Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008197.1 Hibiscus syriacus cultivar Beakdansim tig00110816_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 560007
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 2 of 2
Found at i:239332 original size:37 final size:37
Alignment explanation
Indices: 239282--239356 Score: 125
Period size: 37 Copynumber: 2.0 Consensus size: 37
239272 AATTTAAAAA
239282 TCGCGTTGCGATAGTACTGTTTACC-TATATCGGTAAT
1 TCGCGTTGCGATAGTACTGTTT-CCTTATATCGGTAAT
*
239319 TCGCGTTGCGATAGTACTGTTTCCTTATGTCGGTAAT
1 TCGCGTTGCGATAGTACTGTTTCCTTATATCGGTAAT
239356 T
1 T
239357 AAGTTACGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
36 2 0.06
37 34 0.94
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.40
Consensus pattern (37 bp):
TCGCGTTGCGATAGTACTGTTTCCTTATATCGGTAAT
Found at i:239481 original size:57 final size:57
Alignment explanation
Indices: 239393--239719 Score: 483
Period size: 57 Copynumber: 5.7 Consensus size: 57
239383 TGCGAAATTT
** *
239393 GCGTTGCGATAGTTGTATTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATC
1 GCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATC
* *
239450 GCGTTGCGATAGTATTGTTTACCTATATCGGTAATTAGCATTGCGAATTTGAAAATC
1 GCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATC
* * *
239507 GCGATGCGGTAGTACTGTTTACCTATGTCGGTAATTAGCGTTGCGAATTTGAAAATC
1 GCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATC
* * * *
239564 GAGTTGCGGTAGTACTGTTTACCTATATAGATAATTAGCGTTGCGAATTTGAAAATC
1 GCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATC
* **
239621 TCGTTGCGATAGTACTGTTTACCTATATCAATAATTAGCGTTGCGAATTTGAAAATC
1 GCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATC
* ** *
239678 TCGTTGTAATAGTATTGTTTACCTATATCGGTAATTAGCGTT
1 GCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTT
239720 ATGATTTACA
Statistics
Matches: 246, Mismatches: 24, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 246 1.00
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.37
Consensus pattern (57 bp):
GCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATC
Found at i:239717 original size:114 final size:114
Alignment explanation
Indices: 239222--239719 Score: 500
Period size: 114 Copynumber: 4.4 Consensus size: 114
239212 TACAGTTTCC
* * * * *
239222 AAAATCGCGTTGTGATAGTACTGTTTACCTATATCAG-AATTAGCGTTGTGAATTTAAAAATCGC
1 AAAATCGCGTTGCGATAGTATTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATCGC
*
239286 GTTGCGATAGTACTGTTTACCTATATCGGTAATTCGCGTTGCG-A--T-
66 GTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTG
** * * ** ** ** * *
239331 AGTA-C-TGTTTCCTTATGT-CGGTAATTAAGT-TA-C-GAAATTGGCGAATT-CG-ATTTGCGA
1 AAAATCGCGTTGCGATA-GTATTGT--TTACCTATATCGGTAATTAGCG--TTGCGAATTT--GA
* * ** *
239388 AATTTGCGTTGCGATAGTTGTATTTACCTATATCGGTAATTAGCGTTGCGAATTTG
59 AAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTG
*
239444 AAAATCGCGTTGCGATAGTATTGTTTACCTATATCGGTAATTAGCATTGCGAATTTGAAAATCGC
1 AAAATCGCGTTGCGATAGTATTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATCGC
* * *
239509 GATGCGGTAGTACTGTTTACCTATGTCGGTAATTAGCGTTGCGAATTTG
66 GTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTG
* * * * * *
239558 AAAATCGAGTTGCGGTAGTACTGTTTACCTATATAGATAATTAGCGTTGCGAATTTGAAAATCTC
1 AAAATCGCGTTGCGATAGTATTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATCGC
**
239623 GTTGCGATAGTACTGTTTACCTATATCAATAATTAGCGTTGCGAATTTG
66 GTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTG
* **
239672 AAAATCTCGTTGTAATAGTATTGTTTACCTATATCGGTAATTAGCGTT
1 AAAATCGCGTTGCGATAGTATTGTTTACCTATATCGGTAATTAGCGTT
239720 ATGATTTACA
Statistics
Matches: 309, Mismatches: 60, Indels: 35
0.76 0.15 0.09
Matches are distributed among these distances:
106 1 0.00
107 20 0.06
108 6 0.02
109 53 0.17
110 1 0.00
112 1 0.00
113 6 0.02
114 199 0.64
115 11 0.04
116 11 0.04
ACGTcount: A:0.27, C:0.14, G:0.21, T:0.37
Consensus pattern (114 bp):
AAAATCGCGTTGCGATAGTATTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATCGC
GTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTG
Found at i:240954 original size:16 final size:17
Alignment explanation
Indices: 240918--240960 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
240908 TCGTCCCTGT
*
240918 TAAAATTTTTATATTTGA
1 TAAAA-TTTTATATTTAA
240936 TAAAATTTTA-ATTTAA
1 TAAAATTTTATATTTAA
*
240952 TAATATTTT
1 TAAAATTTT
240961 GGTTCGTGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 13 0.57
17 5 0.22
18 5 0.22
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
TAAAATTTTATATTTAA
Found at i:241909 original size:40 final size:40
Alignment explanation
Indices: 241864--241985 Score: 244
Period size: 40 Copynumber: 3.0 Consensus size: 40
241854 CAAAAACTTA
241864 TTTATAAAAATAAGTATTTTTATTTTAATTATTAAAATCG
1 TTTATAAAAATAAGTATTTTTATTTTAATTATTAAAATCG
241904 TTTATAAAAATAAGTATTTTTATTTTAATTATTAAAATCG
1 TTTATAAAAATAAGTATTTTTATTTTAATTATTAAAATCG
241944 TTTATAAAAATAAGTATTTTTATTTTAATTATTAAAATCG
1 TTTATAAAAATAAGTATTTTTATTTTAATTATTAAAATCG
241984 TT
1 TT
241986 AAATGTTAAG
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 82 1.00
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (40 bp):
TTTATAAAAATAAGTATTTTTATTTTAATTATTAAAATCG
Found at i:247094 original size:24 final size:24
Alignment explanation
Indices: 247058--247109 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
247048 TTTTATGTAC
*
247058 AATATGACC-AAAATTTTAAAAGAA
1 AATATGACCAAAAAATTT-AAAGAA
**
247082 AATATGATTAAAAAATTTAAAGAA
1 AATATGACCAAAAAATTTAAAGAA
247106 AATA
1 AATA
247110 AAAACAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 17 0.71
25 7 0.29
ACGTcount: A:0.62, C:0.04, G:0.08, T:0.27
Consensus pattern (24 bp):
AATATGACCAAAAAATTTAAAGAA
Found at i:247259 original size:29 final size:29
Alignment explanation
Indices: 247168--247275 Score: 80
Period size: 29 Copynumber: 3.7 Consensus size: 29
247158 TTTGCATGAA
*
247168 TTTAGGGATAAAATTAGAATATTCAAAA-
1 TTTAGGGATGAAATTAGAATATTCAAAAG
* * *
247196 TTT-GAGGACT-AATTTAGAAAAAGGTTC-ATAG
1 TTTAG-GGA-TGAAATTAG-AATA--TTCAAAAG
247227 TTTAGGGATGAAATTAGAATATTCAAAAG
1 TTTAGGGATGAAATTAGAATATTCAAAAG
* * *
247256 TTTAAGGATGCATTTAGAAT
1 TTTAGGGATGAAATTAGAAT
247276 GAGAATCATA
Statistics
Matches: 62, Mismatches: 9, Indels: 17
0.70 0.10 0.19
Matches are distributed among these distances:
27 1 0.02
28 15 0.24
29 24 0.39
30 6 0.10
31 15 0.24
32 1 0.02
ACGTcount: A:0.43, C:0.05, G:0.19, T:0.33
Consensus pattern (29 bp):
TTTAGGGATGAAATTAGAATATTCAAAAG
Found at i:247301 original size:60 final size:59
Alignment explanation
Indices: 247166--247331 Score: 181
Period size: 60 Copynumber: 2.8 Consensus size: 59
247156 TATTTGCATG
* **
247166 AATTTAGGGATAAAATTAGAATATTCAAAATTTGAGGACTAATTTAGAAAAAGGTTCAT
1 AATTTAGGGATAAAATTAGAATATTCAAAATTTAAGGACTAATTTAGAAAAAGAATCAT
* * * **
247225 AGTTTAGGGATGAAATTAGAATATTCAAAAGTTTAAGGA-TGCATTTAGAATGAGAATCAT
1 AATTTAGGGATAAAATTAGAATATTCAAAA-TTTAAGGACT-AATTTAGAAAAAGAATCAT
* * * * *
247285 AATTTAAGGATAAAATTAAAATATTTAAAAATTTAAAGACCAATTTA
1 AATTTAGGGATAAAATTAGAATA-TTCAAAATTTAAGGACTAATTTA
247332 AAATAATAGT
Statistics
Matches: 87, Mismatches: 16, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
59 29 0.33
60 52 0.60
61 6 0.07
ACGTcount: A:0.47, C:0.05, G:0.16, T:0.33
Consensus pattern (59 bp):
AATTTAGGGATAAAATTAGAATATTCAAAATTTAAGGACTAATTTAGAAAAAGAATCAT
Found at i:256899 original size:2 final size:2
Alignment explanation
Indices: 256892--256929 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
256882 TTCCATTTCA
256892 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
256930 TTCCCAGCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:257301 original size:29 final size:29
Alignment explanation
Indices: 257197--257293 Score: 185
Period size: 29 Copynumber: 3.3 Consensus size: 29
257187 TCTTTAGTTG
*
257197 GTGAGAAAATGAGAGAAAATCGAGGATGA
1 GTGAGAAAATGAGAGAAATTCGAGGATGA
257226 GTGAGAAAATGAGAGAAATTCGAGGATGA
1 GTGAGAAAATGAGAGAAATTCGAGGATGA
257255 GTGAGAAAATGAGAGAAATTCGAGGATGA
1 GTGAGAAAATGAGAGAAATTCGAGGATGA
257284 GTGAGAAAAT
1 GTGAGAAAAT
257294 ATAAGAAAAC
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
29 67 1.00
ACGTcount: A:0.46, C:0.03, G:0.34, T:0.16
Consensus pattern (29 bp):
GTGAGAAAATGAGAGAAATTCGAGGATGA
Found at i:288893 original size:2 final size:2
Alignment explanation
Indices: 288886--288923 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
288876 GTAACACATA
* *
288886 AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
288924 GGTAATAGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:291162 original size:13 final size:14
Alignment explanation
Indices: 291119--291170 Score: 52
Period size: 16 Copynumber: 3.6 Consensus size: 14
291109 GTTTTTCGAT
*
291119 CTTTCGTTATAAGGTA
1 CTTTTGTTATAA--TA
291135 CTTTTGTTATAATA
1 CTTTTGTTATAATA
*
291149 CTTTT-TTATTATA
1 CTTTTGTTATAATA
291162 CTTATTGTT
1 CTT-TTGTT
291171 TATTATGATT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
13 10 0.31
14 9 0.28
15 2 0.06
16 11 0.34
ACGTcount: A:0.23, C:0.10, G:0.10, T:0.58
Consensus pattern (14 bp):
CTTTTGTTATAATA
Found at i:296814 original size:42 final size:42
Alignment explanation
Indices: 296751--296916 Score: 233
Period size: 42 Copynumber: 4.0 Consensus size: 42
296741 GAAAAGTGAA
* * * *
296751 TAAAGTAGAACGGAAGAAGGCATTGTACTTTTGATTCTCGTC
1 TAAAGTAGAACGGAAGGAGGCATCGCACTTTCGATTCTCGTC
**
296793 TAAAGTAGAACGGAAGGAGGCATAACACTTTCGATTCTCGTC
1 TAAAGTAGAACGGAAGGAGGCATCGCACTTTCGATTCTCGTC
* ** *
296835 TAAAGTAGAACGGAATGAGGCATCGCACTTTTAATTATCGTC
1 TAAAGTAGAACGGAAGGAGGCATCGCACTTTCGATTCTCGTC
*
296877 TAAAGTAGAACGGAAGGAGACATCGCACTTTCGATTCTCG
1 TAAAGTAGAACGGAAGGAGGCATCGCACTTTCGATTCTCG
296917 ATGAATCACG
Statistics
Matches: 108, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 108 1.00
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (42 bp):
TAAAGTAGAACGGAAGGAGGCATCGCACTTTCGATTCTCGTC
Found at i:297085 original size:28 final size:28
Alignment explanation
Indices: 297021--297085 Score: 121
Period size: 28 Copynumber: 2.3 Consensus size: 28
297011 TTCTTTACAT
*
297021 AGAACCAGATCTTTCCATTTCTTGGCTG
1 AGAACCAGCTCTTTCCATTTCTTGGCTG
297049 AGAACCAGCTCTTTCCATTTCTTGGCTG
1 AGAACCAGCTCTTTCCATTTCTTGGCTG
297077 AGAACCAGC
1 AGAACCAGC
297086 AACTCATTGC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.23, C:0.28, G:0.18, T:0.31
Consensus pattern (28 bp):
AGAACCAGCTCTTTCCATTTCTTGGCTG
Found at i:297545 original size:30 final size:30
Alignment explanation
