Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002890.1 Hibiscus syriacus cultivar Beakdansim tig00005974_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: 5046466
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 21
Found at i:383744 original size:20 final size:20
Alignment explanation
Indices: 383716--383845 Score: 217
Period size: 20 Copynumber: 6.5 Consensus size: 20
383706 ATGATCAATG
*
383716 GTATTGATACCTTCCTCATA
1 GTATCGATACCTTCCTCATA
383736 GTATCGATACCTTCCTCATA
1 GTATCGATACCTTCCTCATA
383756 GTATCGATACCTTCCTCATA
1 GTATCGATACCTTCCTCATA
*
383776 GTATTGATACCTTCCTCATA
1 GTATCGATACCTTCCTCATA
383796 GTATCGATACCTTCCTCATA
1 GTATCGATACCTTCCTCATA
*
383816 GTATCGATACCCTT-CTCTTA
1 GTATCGATA-CCTTCCTCATA
383836 GTATCGATAC
1 GTATCGATAC
383846 TAATTACATC
Statistics
Matches: 105, Mismatches: 4, Indels: 3
0.94 0.04 0.03
Matches are distributed among these distances:
19 1 0.01
20 100 0.95
21 4 0.04
ACGTcount: A:0.25, C:0.28, G:0.11, T:0.37
Consensus pattern (20 bp):
GTATCGATACCTTCCTCATA
Found at i:385430 original size:46 final size:47
Alignment explanation
Indices: 385363--385454 Score: 168
Period size: 46 Copynumber: 2.0 Consensus size: 47
385353 CATGCCTTTA
*
385363 ACATATCCTCTATTATTTGAATAGCTCGCTCTGACTG-CCATCTGTT
1 ACATATCCTCTATTATTTGAATAGCTCACTCTGACTGCCCATCTGTT
385409 ACATATCCTCTATTATTTGAATAGCTCACTCTGACTGCCCATCTGT
1 ACATATCCTCTATTATTTGAATAGCTCACTCTGACTGCCCATCTGT
385455 CTGCGGATGA
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
46 36 0.82
47 8 0.18
ACGTcount: A:0.23, C:0.27, G:0.12, T:0.38
Consensus pattern (47 bp):
ACATATCCTCTATTATTTGAATAGCTCACTCTGACTGCCCATCTGTT
Found at i:387267 original size:15 final size:15
Alignment explanation
Indices: 387247--387279 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
387237 TAATTGTTCT
387247 TTATCATTACTTTGA
1 TTATCATTACTTTGA
387262 TTATCATTACTTTGA
1 TTATCATTACTTTGA
387277 TTA
1 TTA
387280 ATTGACGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.27, C:0.12, G:0.06, T:0.55
Consensus pattern (15 bp):
TTATCATTACTTTGA
Found at i:389979 original size:54 final size:53
Alignment explanation
Indices: 389918--390409 Score: 526
Period size: 54 Copynumber: 9.3 Consensus size: 53
389908 ATTATATGGT
* * *
389918 TTGCACACATAGTTCTGAAACGATTATTCATCAACATATGATGAATTATGTGAA
1 TTGCACACTTAGTGC-GAAACGATTATTCATCAACATATGATGAATTCTGTGAA
* * * *
389972 TTACACACTTAGAGCCGAAAC-ATTTATTTATCAACATATGATGAATTCAGTGAA
1 TTGCACACTTAGTG-CGAAACGA-TTATTCATCAACATATGATGAATTCTGTGAA
* * * **
390026 TTGCACACCTAGTTCTGAAA-TAGTTATTCATCAACATATGATGAATTCCATGAA
1 TTGCACACTTAGTGC-GAAACGA-TTATTCATCAACATATGATGAATTCTGTGAA
390080 TTGCACACTTAGTGACGAAAC-AGTTATTCATCAACATATGATGAATTC--TG--
1 TTGCACACTTAGTG-CGAAACGA-TTATTCATCAACATATGATGAATTCTGTGAA
**
390130 -TG-A-A-TT-GTGCTGAAATAATTATTCATCAACATATGATGAATT-TCGTGAA
1 TTGCACACTTAGTGC-GAAACGATTATTCATCAACATATGATGAATTCT-GTGAA
* * * *
390179 TTGCACACTTAGTGCCGAAACGATTAGTCATCAACATATAATGAATTTTATGAA
1 TTGCACACTTAGTG-CGAAACGATTATTCATCAACATATGATGAATTCTGTGAA
*
390233 TTGCACACTTAGTGTCGAAACGGTTATTCATCAACATATGATGAATTCTGTGAA
1 TTGCACACTTAGTG-CGAAACGATTATTCATCAACATATGATGAATTCTGTGAA
* * * **
390287 TTGCACACTTAGTATCAAAATGATTATTCATCAAGTTATGATGAATTCTGTGAA
