAAGGGAT-ATGCTCTTTAAGGACT-AAACA-
303875 TAAA
62 TAAA
* * * *
303879 AGGTGCCACTAGCTTGTATAGGCTTTA-AAGAAAA
1 ATGTGCCACCAACTTGTATGGGCTTTAGAAGAAAA
303913 AAGCATCCTA
Statistics
Matches: 85, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
65 29 0.34
66 23 0.27
67 7 0.08
68 26 0.31
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.27
Consensus pattern (65 bp):
ATGTGCCACCAACTTGTATGGGCTTTAGAAGAAAAGGGATATGCTCTTTAAGGACTAAACATAAA
Found at i:303903 original size:68 final size:68
Alignment explanation
Indices: 303707--303955 Score: 231
Period size: 68 Copynumber: 3.7 Consensus size: 68
303697 AAAAAAAAAG
* * * * *
303707 AAAAACGTCCTGCTCTTTGAAGATTAAAAGGATAAAAAGATGTGCCACCAACTTGTGTGGGCTTT
1 AAAAACGTCCTGCTCTTTGAGGACTAAAAAGAT-AAAAG--GTGCCACCAACTTGTATAGGCTTT
303772 AGAAG-
63 AGAAGA
** * * * * * *
303777 AAAAGGGAT-ATGCTCTTTAAGGACT--AAACATAAAATGTGCTACCAACTTGTATTGGCTTTAG
1 AAAAACG-TCCTGCTCTTTGAGGACTAAAAAGATAAAAGGTGCCACCAACTTGTATAGGCTTTAG
303839 AAGA
65 AAGA
* *
303843 AAAAACGTCCTGCTCTTTGAGGACTAAAAA-AGTAAAAGGTGCCACTAGCTTGTATAGGCTTTA-
1 AAAAACGTCCTGCTCTTTGAGGACTAAAAAGA-TAAAAGGTGCCACCAACTTGTATAGGCTTTAG
303906 AAGA
65 AAGA
* * * *
303910 AAAAAGCATCCTACTCTTTGAGGACTGAAAAGATAAAAAGTGCCAC
1 AAAAA-CGTCCTGCTCTTTGAGGACTAAAAAGATAAAAGGTGCCAC
303956 TAGCTTGTGT
Statistics
Matches: 146, Mismatches: 25, Indels: 18
0.77 0.13 0.10
Matches are distributed among these distances:
65 27 0.18
66 19 0.13
67 14 0.10
68 67 0.46
69 1 0.01
70 17 0.12
71 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.25
Consensus pattern (68 bp):
AAAAACGTCCTGCTCTTTGAGGACTAAAAAGATAAAAGGTGCCACCAACTTGTATAGGCTTTAGA
AGA
Found at i:304990 original size:11 final size:12
Alignment explanation
Indices: 304974--305042 Score: 63
Period size: 11 Copynumber: 5.9 Consensus size: 12
304964 CTTAAGTTGG
304974 TTCT-TTTTTTT
1 TTCTGTTTTTTT
*
304985 TTCTTTTTTCTTT
1 TTCTGTTTT-TTT
* *
304998 TTGTGTTCTTTT
1 TTCTGTTTTTTT
*
305010 TT-TGTTTTGTT
1 TTCTGTTTTTTT
*
305021 TTCTGTTTTGTT
1 TTCTGTTTTTTT
305033 TT-TGTTTTTT
1 TTCTGTTTTTT
305043 CCTCTTTTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
11 20 0.41
12 20 0.41
13 9 0.18
ACGTcount: A:0.00, C:0.07, G:0.10, T:0.83
Consensus pattern (12 bp):
TTCTGTTTTTTT
Found at i:304997 original size:18 final size:18
Alignment explanation
Indices: 304974--305040 Score: 82
Period size: 18 Copynumber: 3.7 Consensus size: 18
304964 CTTAAGTTGG
*
304974 TTCTTTTTTTTTTCTTTT
1 TTCTTTTTGTTTTCTTTT
*
304992 TTCTTTTTGTGTTCTTTT
1 TTCTTTTTGTTTTCTTTT
*
305010 TT-TGTTTTGTTTTCTGTT
1 TTCT-TTTTGTTTTCTTTT
*
305028 TTGTTTTTGTTTT
1 TTCTTTTTGTTTT
305041 TTCCTCTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
17 1 0.02
18 41 0.95
19 1 0.02
ACGTcount: A:0.00, C:0.07, G:0.10, T:0.82
Consensus pattern (18 bp):
TTCTTTTTGTTTTCTTTT
Done.