Indices: 297505--297570 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
297495 AAATATATTT
* *
297505 TCTTTGAAAAAAATCTCAAAAGTTTTGAAAA
1 TCTTTAAAAAAAATCTCAAAACTTTT-AAAA
297536 T-TTTAAAAAAAATCTCAAAACTTTTAAAA
1 TCTTTAAAAAAAATCTCAAAACTTTTAAAA
297565 TCTTTA
1 TCTTTA
297571 TTTCAATCAC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
29 5 0.16
30 26 0.81
31 1 0.03
ACGTcount: A:0.48, C:0.11, G:0.05, T:0.36
Consensus pattern (30 bp):
TCTTTAAAAAAAATCTCAAAACTTTTAAAA
Found at i:299454 original size:22 final size:22
Alignment explanation
Indices: 299429--299471 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
299419 ATAATTATAC
299429 ATTTGATCCTCAATACTTACAA
1 ATTTGATCCTCAATACTTACAA
299451 ATTTGATCCTCAATACTTACA
1 ATTTGATCCTCAATACTTACA
299472 TATTCTATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.23, G:0.05, T:0.37
Consensus pattern (22 bp):
ATTTGATCCTCAATACTTACAA
Found at i:301010 original size:28 final size:28
Alignment explanation
Indices: 300966--301022 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
300956 TTGTCTTTCC
* *
300966 TTTCAAGTACTTGCTCAACGATATAATG
1 TTTCAAGCACTTGCTCAACGACATAATG
*
300994 TTTCAAGCA-TTGACTCAATGACATAATG
1 TTTCAAGCACTTG-CTCAACGACATAATG
301022 T
1 T
301023 AGACAAAGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 3 0.12
28 22 0.88
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (28 bp):
TTTCAAGCACTTGCTCAACGACATAATG
Found at i:308146 original size:21 final size:21
Alignment explanation
Indices: 308120--308181 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
308110 TAAATAACAA
308120 AAAAACGTGCCACAAAGATAG
1 AAAAACGTGCCACAAAGATAG
* *
308141 AAAAACGTGCCATAAAGGTAG
1 AAAAACGTGCCACAAAGATAG
*
308162 AGATAAACGTGCCCCAAAGA
1 A-A-AAACGTGCCACAAAGA
308182 CATAATTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 20 0.59
22 1 0.03
23 13 0.38
ACGTcount: A:0.48, C:0.19, G:0.21, T:0.11
Consensus pattern (21 bp):
AAAAACGTGCCACAAAGATAG
Found at i:308620 original size:29 final size:29
Alignment explanation
Indices: 308566--308649 Score: 96
Period size: 29 Copynumber: 2.9 Consensus size: 29
308556 ACCCAACCCA
* **
308566 TAGGTCGCCATGCACTCCCAGTGACCTCC
1 TAGGTCGCCATGCACTCCCAGCGACCAAC
* *
308595 TAGGTCGCCATGCACTCCGAGCGACCAAG
1 TAGGTCGCCATGCACTCCCAGCGACCAAC
* * *
308624 GAGGTCGCCATGCACGCCCGGCGACC
1 TAGGTCGCCATGCACTCCCAGCGACC
308650 TTGTCTCCTT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.19, C:0.39, G:0.27, T:0.14
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCCAGCGACCAAC
Found at i:308771 original size:29 final size:29
Alignment explanation
Indices: 308724--308808 Score: 145
Period size: 29 Copynumber: 2.9 Consensus size: 29
308714 GGGTTAAAAG
*
308724 CTTGGTCGCCGGGCA-TGCATGGCGACCTC
1 CTTGGTCGCCCGG-AGTGCATGGCGACCTC
308753 CTTGGTCGCCCGGAGTGCATGGCGACCTC
1 CTTGGTCGCCCGGAGTGCATGGCGACCTC
308782 CTTGGTCGCCCGGAGTGCATGGCGACC
1 CTTGGTCGCCCGGAGTGCATGGCGACC
308809 GGGAGTGTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
28 1 0.02
29 53 0.98
ACGTcount: A:0.11, C:0.34, G:0.35, T:0.20
Consensus pattern (29 bp):
CTTGGTCGCCCGGAGTGCATGGCGACCTC
Found at i:308815 original size:17 final size:17
Alignment explanation
Indices: 308793--308825 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
308783 TTGGTCGCCC
308793 GGAGTGCATGGCGACCG
1 GGAGTGCATGGCGACCG
*
308810 GGAGTGTATGGCGACC
1 GGAGTGCATGGCGACC
308826 TATGGGTTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.21, G:0.45, T:0.15
Consensus pattern (17 bp):
GGAGTGCATGGCGACCG
Found at i:309718 original size:45 final size:45
Alignment explanation
Indices: 309669--309755 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
309659 AGAACCCGAA
**
309669 GAAGAGATCCGTGAAGAACCCGATTTAGGTGAGACCCAAACCCCG
1 GAAGAGATCCGTGAAGAACCCGATGAAGGTGAGACCCAAACCCCG
* *
309714 GAAGAGATCCGTGAAGAACCCGATGAAGTTGAGACGCAAACC
1 GAAGAGATCCGTGAAGAACCCGATGAAGGTGAGACCCAAACC
309756 AAGGGAGAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.36, C:0.24, G:0.28, T:0.13
Consensus pattern (45 bp):
GAAGAGATCCGTGAAGAACCCGATGAAGGTGAGACCCAAACCCCG
Found at i:309765 original size:45 final size:45
Alignment explanation
Indices: 309669--309776 Score: 135
Period size: 45 Copynumber: 2.4 Consensus size: 45
309659 AGAACCCGAA
** **
309669 GAAGAGATCCGTGAAGAACCCGATTTAGGTGAGACCCAAACCCCG
1 GAAGAGATCCGTGAAGAACCCGATGAAGGTGAGACCCAAACCAAG
* *
309714 GAAGAGATCCGTGAAGAACCCGATGAAGTTGAGACGCAAACCAAG
1 GAAGAGATCCGTGAAGAACCCGATGAAGGTGAGACCCAAACCAAG
* * *
309759 GGAGAGATCAGAGAAGAA
1 GAAGAGATCCGTGAAGAA
309777 GCCAGTGAAG
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 54 1.00
ACGTcount: A:0.39, C:0.20, G:0.30, T:0.11
Consensus pattern (45 bp):
GAAGAGATCCGTGAAGAACCCGATGAAGGTGAGACCCAAACCAAG
Found at i:343532 original size:144 final size:144
Alignment explanation
Indices: 343272--343561 Score: 562
Period size: 144 Copynumber: 2.0 Consensus size: 144
343262 CAGTATGTTC
343272 TAGTTGGTGGTAACTTAGTGTCCTGGAGTACAAATAAGTAGAAAGTTGTCTCTAGATCCACCATG
1 TAGTTGGTGGTAACTTAGTGTCCTGGAGTACAAATAAGTAGAAAGTTGTCTCTAGATCCACCATG
343337 GAAGCAGAATATCACAGCCTAGCAGATATGGTTGCAGAAGTTACTTGGATCGATGCATTGTTGAA
66 GAAGCAGAATATCACAGCCTAGCAGATATGGTTGCAGAAGTTACTTGGATCGATGCATTGTTGAA
343402 TGATATTGGAGTAA
131 TGATATTGGAGTAA
*
343416 TAGTTGGTGGTAACTTAGTGTCCTGGAGTACAAATAAGTATAAAGTTGTCTCTAGATCCACCATG
1 TAGTTGGTGGTAACTTAGTGTCCTGGAGTACAAATAAGTAGAAAGTTGTCTCTAGATCCACCATG
*
343481 GAAGCAGAATATCATAGCCTAGCAGATATGGTTGCAGAAGTTACTTGGATCGATGCATTGTTGAA
66 GAAGCAGAATATCACAGCCTAGCAGATATGGTTGCAGAAGTTACTTGGATCGATGCATTGTTGAA
343546 TGATATTGGAGTAA
131 TGATATTGGAGTAA
343560 TA
1 TA
343562 AGGCAAGAAA
Statistics
Matches: 144, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
144 144 1.00
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.30
Consensus pattern (144 bp):
TAGTTGGTGGTAACTTAGTGTCCTGGAGTACAAATAAGTAGAAAGTTGTCTCTAGATCCACCATG
GAAGCAGAATATCACAGCCTAGCAGATATGGTTGCAGAAGTTACTTGGATCGATGCATTGTTGAA
TGATATTGGAGTAA
Found at i:345910 original size:18 final size:17
Alignment explanation
Indices: 345869--345910 Score: 66
Period size: 18 Copynumber: 2.4 Consensus size: 17
345859 TATTGAAAAA
345869 AATAAATTATGACATAT
1 AATAAATTATGACATAT
345886 AATTAAATTATGACATATT
1 AA-TAAATTATGACATA-T
345905 AATAAA
1 AATAAA
345911 ACGAATAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 2 0.09
18 18 0.78
19 3 0.13
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.36
Consensus pattern (17 bp):
AATAAATTATGACATAT
Found at i:347400 original size:4 final size:4
Alignment explanation
Indices: 347391--347428 Score: 51
Period size: 4 Copynumber: 9.5 Consensus size: 4
347381 TTGGGTTGGG
*
347391 ATTT ATTT ATTT A-AT ATTGT ATTT ATTT ATTT ATTT AT
1 ATTT ATTT ATTT ATTT ATT-T ATTT ATTT ATTT ATTT AT
347429 ACATAATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
3 2 0.07
4 24 0.80
5 4 0.13
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (4 bp):
ATTT
Found at i:371339 original size:16 final size:16
Alignment explanation
Indices: 371301--371342 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
371291 TATTTAAAGT
371301 TTTAAGTAAAA-TTAAA
1 TTTAA-TAAAATTTAAA
*
371317 TTT-ATAAAATTTGAA
1 TTTAATAAAATTTAAA
371332 TTTAATAAAAT
1 TTTAATAAAAT
371343 ATATTTGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 5 0.22
15 8 0.35
16 10 0.43
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (16 bp):
TTTAATAAAATTTAAA
Found at i:371363 original size:12 final size:12
Alignment explanation
Indices: 371346--371370 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
371336 ATAAAATATA
371346 TTTGTTTAAATT
1 TTTGTTTAAATT
371358 TTTGTTTAAATT
1 TTTGTTTAAATT
371370 T
1 T
371371 AAATATAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (12 bp):
TTTGTTTAAATT
Found at i:395714 original size:39 final size:36
Alignment explanation
Indices: 395660--395750 Score: 128
Period size: 39 Copynumber: 2.4 Consensus size: 36
395650 CGAGGGTTTG
*
395660 GTGTTTCAAGAGAAACATTTTCAAAGGTTTTTTGTGTGT
1 GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTT-T-T-T
* *
395699 GTGTTTCAAGAGAAACAATTTCTAGGGTTTTTTTTT
1 GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTTTTT
395735 GTGTTTCAAGAGAAAC
1 GTGTTTCAAGAGAAAC
395751 TGTCTCAAGA
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
36 17 0.35
37 1 0.02
38 1 0.02
39 30 0.61
ACGTcount: A:0.27, C:0.09, G:0.22, T:0.42
Consensus pattern (36 bp):
GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTTTTT
Found at i:395776 original size:36 final size:36
Alignment explanation
Indices: 395736--395969 Score: 211
Period size: 36 Copynumber: 6.6 Consensus size: 36
395726 TTTTTTTTTG
*
395736 TGTTTCAAGAGAAACTGTCTCAAGAGGGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
*
395772 TGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * *
395809 AG-TTCTAAAAGAAACTGTCTCAAGGGAGACGAAATT
1 TGTTTC-AAGAGAAACTGTCTCAAGAGAGACAAAATT
* * *
395845 TGTTTCAAG-GAAA-AGATATTC-A-A-AG----ATTT
1 TGTTTCAAGAGAAACTG-T-CTCAAGAGAGACAAAATT
*
395874 TGTTTCAAG-GAAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGAG-AAACTGTCTCAAGAGAGACAAAATT
* * *
395910 TGTTTCAAGGGAAACCGTCTCAAGAGAGACAAGATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAA-AATT
*
395947 TGTTTCAAGGGAAACTGTCTCAA
1 TGTTTCAAGAGAAACTGTCTCAA
395970 AACTAGTTTA
Statistics
Matches: 163, Mismatches: 19, Indels: 31
0.77 0.09 0.15
Matches are distributed among these distances:
29 15 0.09
30 5 0.03
31 1 0.01
32 2 0.01
33 2 0.01
34 1 0.01
35 6 0.04
36 73 0.45
37 58 0.36
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:395970 original size:102 final size:102
Alignment explanation
Indices: 395770--395956 Score: 247
Period size: 102 Copynumber: 1.8 Consensus size: 102
395760 AGGGACAAAA
* * *
395770 TTTGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCTAAAAGAAACTGTCTCAAGGG
1 TTTGTTTCAAAAGAAACTATCTCAAGAGAGACAAAACTTAGTTCTAAAAGAAACCGTCTCAAGAG
395835 AGACGAAATTTGTTTCAAGGAAAAGATATTCAAAGAT
66 AGACGAAATTTGTTTCAAGGAAAAGATATTCAAAGAT
* * **
395872 TTTGTTTC-AAGGAAAACTATCTCAAGAGAGACAAAA-TTTGTT-TCAAGGGAAACCGTCTCAAG
1 TTTGTTTCAAAAG-AAACTATCTCAAGAGAGACAAAACTTAGTTCT-AAAAGAAACCGTCTCAAG
395934 AGAGAC-AAGATTTTGTTTCAAGG
64 AGAGACGAA-A-TTTGTTTCAAGG
395957 GAAACTGTCT
Statistics
Matches: 74, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
100 3 0.04
101 29 0.39
102 42 0.57
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (102 bp):
TTTGTTTCAAAAGAAACTATCTCAAGAGAGACAAAACTTAGTTCTAAAAGAAACCGTCTCAAGAG