1 TTGCACACTTAGT-GCGAAACGATTATTCATCAACATATGATGAATTCTGTGAA
* *
390341 TTGCACACTTAATGCCGAAAC-ATCTATTCATCAACATATGATGAATTCCGTGAA
1 TTGCACACTTAGTG-CGAAACGAT-TATTCATCAACATATGATGAATTCTGTGAA
390395 TTGCACACTTAGTGC
1 TTGCACACTTAGTGC
390410 CTATTTGGTA
Statistics
Matches: 372, Mismatches: 43, Indels: 47
0.81 0.09 0.10
Matches are distributed among these distances:
44 1 0.00
45 31 0.08
46 3 0.01
47 3 0.01
48 1 0.00
49 2 0.01
50 2 0.01
51 1 0.00
52 3 0.01
53 7 0.02
54 314 0.84
55 4 0.01
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (53 bp):
TTGCACACTTAGTGCGAAACGATTATTCATCAACATATGATGAATTCTGTGAA
Found at i:390246 original size:153 final size:156
Alignment explanation
Indices: 389995--390408 Score: 541
Period size: 153 Copynumber: 2.6 Consensus size: 156
389985 GCCGAAACAT
* * * * *
389995 TTATTTATCAACATATGATGAATTCAGTGAATTGCACACCTAGTTCTGAAATAGTTATTCATCAA
1 TTATTCATCAACATATGATGAATTCAGTGAATTGCACACTTAGTGCCGAAACA-TTATTCATCAA
390060 CATATGATGAATTCCATGAATTGCACACTTAGTGACGAAACAGTTATTCATCAACATATGATGAA
65 CATATGATGAATTCCATGAATTGCACACTTAGTGACGAAACAGTTATTCATCAACATATGATGAA
* *
390125 TTCTGTGAATTG-T-G-CT-GAAATAA
130 TTCTGTGAATTGCTAGTATCAAAATAA
*
390148 TTATTCATCAACATATGATGAATTTC-GTGAATTGCACACTTAGTGCCGAAACGATTAGTCATCA
1 TTATTCATCAACATATGATGAA-TTCAGTGAATTGCACACTTAGTGCCGAAAC-ATTATTCATCA
* ** * *
390212 ACATATAATGAATTTTATGAATTGCACACTTAGTGTCGAAACGGTTATTCATCAACATATGATGA
64 ACATATGATGAATTCCATGAATTGCACACTTAGTGACGAAACAGTTATTCATCAACATATGATGA
*
390277 ATTCTGTGAATTGCACACTTAGTATCAAAATGA
129 ATTCTGTGAATTG----C-TAGTATCAAAATAA
** * *
390310 TTATTCATCAAGTTATGATGAATTCTGTGAATTGCACACTTAATGCCGAAACATCTATTCATCAA
1 TTATTCATCAACATATGATGAATTCAGTGAATTGCACACTTAGTGCCGAAACAT-TATTCATCAA
*
390375 CATATGATGAATTCCGTGAATTGCACACTTAGTG
65 CATATGATGAATTCCATGAATTGCACACTTAGTG
390409 CCTATTTGGT
Statistics
Matches: 226, Mismatches: 22, Indels: 17
0.85 0.08 0.06
Matches are distributed among these distances:
153 125 0.55
154 4 0.02
159 1 0.00
160 1 0.00
161 6 0.03
162 89 0.39
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (156 bp):
TTATTCATCAACATATGATGAATTCAGTGAATTGCACACTTAGTGCCGAAACATTATTCATCAAC
ATATGATGAATTCCATGAATTGCACACTTAGTGACGAAACAGTTATTCATCAACATATGATGAAT
TCTGTGAATTGCTAGTATCAAAATAA
Found at i:390295 original size:207 final size:207
Alignment explanation
Indices: 389940--390410 Score: 589
Period size: 207 Copynumber: 2.2 Consensus size: 207
389930 TTCTGAAACG
* * * *
389940 ATTATTCATCAACATATGATGAATTAT-GTGAATTACACACTTAGAGCCGAAACATTTATTTATC
1 ATTATTCATCAACATATGATGAATT-TCGTGAATTGCACACTTAGTGCCGAAACATTTAGTCATC
* *
390004 AACATATGATGAATTCAGTGAATTGCACACCTAGTTCTGAAATAGTTATTCATCAACATATGATG
65 AACATATAATGAATTCAGTGAATTGCACACCTAGTTCTGAAACAGTTATTCATCAACATATGATG
390069 AATTCCATGAATTGCACACTTAGTGA-CGAAACA-G-TTATTCATCAACATATGATGAATTCTGT
130 AATTCCATGAATTGCACACTTAGT-ATC-AAA-ATGATTATTCATCAACATATGATGAATTCTGT
*
390131 GAATTG-TGCTGAAATA
192 GAATTGATGCCGAAA-A
390147 ATTATTCATCAACATATGATGAATTTCGTGAATTGCACACTTAGTGCCGAAACGA-TTAGTCATC
1 ATTATTCATCAACATATGATGAATTTCGTGAATTGCACACTTAGTGCCGAAAC-ATTTAGTCATC
* * *
390211 AACATATAATGAATTTTA-TGAATTGCACACTTAGTGTC-GAAACGGTTATTCATCAACATATGA
65 AACATATAATGAA-TTCAGTGAATTGCACACCTAGT-TCTGAAACAGTTATTCATCAACATATGA