AGACGAAATTTGTTTCAAGGAAAAGATATTCAAAGAT
Found at i:396084 original size:37 final size:37
Alignment explanation
Indices: 396033--396221 Score: 141
Period size: 37 Copynumber: 5.4 Consensus size: 37
396023 TCAAGGTTTA
*
396033 TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAACTATCTCAAGGGAGACAAAATTT
*
396070 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGGGAAACTATCTCAAGGGAGACAAAATTT
** * * *
396106 AATTTCAAAGGAAA-TATTTTCAA---TG------TTT
1 TGTTTCAAGGGAAACTA-TCTCAAGGGAGACAAAATTT
* *
396134 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 -TGTTTCAAGGGAAACTATCTCAAGGGAGACAAAATTT
* * * *
396172 TGTTTCAAGGGAAACTACCCCAAGCGAGATAAAA-TT
1 TGTTTCAAGGGAAACTATCTCAAGGGAGACAAAATTT
**
396208 CATTTCAAGGGAAA
1 TGTTTCAAGGGAAA
396222 TGTTTTCAAT
Statistics
Matches: 117, Mismatches: 22, Indels: 27
0.70 0.13 0.16
Matches are distributed among these distances:
28 2 0.02
29 15 0.13
30 1 0.01
32 1 0.01
33 1 0.01
35 2 0.02
36 32 0.27
37 60 0.51
38 3 0.03
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.28
Consensus pattern (37 bp):
TGTTTCAAGGGAAACTATCTCAAGGGAGACAAAATTT
Found at i:396126 original size:102 final size:102
Alignment explanation
Indices: 396006--396245 Score: 390
Period size: 102 Copynumber: 2.4 Consensus size: 102
395996 ATATTTTGTG
* *
396006 TTTCAAGGGAAACGTTTTCAAGGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTT
* *
396071 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTAA
66 GTTTCAAGGGAAACTACCCCAAGAGAGACAAAATTAA
* * *
396108 TTTCAAAGGAAATATTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTT
* * *
396173 GTTTCAAGGGAAACTACCCCAAGCGAGATAAAATTCA
66 GTTTCAAGGGAAACTACCCCAAGAGAGACAAAATTAA
396210 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAG
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAG
396246 GGAGACAAAA
Statistics
Matches: 126, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
102 126 1.00
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (102 bp):
TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTT
GTTTCAAGGGAAACTACCCCAAGAGAGACAAAATTAA
Found at i:396245 original size:87 final size:87
Alignment explanation
Indices: 396154--396332 Score: 313
Period size: 87 Copynumber: 2.1 Consensus size: 87
396144 AGAAACTGTC
*
396154 TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTACCCCAAGCGAGATAAAATTCATTTCAAGGG
1 TCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTACCCCAAGCGAGATAAAATTCATTTCAAGGG
396219 AAATGTTTTCAATGTTTATGTT
66 AAATGTTTTCAATGTTTATGTT
* * **
396241 TCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTATCTCAATTGAGATAAAATTCATTTCAAGGG
1 TCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTACCCCAAGCGAGATAAAATTCATTTCAAGGG
396306 AAATGTTTTCAATGTTTATGTT
66 AAATGTTTTCAATGTTTATGTT
396328 TCAAG
1 TCAAG
396333 AGAAACTGTC
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 87 1.00
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.32
Consensus pattern (87 bp):
TCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTACCCCAAGCGAGATAAAATTCATTTCAAGGG
AAATGTTTTCAATGTTTATGTT
Found at i:396432 original size:189 final size:189
Alignment explanation
Indices: 396052--396437 Score: 508
Period size: 189 Copynumber: 2.0 Consensus size: 189
396042 AGAAACTATC
*
396052 TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTAATTTCAAAGG
1 TCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTAATTTCAAAGG
* * **
396117 AAATATTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGG
66 AAATATTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTAGTTCCAAAA
* * * * * *
396182 GAAACTACCCCAAGCGAGATAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTT
131 GAAAATACCCCAAGCGAGACAAAATTCATTTCAAGGAAAAAGTATTCAATATTTATGTT
** * * *
396241 TCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTATCTCAATTGAGATAAAATTCATTTCAAGGG
1 TCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTAATTTCAAAGG
* *
396306 AAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGATAAAATTTAGTTCCAAAA
66 AAATATTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTAGTTCCAAAA
** * * * *
396371 GAAAATGTCTCAAGGGAGACGAAATT-AGTTTCAATGAAAACAG-ATTCAAATATTT-TGTT
131 GAAAATACCCCAAGCGAGACAAAATTCA-TTTCAAGGAAAA-AGTATTC-AATATTTATGTT
396430 TCAAGGGA
1 TCAAGGGA
396438 AACTTGGAAA
Statistics
Matches: 170, Mismatches: 24, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
188 1 0.01
189 162 0.95
190 7 0.04
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.30
Consensus pattern (189 bp):
TCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTAATTTCAAAGG
AAATATTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTAGTTCCAAAA
GAAAATACCCCAAGCGAGACAAAATTCATTTCAAGGAAAAAGTATTCAATATTTATGTT
Found at i:396774 original size:106 final size:106
Alignment explanation
Indices: 396589--396836 Score: 343
Period size: 106 Copynumber: 2.3 Consensus size: 106
396579 TGTATTGTTC
* * * * * *
396589 CGAGTCCAATATCCTCCGCCGTGAAGTTAAAATTGGCTCTGGAACTAAGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAACTAAGAAATTATTTGTTGACA
* *
396654 GCCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCT
66 ACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCT
* * **
396695 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTATTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAACTAAGAAATTATTTGTTGACA
* * * *
396760 ACCAGCCGTCCCTTCGTTTTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCT
*
396801 CGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGG
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGG
396837 GAAATTGTTT
Statistics
Matches: 124, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
106 124 1.00
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (106 bp):
CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAACTAAGAAATTATTTGTTGACA
ACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCT
Found at i:397516 original size:32 final size:32
Alignment explanation
Indices: 397475--397587 Score: 140
Period size: 32 Copynumber: 3.5 Consensus size: 32
397465 TTTGCATCAG
* * *
397475 GATGTTGAAT-TCCCAAAGATGCCCCAATATTC
1 GATGTTGAATCT-CAAAAAATGCCCCAATATTT
*
397507 GATGTTGAATCTCAAAAAATGCCCCAACATTT
1 GATGTTGAATCTCAAAAAATGCCCCAATATTT
*
397539 GATGTT-AAGTCTAAAAAAATGCCCCAATATTT
1 GATGTTGAA-TCTCAAAAAATGCCCCAATATTT
397571 GATGTTGAATCTTCAAA
1 GATGTTGAATC-TCAAA
397588 GATGCCCTCA
Statistics
Matches: 70, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
31 2 0.03
32 61 0.87
33 7 0.10
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.30
Consensus pattern (32 bp):
GATGTTGAATCTCAAAAAATGCCCCAATATTT
Found at i:398635 original size:69 final size:69
Alignment explanation
Indices: 398514--398651 Score: 204
Period size: 69 Copynumber: 2.0 Consensus size: 69
398504 TGTCTCTCTC
* * * *
398514 TTGATGCTCCATGATCTTCGAGTGGAGTGATTTAGTAATTCAGAAGTGATTGTGCTTGATCAATC
1 TTGAGGCTCCATGATCTTCGAGTGAAGTGATTCAGTAATTCAGAAATGATTGTGCTTGATCAATC
398579 TCAT
66 TCAT
* * * *
398583 TTGAGGCTCTATGATCTTCGAGTGAAGTGGTTCAGTGATTCGGAAATGATTGTGCTTGATCAATC
1 TTGAGGCTCCATGATCTTCGAGTGAAGTGATTCAGTAATTCAGAAATGATTGTGCTTGATCAATC
398648 TCAT
66 TCAT
398652 AGTTTGAATC
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
69 61 1.00
ACGTcount: A:0.24, C:0.14, G:0.25, T:0.37
Consensus pattern (69 bp):
TTGAGGCTCCATGATCTTCGAGTGAAGTGATTCAGTAATTCAGAAATGATTGTGCTTGATCAATC
TCAT
Found at i:398748 original size:21 final size:21
Alignment explanation
Indices: 398724--398775 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
398714 TTTTCTTCAA
* *
398724 TTTTCCTTTGTTTTTTTCTCT
1 TTTTACTTTGTCTTTTTCTCT
* *
398745 TTTTATTTTCTCTTTTTCTCT
1 TTTTACTTTGTCTTTTTCTCT
*
398766 TTTTGCTTTG
1 TTTTACTTTG
398776 ATTAAATCTT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.02, C:0.17, G:0.06, T:0.75
Consensus pattern (21 bp):
TTTTACTTTGTCTTTTTCTCT
Found at i:398753 original size:13 final size:13
Alignment explanation
Indices: 398723--398761 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
398713 TTTTTCTTCA
398723 ATTTTC-CTTTGTT
1 ATTTTCTCTTT-TT
*
398736 TTTTTCTCTTTTT
1 ATTTTCTCTTTTT
398749 ATTTTCTCTTTTT
1 ATTTTCTCTTTTT
398762 CTCTTTTTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 19 0.83
14 4 0.17
ACGTcount: A:0.05, C:0.15, G:0.03, T:0.77
Consensus pattern (13 bp):
ATTTTCTCTTTTT
Found at i:401912 original size:16 final size:16
Alignment explanation
Indices: 401891--401923 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
401881 TTTTAGAATC
401891 CTATTAACAATATAAT
1 CTATTAACAATATAAT
401907 CTATTAACAATATAAT
1 CTATTAACAATATAAT
401923 C
1 C
401924 CTAATGCAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.36
Consensus pattern (16 bp):
CTATTAACAATATAAT
Found at i:410369 original size:2 final size:2
Alignment explanation
Indices: 410362--410389 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
410352 TGAAAACTAC
410362 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
410390 CTGTGGGTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:416778 original size:13 final size:13
Alignment explanation
Indices: 416760--416785 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
416750 TATATACAAA
416760 TTAATCTAATTTT
1 TTAATCTAATTTT
416773 TTAATCTAATTTT
1 TTAATCTAATTTT
416786 CATTTCATAT
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:0.08, G:0.00, T:0.62
Consensus pattern (13 bp):
TTAATCTAATTTT
Found at i:418852 original size:28 final size:28
Alignment explanation
Indices: 418799--418855 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
418789 CCATTGTTGC
*
418799 TTTTAAGCACTGACTCGACAACATAATG
1 TTTTAAGCACTGACTCAACAACATAATG
* *
418827 TTTTAAGCACATG-CTCAACGATATAATG
1 TTTTAAGCAC-TGACTCAACAACATAATG
418855 T
1 T
418856 AAACATAGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 23 0.92
29 2 0.08
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32
Consensus pattern (28 bp):
TTTTAAGCACTGACTCAACAACATAATG
Found at i:430133 original size:21 final size:22
Alignment explanation
Indices: 430095--430140 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
430085 GTCTGTTGAA
* **
430095 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGATGCGGAGTACT
430116 ACTCCACCTGATGCGGAGTACT
1 ACTCCACCTGATGCGGAGTACT
430138 ACT
1 ACT
430141 TGTCTGGACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGATGCGGAGTACT
Found at i:443525 original size:30 final size:31
Alignment explanation
Indices: 443489--443549 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
443479 TAGCTGAGAG
*
443489 ACTAAAATCGAAC-ATATCGATAAC-TTATGA
1 ACTAAAATCGAACGA-ACCGATAACGTTATGA
443519 ACTAAAATCGAACGAACCGATAACGTTATGA
1 ACTAAAATCGAACGAACCGATAACGTTATGA
443550 CCATGTAATC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 21 0.75
31 7 0.25
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.23
Consensus pattern (31 bp):
ACTAAAATCGAACGAACCGATAACGTTATGA
Found at i:445379 original size:118 final size:117
Alignment explanation
Indices: 445171--445870 Score: 435
Period size: 118 Copynumber: 6.1 Consensus size: 117
445161 AAAAAATATA
** * *
445171 GACGATAACATAACCGGTTAATTACTGGAAACATTATCAAGCACAATAACATATTAGG-AAGCGC
1 GACGATAACATAACCAATTAATTACTGGAAACATTATCAAGCATAATAACATATTAGGTAA-CAC
* * *
445235 TTATATAACGTAATATGTAGCGCCTTTTTAAAGCTGATGGGGCTTTGGAAATCT
65 TTATATAACGTAATATGTAGCGCCTTTTT-AAGCTGATAGGGCTTTAGAAATCC
* * * *
445289 GACGATAACATAATCAATTAATTATTGTAAACATTATCAAGCATAATAACATATTAGGTAGCACT
1 GACGATAACATAACCAATTAATTACTGGAAACATTATCAAGCATAATAACATATTAGGTAACACT
* * *
445354 TATATAACGTAATATGTAGCGCCTTTTTAAGTTGATAGGGTTTTGGAAATCC
66 TATATAACGTAATATGTAGCGCCTTTTTAAGCTGATAGGGCTTTAGAAATCC
* ** * *** * * *
445406 GACAATAACA-AAATAAGTTAATTACT-TAATTTGTTAT-TAGTATTATTAACATATTAGGTAAC
1 GACGATAACATAACCAA-TTAATTACTGGAA-ACATTATCAAGCA-TAATAACATATTAGGTAAC
* * ** ** * *
445468 ACCTA-A-AATGT--TA-CCAAAG----TTTAAGCTGATAGAGCCTTAGAAATCC
63 ACTTATATAACGTAATATGTAGCGCCTTTTTAAGCTGATAGGGCTTTAGAAATCC
* * *
445514 GACGATAACATAACCGATTAATTACTGGAAACATTATCAAGCATAATAACATATTAGGCAACGCT
1 GACGATAACATAACCAATTAATTACTGGAAACATTATCAAGCATAATAACATATTAGGTAACACT
* * **
445579 TATATAACGTAATAGGTAGCGCCCTTTTAAAGCTGAT-GGGACTTTAGAAATTT
66 TATATAACGTAATATGTAGCG-CCTTTTTAAGCTGATAGGG-CTTTAGAAATCC
* * ** * * *** ** * *
445632 GGCGATAA-AAAAATAGGTTAATTACT-TAATTTGTTAT-TTGTATTATTAACATATTAGGTAAC
1 GACGATAACATAACCA-ATTAATTACTGGAA-ACATTATCAAGCA-TAATAACATATTAGGTAAC
* * * ** * * *
445694 GCCTA-A-AATGTTACAT-TG-AAAG----TTTAAGCTGATAGAGCCTTAGAAATCT
63 ACTTATATAACG-TA-ATATGTAGCGCCTTTTTAAGCTGATAGGGCTTTAGAAATCC
* ** * * *
445743 GACCATAACATAACCGGTTAATTAATGGAAACATTATCAAGCATAATAACATATTAGGTAGCGCT
1 GACGATAACATAACCAATTAATTACTGGAAACATTATCAAGCATAATAACATATTAGGTAACACT
* * * * * * *
445808 TATGTAACGTAATAAGTTGCGCATTATTAAAGTTGAT-GTGGCCTTAGAAATCC
66 TATATAACGTAATATGTAGCGCCTT-TTTAAGCTGATAG-GGCTTTAGAAATCC
445861 GACGATAACA
1 GACGATAACA
445871 AAATATGTTA
Statistics
Matches: 435, Mismatches: 110, Indels: 74
0.70 0.18 0.12
Matches are distributed among these distances:
108 64 0.15
109 9 0.02
110 4 0.01
111 62 0.14
112 16 0.04
113 8 0.02
115 4 0.01
116 16 0.04
117 76 0.17
118 175 0.40
119 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.31
Consensus pattern (117 bp):
GACGATAACATAACCAATTAATTACTGGAAACATTATCAAGCATAATAACATATTAGGTAACACT
TATATAACGTAATATGTAGCGCCTTTTTAAGCTGATAGGGCTTTAGAAATCC
Found at i:445776 original size:229 final size:224
Alignment explanation
Indices: 445282--445979 Score: 934
Period size: 229 Copynumber: 3.1 Consensus size: 224
445272 TGGGGCTTTG
* * * *
445282 GAAATCTGACGATAACATAATCAATTAATTATTGTAAACATTATCAAGCATAATAACATATTAGG
1 GAAATCTGACGATAACATAACCGATTAATTAATGGAAACATTATCAAGCATAATAACATATTAGG
* * * * * *
445347 TAGCACTTATATAACGTAATATGTAGCGCCTTTTTAAGTTGATAGGGTTTTGGAAATCCGACAAT
66 TAGCGCTTATATAACGTAATAAGTAGCGCCTTTTAAAGTTGAT-GGGCTTTAGAAATCCGACGAT
445412 AACAAAATAAGTTAATTACTTAATTTGTTATTAGTATTATTAACATATTAGGTAACACCTAAAAT
130 AACAAAATAAGTTAATTACTTAATTTGTTATTAGTATTATTAACATATTAGGTAACACCTAAAAT
445477 GTTACCAAAGTTTAAGCTGATAGAGCCTTA
195 GTTACCAAAGTTTAAGCTGATAGAGCCTTA
* *
445507 GAAATCCGACGATAACATAACCGATTAATTACTGGAAACATTATCAAGCATAATAACATATTAGG
1 GAAATCTGACGATAACATAACCGATTAATTAATGGAAACATTATCAAGCATAATAACATATTAGG
* * * * ** *
445572 CAACGCTTATATAACGTAATAGGTAGCGCCCTTTTAAAGCTGATGGGACTTTAGAAATTTGGCGA
66 TAGCGCTTATATAACGTAATAAGTAGCG-CCTTTTAAAGTTGATGGG-CTTTAGAAATCCGACGA
* * * *
445637 TAAAAAAATAGGTTAATTACTTAATTTGTTATTTGTATTATTAACATATTAGGTAACGCCTAAAA
129 TAACAAAATAAGTTAATTACTTAATTTGTTATTAGTATTATTAACATATTAGGTAACACCTAAAA
*
445702 TGTTACATTGAAAGTTTAAGCTGATAGAGCCTTA
194 TGTTAC---CAAAGTTTAAGCTGATAGAGCCTTA
* *
445736 GAAATCTGACCATAACATAACCGGTTAATTAATGGAAACATTATCAAGCATAATAACATATTAGG
1 GAAATCTGACGATAACATAACCGATTAATTAATGGAAACATTATCAAGCATAATAACATATTAGG
* * * *
445801 TAGCGCTTATGTAACGTAATAAGTTGCGCATTATTAAAGTTGATGTGGCCTTAGAAATCCGACGA
66 TAGCGCTTATATAACGTAATAAGTAGCGCCTT-TTAAAGTTGATG-GGCTTTAGAAATCCGACGA
* * * *
445866 TAACAAAATATGTTAATTATTTAATTTGTTATCAGTATTATCAACATATTAGGTAACACCT-AAA
129 TAACAAAATAAGTTAATTACTTAATTTGTTATTAGTATTATTAACATATTAGGTAACACCTAAAA
* * * * *
445930 TGTTAACAAAATTTAA-TTAATGGAGCCTTA
194 TGTTACCAAAGTTTAAGCTGATAGAGCCTTA
*
445960 GGAAT-TCGACGATAACATAA
1 GAAATCT-GACGATAACATAA
445980 TCGGTTAACC
Statistics
Matches: 413, Mismatches: 52, Indels: 17
0.86 0.11 0.04
Matches are distributed among these distances:
223 1 0.00
224 27 0.07
225 95 0.23
226 91 0.22
228 11 0.03
229 186 0.45
230 2 0.00
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (224 bp):
GAAATCTGACGATAACATAACCGATTAATTAATGGAAACATTATCAAGCATAATAACATATTAGG
TAGCGCTTATATAACGTAATAAGTAGCGCCTTTTAAAGTTGATGGGCTTTAGAAATCCGACGATA
ACAAAATAAGTTAATTACTTAATTTGTTATTAGTATTATTAACATATTAGGTAACACCTAAAATG
TTACCAAAGTTTAAGCTGATAGAGCCTTA
Found at i:447200 original size:161 final size:162
Alignment explanation
Indices: 446934--447256 Score: 639
Period size: 161 Copynumber: 2.0 Consensus size: 162
446924 TTACCATTTT
446934 CTCAAAATTTAATCGGTTTAGAAATTATAAGTATGAAAACTTTGTTGTCGAGATTATAAAAAATA
1 CTCAAAATTTAATCGGTTTAGAAATTATAAGTATGAAAACTTTGTTGTCGAGATTATAAAAAATA
446999 ATACTTTAATAATGTAACACCCCAACCCGTACCCGACCCGGATACGAGTCCTAGATGTCACATTG
66 ATACTTTAATAATGTAACACCCCAACCCGTACCCGACCCGGATACGAGTCCTAGATGTCACATTG
447064 AAATTTTAAAACGATGTTCTTCCAAAATAACC
131 AAATTTTAAAACGATGTTCTTCCAAAATAACC
447096 CTCAAAATTTAATCGGTTTAGAAA-TATAAGTATGAAAACTTTGTTGTCGAGATTATAAAAAATA
1 CTCAAAATTTAATCGGTTTAGAAATTATAAGTATGAAAACTTTGTTGTCGAGATTATAAAAAATA
447160 ATACTTTAATAATGTAACACCCCAACCCGTACCCGACCCGGATACGAGTCCTAGATGTCACATTG
66 ATACTTTAATAATGTAACACCCCAACCCGTACCCGACCCGGATACGAGTCCTAGATGTCACATTG
447225 AAATTTTAAAACGATGTTCTTCCAAAATAACC
131 AAATTTTAAAACGATGTTCTTCCAAAATAACC
447257 AAACATTTGA
Statistics
Matches: 161, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
161 137 0.85
162 24 0.15
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.29
Consensus pattern (162 bp):
CTCAAAATTTAATCGGTTTAGAAATTATAAGTATGAAAACTTTGTTGTCGAGATTATAAAAAATA
ATACTTTAATAATGTAACACCCCAACCCGTACCCGACCCGGATACGAGTCCTAGATGTCACATTG
AAATTTTAAAACGATGTTCTTCCAAAATAACC
Found at i:447442 original size:21 final size:21
Alignment explanation
Indices: 447403--447443 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
447393 TCGTGAACAA
*
447403 TGCTACAATGCATCAATGCAT
1 TGCTACAATGCACCAATGCAT
* *
447424 TGCTACAGTGCACCGATGCA
1 TGCTACAATGCACCAATGCA
447444 CTAAAATTTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (21 bp):
TGCTACAATGCACCAATGCAT
Found at i:448406 original size:27 final size:27
Alignment explanation
Indices: 448374--448442 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
448364 ATATATACTT
*
448374 TATGCATGTATCATAATAATCATCATG
1 TATGCATGTATCATAATAATCATAATG
*
448401 TATGCATGTATCATAATAATTATAATG
1 TATGCATGTATCATAATAATCATAATG
448428 TATGCATGT-TCATAA
1 TATGCATGTATCATAA
448443 CTATTGTACT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
26 6 0.15
27 34 0.85
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.39
Consensus pattern (27 bp):
TATGCATGTATCATAATAATCATAATG
Found at i:450843 original size:18 final size:18
Alignment explanation
Indices: 450820--450858 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
450810 GCCGAAATTT
450820 AAATTAAAATTCAAACTC
1 AAATTAAAATTCAAACTC
* *
450838 AAATTAAAATTGAAATTC
1 AAATTAAAATTCAAACTC
450856 AAA
1 AAA
450859 CTCCAACTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.59, C:0.10, G:0.03, T:0.28
Consensus pattern (18 bp):
AAATTAAAATTCAAACTC
Found at i:450847 original size:24 final size:24
Alignment explanation
Indices: 450814--450870 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
450804 AGTGGAGCCG
*
450814 AAATTTAAATTAAAATTCAAACTC
1 AAATTAAAATTAAAATTCAAACTC
*
450838 AAATTAAAATTGAAATTCAAACTC
1 AAATTAAAATTAAAATTCAAACTC
* *
450862 CAACTAAAA
1 AAATTAAAA
450871 ATGAAATGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.56, C:0.14, G:0.02, T:0.28
Consensus pattern (24 bp):
AAATTAAAATTAAAATTCAAACTC
Found at i:450875 original size:24 final size:24
Alignment explanation
Indices: 450826--450877 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
450816 ATTTAAATTA
* *
450826 AAATTCAAACTCAAATTAAAATTG
1 AAATTCAAACTCAAACTAAAAATG
*
450850 AAATTCAAACTCCAACTAAAAATG
1 AAATTCAAACTCAAACTAAAAATG
450874 AAAT
1 AAAT
450878 GAACATGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.15, G:0.04, T:0.25
Consensus pattern (24 bp):
AAATTCAAACTCAAACTAAAAATG
Found at i:452571 original size:46 final size:46
Alignment explanation
Indices: 452521--452625 Score: 176
Period size: 46 Copynumber: 2.3 Consensus size: 46
452511 CTATGTGACT
*
452521 ATATGAAATGACATATGAATATGCAATACGTGATACATATGATATG
1 ATATGAAATGACATATGAATATACAATACGTGATACATATGATATG
* *
452567 ATATGAAATGACATATGAATATATAATACGTGATACATGTGATATG
1 ATATGAAATGACATATGAATATACAATACGTGATACATATGATATG
452613 ATATGAAAT-ACAT
1 ATATGAAATGACAT
452626 GGTTACACAT
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
45 4 0.07
46 52 0.93
ACGTcount: A:0.45, C:0.08, G:0.16, T:0.31
Consensus pattern (46 bp):
ATATGAAATGACATATGAATATACAATACGTGATACATATGATATG
Found at i:452831 original size:38 final size:38
Alignment explanation
Indices: 452776--452871 Score: 129
Period size: 38 Copynumber: 2.5 Consensus size: 38
452766 TATAAGACAT
* * *
452776 ATGATAGGTTCTACGGGACACAGATTACATCATTCAGA
1 ATGATAGGTCCTTCGGGACACAGATGACATCATTCAGA
* * * *
452814 ATGATAGGTCCTTCGGGACACAGATGATATCCTTCGGG
1 ATGATAGGTCCTTCGGGACACAGATGACATCATTCAGA
452852 ATGATAGGTCCTTCGGGACA
1 ATGATAGGTCCTTCGGGACA
452872 TTTATACGAG
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 51 1.00
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (38 bp):
ATGATAGGTCCTTCGGGACACAGATGACATCATTCAGA
Found at i:452856 original size:15 final size:16
Alignment explanation
Indices: 452836--452869 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
452826 TCGGGACACA
452836 GATGATA-TCCTTCGG
1 GATGATAGTCCTTCGG
452851 GATGATAGGTCCTTCGG
1 GATGATA-GTCCTTCGG
452868 GA
1 GA
452870 CATTTATACG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
17 10 0.59
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (16 bp):
GATGATAGTCCTTCGG
Found at i:454854 original size:2 final size:2
Alignment explanation
Indices: 454847--454871 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
454837 TATCATTGGA
454847 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
454872 ATAATAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:454877 original size:3 final size:3
Alignment explanation
Indices: 454869--454897 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
454859 ATATATATAT
454869 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
454898 TTGATTGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:458225 original size:21 final size:20
Alignment explanation
Indices: 458201--458239 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
458191 AGTATGTGCA
458201 GGGGCAACAGATTCCCCCTGG
1 GGGGCAAC-GATTCCCCCTGG
* *
458222 GGGGTATCGATTCCCCCT
1 GGGGCAACGATTCCCCCT
458240 TAAATGAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.15, C:0.33, G:0.31, T:0.21
Consensus pattern (20 bp):
GGGGCAACGATTCCCCCTGG
Found at i:458695 original size:46 final size:46
Alignment explanation
Indices: 458645--458749 Score: 185
Period size: 46 Copynumber: 2.3 Consensus size: 46
458635 CAATGTGACT
*
458645 ATATGAAATGACATATGAATATGCAATACGTGATACATGTGATATG
1 ATATGAAATGACATATGAATATACAATACGTGATACATGTGATATG
*
458691 ATATGAAATGACATATGAATATATAATACGTGATACATGTGATATG
1 ATATGAAATGACATATGAATATACAATACGTGATACATGTGATATG
458737 ATATGAAAT-ACAT
1 ATATGAAATGACAT
458750 GGTTACACAT
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
45 4 0.07
46 53 0.93
ACGTcount: A:0.44, C:0.08, G:0.17, T:0.31
Consensus pattern (46 bp):
ATATGAAATGACATATGAATATACAATACGTGATACATGTGATATG
Found at i:458953 original size:38 final size:38
Alignment explanation
Indices: 458898--458993 Score: 129
Period size: 38 Copynumber: 2.5 Consensus size: 38
458888 TATAAGACAT
* * *
458898 ATGATAGGTTCTACGGGACACAGATTACATCATTCAGG
1 ATGATAGGTCCTTCGGGACACAGATGACATCATTCAGG
* * **
458936 ATGATAGGTCCTTCGGGACACAGATGATATCCTTTGGG
1 ATGATAGGTCCTTCGGGACACAGATGACATCATTCAGG
458974 ATGATAGGTCCTTCGGGACA
1 ATGATAGGTCCTTCGGGACA
458994 TTTATACGAG
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 51 1.00
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (38 bp):
ATGATAGGTCCTTCGGGACACAGATGACATCATTCAGG
Found at i:462157 original size:763 final size:763
Alignment explanation
Indices: 460693--462226 Score: 2870
Period size: 763 Copynumber: 2.0 Consensus size: 763
460683 CCTTGATATG
**
460693 GAAGGGGAACTGAAGACACAAGAATTTTGTTGTTCAAAAGAAGAGTTTCGAGTATTCAAAGTCAA
1 GAAGGGGAACCAAAGACACAAGAATTTTGTTGTTCAAAAGAAGAGTTTCGAGTATTCAAAGTCAA
* *
460758 TAATGTTAATCGTCAACGTGCTCATACGCCAGTCACAAAAAAATGAATGTAAGGCTAAAGTCGTA
66 TAATGTTAATCGTCAACATGCTCATACGCCAGTCACAAAAAAATGAACGTAAGGCTAAAGTCGTA
460823 ATTACAACAACAAATACAAACAATCAGTGGGTTGTAAGTAAGTTTTCTTAGCAACATAATCATGC
131 ATTACAACAACAAATACAAACAATCAGTGGGTTGTAAGTAAGTTTTCTTAGCAACATAATCATGC
460888 ATTGTGCACACCTGCTATAACACCATTTATGCATTCAAATAGAGCTATGAGTAAGGCTGATGTGG
196 ATTGTGCACACCTGCTATAACACCATTTATGCATTCAAATAGAGCTATGAGTAAGGCTGATGTGG
*
460953 ATGAGGCAACAACATTAAAAGACGTCGGTGTTGGCACATCGCAAGTAATGACTTATTTAACGCAG
261 ATGAGGCAACAACATTAAAAGACGTCGGTGTTGGCACATCGCAAGTAATGAATTATTTAACGCAG
*
461018 CAGACAGATGGTTATTATAATGTTGAATTTACACATAAAGACCTTTACAATGCACTTCAAAGAGG
326 CAGACAGATGGTTATTATAATGTTGAATTTACACATAAAAACCTTTACAATGCACTTCAAAGAGG
461083 TAAAGCAAAGGAAATCTTCAATGGGGATGTCAAAGCGCTTATTGCTTACTTTGATTATAAGAAAC
391 TAAAGCAAAGGAAATCTTCAATGGGGATGTCAAAGCGCTTATTGCTTACTTTGATTATAAGAAAC
461148 ATGATGATCCTGGGTCTTTTATGACATACTCGGTAGACGAATCAGGGGCATTGCATAATCTTATT
456 ATGATGATCCTGGGTCTTTTATGACATACTCGGTAGACGAATCAGGGGCATTGCATAATCTTATT
* *
461213 TGGTCTGATTCTATATCGAGATCAGATTACACGTGTTTCGGTGATGTAATTACGTTCGACACAAC
521 TGGTCTGATTCTACATCGAGATCAGATTACACGTGCTTCGGTGATGTAATTACGTTCGACACAAC
461278 GTACAAATATAATTTGTATGGTCGACCAATTATACCTATTATCGGTGTCAATCATCAACATAACA
586 GTACAAATATAATTTGTATGGTCGACCAATTATACCTATTATCGGTGTCAATCATCAACATAACA
461343 CAATAGTGTTTGCTACTGCCATAATCGCCGACGAAACATCCCAATCTTTCGAGTAGGTGTTAAAG
651 CAATAGTGTTTGCTACTGCCATAATCGCCGACGAAACATCCCAATCTTTCGAGTAGGTGTTAAAG
*
461408 AATTTTTTAGAAGCCATGATGAATAAATCACATATTTCTGTTGTCACC
716 AATTTTTTAGAAGCCATGATGAATAAATCACATATTTCAGTTGTCACC
*
461456 GAAGGGGAACCAAAGACACAAGAATTTTGTTGTTCAAAAGAAGAGTTTTGAGTATTCAAAGTCAA
1 GAAGGGGAACCAAAGACACAAGAATTTTGTTGTTCAAAAGAAGAGTTTCGAGTATTCAAAGTCAA
*
461521 TGATGTTAATCGTCAACATGCTCATACGCCAGTCACAAAAAAATGAACGTAAGGCTAAAGTCGTA
66 TAATGTTAATCGTCAACATGCTCATACGCCAGTCACAAAAAAATGAACGTAAGGCTAAAGTCGTA
* *
461586 ATTCCAACAATAAATACAAACAATCAGTGGGTTGTAAGTAAGTTTTCTTAGCAACATAATCATGC
131 ATTACAACAACAAATACAAACAATCAGTGGGTTGTAAGTAAGTTTTCTTAGCAACATAATCATGC
* *
461651 ATTGTGCACACTTGCTATGACACCATTTATGCATTCAAATAGAGCTATGAGTAAGGCTGATGTGG
196 ATTGTGCACACCTGCTATAACACCATTTATGCATTCAAATAGAGCTATGAGTAAGGCTGATGTGG
*
461716 ATGAGGCAACAACATTAAAAGACGTCGGTGTTGGCACATCGCAAGTAATGAATTATTTAACGCAT
261 ATGAGGCAACAACATTAAAAGACGTCGGTGTTGGCACATCGCAAGTAATGAATTATTTAACGCAG
*
461781 CAGACAGATGGTTATTATAATGTTGAATTTACACATAAAAACCTTTACAATGCACTTTAAAGAGG
326 CAGACAGATGGTTATTATAATGTTGAATTTACACATAAAAACCTTTACAATGCACTTCAAAGAGG
*
461846 TAAAGCAAAGGAAATCTTCAATGGGGATGTCAAAGTGCTTATTGCTTACTTTGATTATAAGAAAC
391 TAAAGCAAAGGAAATCTTCAATGGGGATGTCAAAGCGCTTATTGCTTACTTTGATTATAAGAAAC
461911 ATGATGATCCTGGGTCTTTTATGACATACTCGGTAGACGAATCAGGGGCATTGCATAATCTTATT
456 ATGATGATCCTGGGTCTTTTATGACATACTCGGTAGACGAATCAGGGGCATTGCATAATCTTATT
*
461976 TGGTCTGATTCTACATCGAGATCAGATTACACGTGCTTCGGTGATGTAATTGCGTTCGACACAAC
521 TGGTCTGATTCTACATCGAGATCAGATTACACGTGCTTCGGTGATGTAATTACGTTCGACACAAC
**
462041 GTACAAATATAATTTGTATGGTCGACCAATTATGTCTATTATCGGTGTCAATCATCAACATAACA
586 GTACAAATATAATTTGTATGGTCGACCAATTATACCTATTATCGGTGTCAATCATCAACATAACA
*
462106 CAATAGTGTTTGCTACTGCCATAATCGCCGACGAAACATCCCAATCTTTCGAGTATGTGTTAAAG
651 CAATAGTGTTTGCTACTGCCATAATCGCCGACGAAACATCCCAATCTTTCGAGTAGGTGTTAAAG
462171 AATTTTTTAGAAGCCATGATGAATAAATCACATATTTCAGTTGTCACC
716 AATTTTTTAGAAGCCATGATGAATAAATCACATATTTCAGTTGTCACC
462219 GAAGGGGA
1 GAAGGGGA
462227 TAGGGCAATG
Statistics
Matches: 749, Mismatches: 22, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
763 749 1.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.29
Consensus pattern (763 bp):
GAAGGGGAACCAAAGACACAAGAATTTTGTTGTTCAAAAGAAGAGTTTCGAGTATTCAAAGTCAA
TAATGTTAATCGTCAACATGCTCATACGCCAGTCACAAAAAAATGAACGTAAGGCTAAAGTCGTA
ATTACAACAACAAATACAAACAATCAGTGGGTTGTAAGTAAGTTTTCTTAGCAACATAATCATGC
ATTGTGCACACCTGCTATAACACCATTTATGCATTCAAATAGAGCTATGAGTAAGGCTGATGTGG
ATGAGGCAACAACATTAAAAGACGTCGGTGTTGGCACATCGCAAGTAATGAATTATTTAACGCAG
CAGACAGATGGTTATTATAATGTTGAATTTACACATAAAAACCTTTACAATGCACTTCAAAGAGG
TAAAGCAAAGGAAATCTTCAATGGGGATGTCAAAGCGCTTATTGCTTACTTTGATTATAAGAAAC
ATGATGATCCTGGGTCTTTTATGACATACTCGGTAGACGAATCAGGGGCATTGCATAATCTTATT
TGGTCTGATTCTACATCGAGATCAGATTACACGTGCTTCGGTGATGTAATTACGTTCGACACAAC
GTACAAATATAATTTGTATGGTCGACCAATTATACCTATTATCGGTGTCAATCATCAACATAACA
CAATAGTGTTTGCTACTGCCATAATCGCCGACGAAACATCCCAATCTTTCGAGTAGGTGTTAAAG
AATTTTTTAGAAGCCATGATGAATAAATCACATATTTCAGTTGTCACC
Found at i:468110 original size:183 final size:183
Alignment explanation
Indices: 467800--468267 Score: 717
Period size: 183 Copynumber: 2.6 Consensus size: 183
467790 TTCTTTTAAA
* * *
467800 AGTATCGATACCTTCAACATATCCGGTAGCGCTTTACC-GATTTTGTCATAATGAAACTGGTTTT
1 AGTATCGATACCTTCAACATATCCGGTAGCGATTTACCAG-TTTTGTCATATTGAACCTGGTTTT
** *
467864 GTCATATTTTTACCTGTTATATTGTTATGTATCGATATATGTTTATAAAATATCGATACTTTATA
65 GTCATATTTTTACCTAATATATTGTTATGTATCGATACATGTTTATAAAATATCGATACTTTATA
* *
467929 GGCATTATTATTGTTTTTCTTTTAAA-TTCTAAAAGTATCGATATTTATTTGAAT
130 GGCACTATTATTGTTTTTCTTTTAAATTTC-AAAAGTATCGATACTTATTTGAAT
* * * *
467983 -GATATCGATACCTTCAACTTATCCGGTAACGTTTTACCAGTTTTGTCATATTGAACCTTGTTTT
1 AG-TATCGATACCTTCAACATATCCGGTAGCGATTTACCAGTTTTGTCATATTGAACCTGGTTTT
468047 GTCATATTTTTACCTAATATATTGTTATGTATCGATACATGTTTATAAAATATCGATACTTTATA
65 GTCATATTTTTACCTAATATATTGTTATGTATCGATACATGTTTATAAAATATCGATACTTTATA
* *
468112 GGCGCTATTATTGTTTTTCTTTTAAATTTCAAAAGTATCGATACTTATTTTAAT
130 GGCACTATTATTGTTTTTCTTTTAAATTTCAAAAGTATCGATACTTATTTGAAT
* * * *
468166 AGTATCGCTAGCTTCAACATATCCGGTAGCGATTTACCAGTTTTGTCACATTGAACCCGGTTTTG
1 AGTATCGATACCTTCAACATATCCGGTAGCGATTTACCAGTTTTGTCATATTGAACCTGGTTTTG
*
468231 TCATATTTTTACTTAATATATTGTTATGTATCGATAC
66 TCATATTTTTACCTAATATATTGTTATGTATCGATAC
468268 GTATTTGAAT
Statistics
Matches: 259, Mismatches: 22, Indels: 8
0.90 0.08 0.03
Matches are distributed among these distances:
182 1 0.00
183 253 0.98
184 5 0.02
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.44
Consensus pattern (183 bp):
AGTATCGATACCTTCAACATATCCGGTAGCGATTTACCAGTTTTGTCATATTGAACCTGGTTTTG
TCATATTTTTACCTAATATATTGTTATGTATCGATACATGTTTATAAAATATCGATACTTTATAG
GCACTATTATTGTTTTTCTTTTAAATTTCAAAAGTATCGATACTTATTTGAAT
Found at i:492344 original size:11 final size:11
Alignment explanation
Indices: 492320--492355 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
492310 ACGATAGAAA
492320 TAATAATATTTT
1 TAATAAT-TTTT
492332 TAATAATTTTT
1 TAATAATTTTT
*
492343 TATTAATTTTT
1 TAATAATTTTT
492354 TA
1 TA
492356 TTTAAATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 16 0.70
12 7 0.30
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TAATAATTTTT
Found at i:492510 original size:14 final size:16
Alignment explanation
Indices: 492489--492526 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
492479 TTTACTACTA
*
492489 CTCTTTTTCCTTTCTT
1 CTCTTTTTCCTTCCTT
492505 -TCTTTTTCCTTCCTT
1 CTCTTTTTCCTTCCTT
492520 CTCTTTT
1 CTCTTTT
492527 AATAAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (16 bp):
CTCTTTTTCCTTCCTT
Found at i:492699 original size:17 final size:18
Alignment explanation
Indices: 492671--492704 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
492661 AAGTATAAGA
492671 ATTTATTTAAAATTAATC
1 ATTTATTTAAAATTAATC
492689 ATTTA-TTAAAATTAAT
1 ATTTATTTAAAATTAAT
492705 TATAATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTTATTTAAAATTAATC
Found at i:492807 original size:30 final size:31
Alignment explanation
Indices: 492765--492826 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
492755 TACTTAAATC
*
492765 AATTA-TTATTTTTAATAAAAATTACAATTA
1 AATTATTTATTTTTAATAAAAATAACAATTA
* *
492795 AATTATATT-TTTTTATTAAAAATAATAATTA
1 AATTAT-TTATTTTTAATAAAAATAACAATTA
492826 A
1 A
492827 TTTAAGTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 5 0.19
31 20 0.74
32 2 0.07
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (31 bp):
AATTATTTATTTTTAATAAAAATAACAATTA
Found at i:496912 original size:14 final size:15
Alignment explanation
Indices: 496888--496916 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
496878 CTTTTGGTAG
496888 CAGATGAAATCATTA
1 CAGATGAAATCATTA
496903 CAGA-GAAATCATTA
1 CAGATGAAATCATTA
496917 AGGAGGGGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.48, C:0.14, G:0.14, T:0.24
Consensus pattern (15 bp):
CAGATGAAATCATTA
Found at i:497270 original size:19 final size:19
Alignment explanation
Indices: 497231--497272 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
497221 AAATTATTAA
*
497231 TAAAAAATATAAAAAGTTT
1 TAAAAAATATAAAAAGATT
497250 TAAAAATATATAAAAA-ATT
1 TAAAAA-ATATAAAAAGATT
497269 TAAA
1 TAAA
497273 CATTTTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (19 bp):
TAAAAAATATAAAAAGATT
Found at i:504730 original size:13 final size:13
Alignment explanation
Indices: 504712--504738 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
504702 ATAGTAACAA
504712 TACAAAATTAGCC
1 TACAAAATTAGCC
504725 TACAAAATTAGCC
1 TACAAAATTAGCC
504738 T
1 T
504739 TTATGTTTAT
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:0.44, C:0.22, G:0.07, T:0.26
Consensus pattern (13 bp):
TACAAAATTAGCC
Found at i:509445 original size:60 final size:60
Alignment explanation
Indices: 509328--509460 Score: 160
Period size: 60 Copynumber: 2.2 Consensus size: 60
509318 TCGGGTGATG
* * *
509328 ATTTTGTAACTTTTAATAGTAGAGGGACTCAACAAAGTAACACCCTATAATCGGATGACC
1 ATTTTGTAACTTTTAATAGTAGAGAGACTAAACAAAGTAACACCCTATAATCCGATGACC
* * * * * * *
509388 ATTTTGTAACTTTTAATAGTCGATAGACTAAACAAAGTAATATCTTATTATCCGATGATC
1 ATTTTGTAACTTTTAATAGTAGAGAGACTAAACAAAGTAACACCCTATAATCCGATGACC
509448 ATTTGTGT-ACTTT
1 ATTT-TGTAACTTT
509461 AGCCTTTTTT
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
60 59 0.95
61 3 0.05
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Consensus pattern (60 bp):
ATTTTGTAACTTTTAATAGTAGAGAGACTAAACAAAGTAACACCCTATAATCCGATGACC
Found at i:510116 original size:23 final size:23
Alignment explanation
Indices: 510090--510137 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
510080 ATAAAGTACA
*
510090 ATAACATACTAGGTAGCACTTAT
1 ATAACATAATAGGTAGCACTTAT
** *
510113 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCACTTAT
510136 AT
1 AT
510138 TTACCTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCACTTAT
Found at i:510573 original size:23 final size:23
Alignment explanation
Indices: 510514--510586 Score: 83
Period size: 23 Copynumber: 3.2 Consensus size: 23
510504 ACACTTTACA
* *
510514 ATATAACCACTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
*
510537 ATATAAACGATACCTATTACATT
1 ATATAAACGCTACCTATTACATT
** * *
510560 ATATAAGGGCTACCTATCACATC
1 ATATAAACGCTACCTATTACATT
510583 ATAT
1 ATAT
510587 GTTTACCTAT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.40, C:0.22, G:0.05, T:0.33
Consensus pattern (23 bp):
ATATAAACGCTACCTATTACATT
Found at i:511042 original size:39 final size:39
Alignment explanation
Indices: 510988--511070 Score: 139
Period size: 39 Copynumber: 2.1 Consensus size: 39
510978 TCAAGTTGTA
* *
510988 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
1 GATTTGGATTTCCTTTTGCTTGGCACCATATGAGATTTG
*
511027 GATTTGGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTGGATTTCCTTTTGCTTGGCACCATATGAGATTTG
511066 GATTT
1 GATTT
511071 TGATGAGCAT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.17, C:0.14, G:0.22, T:0.47
Consensus pattern (39 bp):
GATTTGGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:511356 original size:18 final size:18
Alignment explanation
Indices: 511333--511369 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
511323 CGAAATATAT
511333 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
511351 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
511369 A
1 A
511370 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:511646 original size:25 final size:25
Alignment explanation
Indices: 511618--511668 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
511608 TTAATCCAAA
*
511618 TAATGTACCCATAACAATGTTCAAT
1 TAATGTACCCACAACAATGTTCAAT
*
511643 TAATGTACCCACAACAATGTTTAAT
1 TAATGTACCCACAACAATGTTCAAT
511668 T
1 T
511669 GATTTGTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (25 bp):
TAATGTACCCACAACAATGTTCAAT
Found at i:511962 original size:21 final size:22
Alignment explanation
Indices: 511937--511988 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
511927 ACACTTTACA
*
511937 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
511960 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
511983 ATATAA
1 ATATAA
511989 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:511973 original size:23 final size:23
Alignment explanation
Indices: 511947--512009 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
511937 ATATAACCAC
511947 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
511970 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
511993 TACCTATTACATCATAT
1 TACCTATTACATTATAT
512010 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:512400 original size:23 final size:23
Alignment explanation
Indices: 512341--512412 Score: 83
Period size: 23 Copynumber: 3.2 Consensus size: 23
512331 ACACTTTACA
* *
512341 ATATAACCACTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
*
512364 ATATAAACGATACCTATTACATT
1 ATATAAACGCTACCTATTACATT
** *
512387 ATATAAGGGCTACCTA-TACATC
1 ATATAAACGCTACCTATTACATT
512409 ATAT
1 ATAT
512413 GTTTACCTAT
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 9 0.21
23 33 0.79
ACGTcount: A:0.40, C:0.21, G:0.06, T:0.33
Consensus pattern (23 bp):
ATATAAACGCTACCTATTACATT
Found at i:512796 original size:21 final size:22
Alignment explanation
Indices: 512771--512822 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
512761 ACACTTTACA
*
512771 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
512794 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
512817 ATATAA
1 ATATAA
512823 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:512807 original size:23 final size:23
Alignment explanation
Indices: 512781--512843 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
512771 ATATAACCAC
512781 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
512804 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
512827 TACCTATTACATCATAT
1 TACCTATTACATTATAT
512844 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:512882 original size:430 final size:430
Alignment explanation
Indices: 512082--512941 Score: 1686
Period size: 430 Copynumber: 2.0 Consensus size: 430
512072 ACTTATGTAA
*
512082 TTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTT
1 TTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTT
512147 TTTATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATATACCGTAACGTAAAA
66 TTTATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATATACCGTAACGTAAAA
512212 AATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTT
131 AATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTT
512277 AAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAA
196 AAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAA
512342 TATAACCACTACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATACA
261 TATAACCACTACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATACA
512407 TCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTT
326 TCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTT
512472 AAAACTTATGTAATTTATGTTTCAATTTTTTTAACAGTGT
391 AAAACTTATGTAATTTATGTTTCAATTTTTTTAACAGTGT
512512 TTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTT
1 TTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTT
512577 TTTATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATATACCGTAACGTAAAA
66 TTTATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATATACCGTAACGTAAAA
*
512642 AATAAATCATTAGACGCCTGTAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTT
131 AATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTT
512707 AAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAA
196 AAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAA
512772 TATAACCACTACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTAC
261 TATAACCACTACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTA-TAC
512837 ATCATATGTTTACCTATTATATTGAAAGTGTCCATAC-TTTTATAAAAAGGATCGATACTTTTTT
325 ATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTT
512901 TAAAACTTATGTAATTTATGTTTCAATTTTTTTAACAGTGT
390 TAAAACTTATGTAATTTATGTTTCAATTTTTTTAACAGTGT
512942 ACTGCGAATT
Statistics
Matches: 427, Mismatches: 2, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
430 387 0.91
431 40 0.09
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.40
Consensus pattern (430 bp):
TTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTT
TTTATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATATACCGTAACGTAAAA
AATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTT
AAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAA
TATAACCACTACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATACA
TCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTT
AAAACTTATGTAATTTATGTTTCAATTTTTTTAACAGTGT
Found at i:515848 original size:184 final size:184
Alignment explanation
Indices: 515383--515908 Score: 930
Period size: 184 Copynumber: 2.9 Consensus size: 184
515373 TTCAAATTAC
* * *
515383 CGACACTTTTTTAAATGGTATCGACACATTTTTATTCCAATCTGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
* * *
515448 ATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAGACCGGTATATTTATACCGGTT
515513 ATATTACAAAATTATCTA-TACATTATAATTATGGGTTCCGATGTGTAAAATGT
131 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAAATGT
515566 CGACACTTTTTTAAATCGTATCGACACA-TTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
515630 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAGACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAGACCGGTATATTTATACCGGTT
515695 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAAATGT
131 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAAATGT
*
515749 CGACACTTTTTTAAATCGTATCGACATATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
515814 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAGACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAGACCGGTATATTTATACCGGTT
* * * **
515879 ATATTGCAAATTTACCTATTTTATTATAAT
131 ATATTACAAAATTATCTATTACATTATAAT
515909 ATGTTGAAAG
Statistics
Matches: 329, Mismatches: 12, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
182 114 0.35
183 89 0.27
184 126 0.38
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (184 bp):
CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAGACCGGTATATTTATACCGGTT
ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAAATGT
Found at i:517381 original size:6 final size:6
Alignment explanation
Indices: 517354--517439 Score: 55
Period size: 6 Copynumber: 14.3 Consensus size: 6
517344 GTTTGGATCA
* * * * * * * *
517354 TCATCT TCATCA TCGTCA TCATCT TCATCG CCAGCT TCATCG TCATCA
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
* * * * *
517402 TCGTCA TCATCG TCATCT TCATCG TCAGCT TCATCT TC
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TC
517440 TGCGACCGCT
Statistics
Matches: 60, Mismatches: 20, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
6 60 1.00
ACGTcount: A:0.19, C:0.35, G:0.09, T:0.37
Consensus pattern (6 bp):
TCATCT
Found at i:517404 original size:9 final size:9
Alignment explanation
Indices: 517351--517418 Score: 75
Period size: 9 Copynumber: 7.6 Consensus size: 9
517341 CTTGTTTGGA
*
517351 TCATCATCT
1 TCATCATCG
517360 TCATCATCG
1 TCATCATCG
*
517369 TCATCATCT
1 TCATCATCG
**
517378 TCATCGCCAG
1 TCATCATC-G
*
517388 -CTTCATCG
1 TCATCATCG
517396 TCATCATCG
1 TCATCATCG
517405 TCATCATCG
1 TCATCATCG
517414 TCATC
1 TCATC
517419 TTCATCGTCA
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
8 1 0.02
9 47 0.98
ACGTcount: A:0.21, C:0.35, G:0.09, T:0.35
Consensus pattern (9 bp):
TCATCATCG
Found at i:517435 original size:18 final size:18
Alignment explanation
Indices: 517354--517439 Score: 66
Period size: 18 Copynumber: 4.4 Consensus size: 18
517344 GTTTGGATCA
* *
517354 TCATCTTCATCATC-GTCA
1 TCATCTTCATCGTCAG-CT
*
517372 TCATCTTCATCGCCAGCT
1 TCATCTTCATCGTCAGCT
*
517390 TCATCGTCATCATCGTCATCAT
1 TCATC-T--TCATCGTCAGC-T
517412 CGTCATCTTCATCGTCAGCT
1 --TCATCTTCATCGTCAGCT
517432 TCATCTTC
1 TCATCTTC
517440 TGCGACCGCT
Statistics
Matches: 55, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
18 26 0.47
19 2 0.04
20 1 0.02
21 19 0.35
22 1 0.02
23 1 0.02
24 5 0.09
ACGTcount: A:0.19, C:0.35, G:0.09, T:0.37
Consensus pattern (18 bp):
TCATCTTCATCGTCAGCT
Found at i:519235 original size:199 final size:199
Alignment explanation
Indices: 518895--520515 Score: 3075
Period size: 199 Copynumber: 8.1 Consensus size: 199
518885 TTTAAATTAG
518895 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
518960 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
519025 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
519090 AAAA
196 AAAA
519094 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
519159 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
519224 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
519289 AAAA
196 AAAA
519293 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
519358 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
519423 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
131 CGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
519488 AAAAA
195 AAAAA
519493 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
519558 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
519623 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
519688 AAAA
196 AAAA
519692 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
519757 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
519822 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
519887 AAAA
196 AAAA
*
519891 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
519956 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
520021 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTG-TTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
520085 AAAA
196 AAAA
*
520089 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
520154 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCTATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
520219 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGG-AA
131 CGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
520283 AAAAA
195 AAAAA
520288 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
* *
520353 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
520418 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGAAGA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
520483 AAAA
196 AAAA
*
520487 TATCGACACAAACTATATTAGTATCGACA
1 TATCGACACAAACTATATTAGTGTCGACA
520516 TGACCCTTAA
Statistics
Matches: 1401, Mismatches: 17, Indels: 8
0.98 0.01 0.01
Matches are distributed among these distances:
198 213 0.15
199 974 0.70
200 214 0.15
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (199 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
AAAA
Found at i:520030 original size:598 final size:596
Alignment explanation
Indices: 518895--520515 Score: 3109
Period size: 598 Copynumber: 2.7 Consensus size: 596
518885 TTTAAATTAG
518895 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
518960 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
519025 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
519090 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGG
196 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGG
*
519155 TATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
261 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
*
519220 GGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGG
326 GGATCGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGG
519285 AAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAA
391 AAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAA
519350 CCGGTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGAT
456 CCGGTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGAT
519415 TTTGGGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCAT
521 TTTGGGATCGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCTTG-TTTTAATTCAT
519480 TCTGGAAAAAAAA
584 TCTGGAAAAAAAA
519493 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
519558 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
519623 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
519688 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGG
196 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGG
519753 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
261 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
519818 GGATCGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGG
326 GGATCGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGG
*
519883 AAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAA
391 AAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAA
519948 CCGGTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGAT
456 CCGGTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGAT
520013 TTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTAATTCATTC
521 TTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTAATTCATTC
520078 TGGAAAAAAAA
586 TGGAAAAAAAA
*
520089 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
* *
520154 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCTATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
520219 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCT-GGAA
131 CGACAC-TTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGGAA
520283 AAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCG
195 AAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCG
*
520348 GTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTT
260 GTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTT
520413 GGGATCGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTG
325 GGGATCGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTG
* *
520478 GAAGAAAAATATCGACACAAACTATATTAGTATCGACA
390 GAAAAAAAATATCGACACAAACTATATTAGTGTCGACA
520516 TGACCCTTAA
Statistics
Matches: 1011, Mismatches: 11, Indels: 4
0.99 0.01 0.00
Matches are distributed among these distances:
596 391 0.39
597 90 0.09
598 530 0.52
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (596 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGG
TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
GGATCGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGG
AAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAA
CCGGTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGAT
TTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTAATTCATTC
TGGAAAAAAAA
Found at i:520639 original size:19 final size:19
Alignment explanation
Indices: 520593--520641 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
520583 TTATATTCAC
*
520593 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
520612 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
520631 ATACAAAATTA
1 ATACAAAATTA
520642 ACTCGACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:524851 original size:20 final size:19
Alignment explanation
Indices: 524805--524851 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
524795 TCCGGTATCA
*
524805 TTTTACCGTTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
524824 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
524845 TTTTACC
1 TTTTACC
524852 TGTTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.19, C:0.17, G:0.09, T:0.55
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:524998 original size:20 final size:20
Alignment explanation
Indices: 524972--525017 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
524962 CACTTTTAAA
524972 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
524991 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
525012 TTTACC
1 TTTACC
525018 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:528591 original size:20 final size:20
Alignment explanation
Indices: 528566--528604 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
528556 GGGTCTGATT
528566 TTTTATTTTATTTTATATAC
1 TTTTATTTTATTTTATATAC
528586 TTTTATTTTATTTTATATA
1 TTTTATTTTATTTTATATA
528605 AATGTATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTTATTTTATTTTATATAC
Found at i:528612 original size:20 final size:20
Alignment explanation
Indices: 528569--528617 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
528559 TCTGATTTTT
** *
528569 TATTTTATTTTATATACTTT
1 TATTTTATTTTATATAAATG
528589 TATTTTATTTTATATAAATG
1 TATTTTATTTTATATAAATG
528609 TATTTTATT
1 TATTTTATT
528618 CTATTTTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (20 bp):
TATTTTATTTTATATAAATG
Found at i:529463 original size:73 final size:71
Alignment explanation
Indices: 529330--529473 Score: 270
Period size: 73 Copynumber: 2.0 Consensus size: 71
529320 TACGATGCAG
529330 GTAAAACATTACACATCTTTTCTGTTTCCTTTATATTTGACTTTTTTATTTTCAAATAATCAAAG
1 GTAAAACATTACACATCTTTTCTGTTTCCTTTATATTTGACTTTTTTATTTTCAAATAATCAAAG
529395 TGTAAT
66 TGTAAT
529401 GTAAAACATTACACATCTTTTTCTGTTTCCTTTATATTTTGACTTTTTTATTTTCAAATAATCAA
1 GTAAAACATTACACATC-TTTTCTGTTTCCTTTATA-TTTGACTTTTTTATTTTCAAATAATCAA
529466 AGTGTAAT
64 AGTGTAAT
529474 TTAATTATGA
Statistics
Matches: 71, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
71 17 0.24
72 18 0.25
73 36 0.51
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.49
Consensus pattern (71 bp):
GTAAAACATTACACATCTTTTCTGTTTCCTTTATATTTGACTTTTTTATTTTCAAATAATCAAAG
TGTAAT
Found at i:532047 original size:48 final size:49
Alignment explanation
Indices: 531994--532089 Score: 140
Period size: 48 Copynumber: 2.0 Consensus size: 49
531984 TACATATAAA
* *
531994 GAAAAAACATAATCATTACATTAATATTTTGGT-GTTTTAATAAAAAAT
1 GAAAAAACATAATCATTACATCAATATTTTGGTAGGTTTAATAAAAAAT
* * *
532042 GAAAAAACATAATTATTACATCAATCTTTTGGTAGGTTTAGTAAAAAA
1 GAAAAAACATAATCATTACATCAATATTTTGGTAGGTTTAATAAAAAA
532090 ATTGGTATAT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
48 30 0.71
49 12 0.29
ACGTcount: A:0.47, C:0.07, G:0.10, T:0.35
Consensus pattern (49 bp):
GAAAAAACATAATCATTACATCAATATTTTGGTAGGTTTAATAAAAAAT
Found at i:549034 original size:119 final size:119
Alignment explanation
Indices: 548816--549050 Score: 364
Period size: 119 Copynumber: 2.0 Consensus size: 119
548806 ATTTAGTGAT
* * * *
548816 TAATTTGTGTTATTTGATGATTTTAAGAGAAGTGATCAATTAATATGATTAGTCTATTTTTATTT
1 TAATTTGTGTTATTTGATGATTTTAAGAGAAGTAATCAATTAATATAATTAGTCTACTTTCATTT
* * *
548881 ATATTTTTAAGATTATAATTATGTGGTAATCATTGGATCGACATACATGAACCA
66 ATATTTTTAAGATTATAAGTATGTGATAATCATTGAATCGACATACATGAACCA
*
548935 TAATTTGTGTTATTTGATGATTTTAAGAGAAGTAATTAATTAATATAATTAGTCTACTTTCATTT
1 TAATTTGTGTTATTTGATGATTTTAAGAGAAGTAATCAATTAATATAATTAGTCTACTTTCATTT
* *
549000 ATATATTTTTAGATTATAAGTATGTGATAA-CATTGAATGGACATACATGAA
66 ATAT-TTTTAAGATTATAAGTATGTGATAATCATTGAATCGACATACATGAA
549051 ATTTAAGACA
Statistics
Matches: 105, Mismatches: 10, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
119 83 0.79
120 22 0.21
ACGTcount: A:0.35, C:0.06, G:0.14, T:0.44
Consensus pattern (119 bp):
TAATTTGTGTTATTTGATGATTTTAAGAGAAGTAATCAATTAATATAATTAGTCTACTTTCATTT
ATATTTTTAAGATTATAAGTATGTGATAATCATTGAATCGACATACATGAACCA
Found at i:550098 original size:61 final size:60
Alignment explanation
Indices: 550019--550147 Score: 152
Period size: 61 Copynumber: 2.1 Consensus size: 60
550009 GAAAAAAATC
* * * * * *
550019 ATAGTTTAGAGATAAAATTAGAATGGTCAAAAGTTTAAGGA-ATAATTTTAAAATGAGACTT
1 ATAGTTTGGAGATAAAATTAAAATAGTCAAAAGTTCAAGGATA-AAATTT-AAATGAAACTT
* * *
550080 ATAGTTTGGAGATGAAATTAAAATATTCAAAAGTTCAAGGATAAAATTTAAATGAAAGTT
1 ATAGTTTGGAGATAAAATTAAAATAGTCAAAAGTTCAAGGATAAAATTTAAATGAAACTT
550140 ATAGTTTG
1 ATAGTTTG
550148 AAGACATATG
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
60 17 0.29
61 40 0.69
62 1 0.02
ACGTcount: A:0.46, C:0.03, G:0.18, T:0.33
Consensus pattern (60 bp):
ATAGTTTGGAGATAAAATTAAAATAGTCAAAAGTTCAAGGATAAAATTTAAATGAAACTT
Found at i:550310 original size:16 final size:17
Alignment explanation
Indices: 550279--550312 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
550269 ATTCGATTAA
*
550279 TAATTAGAAAATTAATT
1 TAATTAGAAAAATAATT
550296 TAATTA-AAAAATAATT
1 TAATTAGAAAAATAATT
550312 T
1 T
550313 TTTTGAACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (17 bp):
TAATTAGAAAAATAATT
Found at i:550663 original size:3 final size:3
Alignment explanation
Indices: 550649--550684 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
550639 TTCATCCCAA
*
550649 TAT TACT TAT TAT TAT TAT TAT TAT TAT TAC TAT TA
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
550685 ATCTATAGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:553493 original size:22 final size:22
Alignment explanation
Indices: 553464--553553 Score: 108
Period size: 22 Copynumber: 4.1 Consensus size: 22
553454 AGTCGAGGGT
553464 TTCATAGGTCATTCGGGACATA
1 TTCATAGGTCATTCGGGACATA
* * *
553486 CTCATAGGTCTTTCGGGGCATA
1 TTCATAGGTCATTCGGGACATA
* *
553508 TTCATAGGTCCTTCAGGACATA
1 TTCATAGGTCATTCGGGACATA
* * *
553530 TTCATAGGTCCTTTGGGATATA
1 TTCATAGGTCATTCGGGACATA
553552 TT
1 TT
553554 TCACATGCCA
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 58 1.00
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (22 bp):
TTCATAGGTCATTCGGGACATA
Found at i:553553 original size:44 final size:44
Alignment explanation
Indices: 553464--553553 Score: 119
Period size: 44 Copynumber: 2.0 Consensus size: 44
553454 AGTCGAGGGT
* *
553464 TTCATAGGTCATTCGGGACATACTCATAGGTCTTTCGGGGCATA
1 TTCATAGGTCATTCAGGACATACTCATAGGTCTTTCGGGACATA
* * *
553508 TTCATAGGTCCTTCAGGACATATTCATAGGTCCTTT-GGGATATA
1 TTCATAGGTCATTCAGGACATACTCATAGGT-CTTTCGGGACATA
553552 TT
1 TT
553554 TCACATGCCA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
44 36 0.90
45 4 0.10
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (44 bp):
TTCATAGGTCATTCAGGACATACTCATAGGTCTTTCGGGACATA
Found at i:554835 original size:22 final size:21
Alignment explanation
Indices: 554807--554890 Score: 116
Period size: 22 Copynumber: 4.0 Consensus size: 21
554797 TACATATACC
*
554807 CCCAGAGGATACCGATACCCA
1 CCCAGAGGGTACCGATACCCA
*
554828 CTCCAGAGGGTACCAATACCC-
1 C-CCAGAGGGTACCGATACCCA
*
554849 CCCAGAGGGTATCGATACCCA
1 CCCAGAGGGTACCGATACCCA
554870 CCCTAGAGGGTACCGATACCC
1 CCC-AGAGGGTACCGATACCC
554891 CTATATGAGA
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
20 17 0.31
21 5 0.09
22 33 0.60
ACGTcount: A:0.29, C:0.37, G:0.21, T:0.13
Consensus pattern (21 bp):
CCCAGAGGGTACCGATACCCA
Found at i:554865 original size:42 final size:42
Alignment explanation
Indices: 554767--554891 Score: 150
Period size: 42 Copynumber: 3.0 Consensus size: 42
554757 AGAAAGATTG
* * *
554767 CCCAGAGGGTATAGATAACC-CTCCAAAGGGTA-CATATA-CC
1 CCCAGAGGGTATCGATACCCACTCCAGAGGGTACCA-ATACCC
* *
554807 CCCAGAGGATACCGATACCCACTCCAGAGGGTACCAATACCC
1 CCCAGAGGGTATCGATACCCACTCCAGAGGGTACCAATACCC
*
554849 CCCAGAGGGTATCGATACCCAC-CCTAGAGGGTACCGATACCC
1 CCCAGAGGGTATCGATACCCACTCC-AGAGGGTACCAATACCC
554891 C
1 C
554892 TATATGAGAT
Statistics
Matches: 73, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
40 16 0.22
41 16 0.22
42 41 0.56
ACGTcount: A:0.30, C:0.34, G:0.21, T:0.14
Consensus pattern (42 bp):
CCCAGAGGGTATCGATACCCACTCCAGAGGGTACCAATACCC
Found at i:556437 original size:64 final size:63
Alignment explanation
Indices: 556325--556545 Score: 191
Period size: 64 Copynumber: 3.5 Consensus size: 63
556315 TTGAAGGTGT
** ** * *
556325 ATCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAATACATCGAATGCAGTTCGTG
1 ATCGATGCATAAGTAGTGCATCGATGCATC-CCATTAATAA-AAA-ACATCGAATGCAATTAGTG
556388 C
63 C
* * *
556389 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAAGGAAACATCAAATACAATTAGTGC
1 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAA-AAAACATCGAATGCAATTAGTGC
* * * * *
556453 ATCGATGCATAAGGCA-TGCATCGATGCATCCCAGTGATAATACAACATCGAATGCATTTTA-TG
1 ATCGATGCATAA-GTAGTGCATCGATGCATCCCATTAATAA-AAAACATCGAATGCA-ATTAGTG
556516 C
63 C
**
556517 A-CTGATGCATCGGTAGTGCATCGATGCAT
1 ATC-GATGCATAAGTAGTGCATCGATGCAT
556546 ACTTTTATTA
Statistics
Matches: 129, Mismatches: 22, Indels: 12
0.79 0.13 0.07
Matches are distributed among these distances:
63 3 0.02
64 116 0.90
65 10 0.08
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (63 bp):
ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAAAAAACATCGAATGCAATTAGTGC
Found at i:557765 original size:31 final size:32
Alignment explanation
Indices: 557712--557829 Score: 154
Period size: 32 Copynumber: 3.8 Consensus size: 32
557702 ATTCTAAGGA
557712 ACATATGGACAGAATTACCTATGTCTTTCGAG
1 ACATATGGACAGAATTACCTATGTCTTTCGAG
* ***
557744 ACATATGGACAGTA-TACCTATGTTCTAAGGA-
1 ACATATGGACAGAATTACCTATG-TCTTTCGAG
557775 ACATATGGACAGAATTACCTATGTCTTTCGAG
1 ACATATGGACAGAATTACCTATGTCTTTCGAG
557807 ACATATGGAC--AATATACCTATGT
1 ACATATGGACAGAAT-TACCTATGT
557830 TCTAAGGAAC
Statistics
Matches: 74, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
30 3 0.04
31 35 0.47
32 36 0.49
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Consensus pattern (32 bp):
ACATATGGACAGAATTACCTATGTCTTTCGAG
Found at i:557791 original size:63 final size:63
Alignment explanation
Indices: 557692--557881 Score: 294
Period size: 63 Copynumber: 3.0 Consensus size: 63
557682 AGAGTTGAGG
*
557692 GTATACCTATATTCTAAGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
1 GTATACCTATGTTCTAAGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
557755 GTATACCTATGTTCTAAGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
1 GTATACCTATGTTCTAAGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
* * * * * *
557818 ATATACCTATGTTCTAAGGAACATATGAACA-ATTTACCTAGGT-TCTTCGAAACCTATGGACA
1 GTATACCTATGTTCTAAGGAACATATGGACAGAATTACCTATGTCT-TTCGAGACATATGGACA
557880 GT
1 GT
557882 TGTCGAGGAT
Statistics
Matches: 118, Mismatches: 8, Indels: 3
0.91 0.06 0.02
Matches are distributed among these distances:
61 1 0.01
62 26 0.22
63 91 0.77
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (63 bp):
GTATACCTATGTTCTAAGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
Found at i:557842 original size:31 final size:31
Alignment explanation
Indices: 557693--557863 Score: 161
Period size: 31 Copynumber: 5.5 Consensus size: 31
557683 GAGTTGAGGG
*
557693 TATACCTATATTCTAAGGAACATATGGACAGA
1 TATACCTATGTTCTAAGGAACATATGGACA-A
*** *
557725 -ATTACCTATG-TCTTTCGAGACATATGGACAG
1 TA-TACCTATGTTCTAAGGA-ACATATGGACAA
557756 TATACCTATGTTCTAAGGAACATATGGACAGA
1 TATACCTATGTTCTAAGGAACATATGGACA-A
***
557788 -ATTACCTATG-TCTTTCGAGACATATGGACAA
1 TA-TACCTATGTTCTAAGGA-ACATATGGACAA
*
557819 TATACCTATGTTCTAAGGAACATATGAACAA
1 TATACCTATGTTCTAAGGAACATATGGACAA
* *
557850 TTTACCTAGGTTCT
1 TATACCTATGTTCT
557864 TCGAAACCTA
Statistics
Matches: 112, Mismatches: 18, Indels: 19
0.75 0.12 0.13
Matches are distributed among these distances:
31 63 0.56
32 49 0.44
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.32
Consensus pattern (31 bp):
TATACCTATGTTCTAAGGAACATATGGACAA
Done.