** **
390274 TGAATTCTGTGAATTGCACACTTAGTATCAAAATGATTATTCATCAAGTTATGATGAATTCTGTG
128 TGAATTCCATGAATTGCACACTTAGTATCAAAATGATTATTCATCAACATATGATGAATTCTGTG
*
390339 AATTGCACACTTAATGCCGAAAC
193 AATTG--------ATGCCGAAAA
*
390362 ATCTATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCC
1 AT-TATTCATCAACATATGATGAATTTCGTGAATTGCACACTTAGTGCC
390411 TATTTGGTAA
Statistics
Matches: 231, Mismatches: 16, Indels: 25
0.85 0.06 0.09
Matches are distributed among these distances:
205 1 0.00
206 6 0.03
207 164 0.71
208 6 0.03
215 2 0.01
216 52 0.23
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (207 bp):
ATTATTCATCAACATATGATGAATTTCGTGAATTGCACACTTAGTGCCGAAACATTTAGTCATCA
ACATATAATGAATTCAGTGAATTGCACACCTAGTTCTGAAACAGTTATTCATCAACATATGATGA
ATTCCATGAATTGCACACTTAGTATCAAAATGATTATTCATCAACATATGATGAATTCTGTGAAT
TGATGCCGAAAA
Found at i:390371 original size:261 final size:261
Alignment explanation
Indices: 389918--390397 Score: 705
Period size: 261 Copynumber: 1.8 Consensus size: 261
389908 ATTATATGGT
* * * * *
389918 TTGCACACATAGTTCTGAAACGATTATTCATCAACATATGATGAATTATGTGAATTACACACTTA
1 TTGCACACATAGTGCCGAAACGATTAGTCATCAACATATAATGAATTATATGAATTACACACTTA
* * *
389983 GAGCCGAAACATTTATTTATCAACATATGATGAATTCAGTGAATTGCACACCTAGTTCTGAAATA
66 GAGCCGAAACAGTTATTCATCAACATATGATGAATTCAGTGAATTGCACACCTAGTTCTAAAATA
*
390048 GTTATTCATCAACATATGATGAATTCCATGAATTGCACACTTAGTGACGAAACAGTTATTCATCA
131 GTTATTCATCAACATATGATGAATTCCATGAATTGCACACTTAATGACGAAACAGTTATTCATCA
*
390113 ACATATGATGAATTCTGTGAATTGTGCTGAAATAATTATTCATCAACATATGATGAATTTCGTGA
196 ACATATGATGAATTCCGTGAATTGTGCTGAAATAATTATTCATCAACATATGATGAATTTCGTGA
390178 A
261 A
* * *
390179 TTGCACACTTAGTGCCGAAACGATTAGTCATCAACATATAATGAATTTTATGAATTGCACACTTA
1 TTGCACACATAGTGCCGAAACGATTAGTCATCAACATATAATGAATTATATGAATTACACACTTA
* * * * *
390244 GTGTCGAAACGGTTATTCATCAACATATGATGAATTCTGTGAATTGCACACTTAGTATC-AAAAT
66 GAGCCGAAACAGTTATTCATCAACATATGATGAATTCAGTGAATTGCACACCTAGT-TCTAAAAT
** ** *
390308 -GATTATTCATCAAGTTATGATGAATTCTGTGAATTGCACACTTAATGCCGAAACA-TCTATTCA
130 AG-TTATTCATCAACATATGATGAATTCCATGAATTGCACACTTAATGACGAAACAGT-TATTCA
390371 TCAACATATGATGAATTCCGTGAATTG
193 TCAACATATGATGAATTCCGTGAATTG
390398 CACACTTAGT
Statistics
Matches: 193, Mismatches: 23, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
260 2 0.01
261 189 0.98
262 2 0.01
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Consensus pattern (261 bp):
TTGCACACATAGTGCCGAAACGATTAGTCATCAACATATAATGAATTATATGAATTACACACTTA
GAGCCGAAACAGTTATTCATCAACATATGATGAATTCAGTGAATTGCACACCTAGTTCTAAAATA
GTTATTCATCAACATATGATGAATTCCATGAATTGCACACTTAATGACGAAACAGTTATTCATCA
ACATATGATGAATTCCGTGAATTGTGCTGAAATAATTATTCATCAACATATGATGAATTTCGTGA
A
Found at i:393963 original size:18 final size:17
Alignment explanation
Indices: 393940--393973 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
393930 ATTAGATTTT
*
393940 TATTTTTACGTGATTAAA
1 TATTTTT-CATGATTAAA
393958 TATTTTTCATGATTAA
1 TATTTTTCATGATTAA
393974 TGTTAAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.32, C:0.06, G:0.09, T:0.53
Consensus pattern (17 bp):
TATTTTTCATGATTAAA
Found at i:399210 original size:34 final size:32
Alignment explanation
Indices: 399150--399219 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
399140 ACCTTACAAC
*
399150 TCCCTAGTTTTTCCGAGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGAGCTAAACTAGAACCTT
* *
399182 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGAGCTAAACTAGAACCTT
399216 TCCC
1 TCCC
399220 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.31, G:0.14, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGAGCTAAACTAGAACCTT
Found at i:399609 original size:20 final size:20
Alignment explanation
Indices: 399584--399658 Score: 105
Period size: 20 Copynumber: 3.7 Consensus size: 20
399574 TTGCAGCCTT
*
399584 GATGCATGGATGCATCGCAG
1 GATGCATCGATGCATCGCAG
*
399604 GATGCATGGATGCATCGCAG
1 GATGCATCGATGCATCGCAG
* *
399624 GCTGCATCGATGCATGGCAAG
1 GATGCATCGATGCATCGC-AG
399645 GATGCATCGATGCA
1 GATGCATCGATGCA
399659 CTAATTGCAT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
20 35 0.70
21 15 0.30
ACGTcount: A:0.25, C:0.21, G:0.33, T:0.20
Consensus pattern (20 bp):
GATGCATCGATGCATCGCAG
Found at i:399747 original size:21 final size:21
Alignment explanation
Indices: 399721--399778 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
399711 CATTAGTGCA
*
399721 GATGCATGGATGCACTGCAGG
1 GATGCATGGATGCACTACAGG
399742 GATGCATGGATGCACTACAGG
1 GATGCATGGATGCACTACAGG
399763 GATGCATGGATGCACT
1 GATGCATGGATGCACT
399779 TTGACACCCT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.26, C:0.19, G:0.34, T:0.21
Consensus pattern (21 bp):
GATGCATGGATGCACTACAGG
Found at i:399917 original size:30 final size:30
Alignment explanation
Indices: 399860--399917 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
399850 AACTTTGAAT
399860 AAATTCAATTCAAATCCAAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
*
399890 AAATTCAATTCAAGTCCAAAAACATTTT
1 AAATTCAATTCAAATCCAAAAACATTTT
399918 TCCTTAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.47, C:0.19, G:0.03, T:0.31
Consensus pattern (30 bp):
AAATTCAATTCAAATCCAAAAACATTTTGC
Found at i:401213 original size:19 final size:20
Alignment explanation
Indices: 401170--401217 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
401160 TCTAAATCCT
*
401170 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
401190 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
401209 TTTTCAAAA
1 TTTTCAAAA
401218 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:402138 original size:34 final size:32
Alignment explanation
Indices: 402076--402145 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
402066 ACCTTACAAC
* *
402076 TCCCTAGTTTTTCCGGGGTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
*
402108 TCCCTAGCTTTTACACGGGCTAATCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
402142 TCCC
1 TCCC
402146 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.21, C:0.30, G:0.16, T:0.33
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:402703 original size:30 final size:30
Alignment explanation
Indices: 402669--402728 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
402659 AACTTTGAAT
*
402669 AAATTCAATTCAAATCCAAAAATTTTTTGC
1 AAATTCAATTCAAATCCAAAAATATTTTGC
*
402699 AAATTCAATTCAAGTCCAAAAATATTTTGC
1 AAATTCAATTCAAATCCAAAAATATTTTGC
402729 CTTAAATTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.43, C:0.17, G:0.05, T:0.35
Consensus pattern (30 bp):
AAATTCAATTCAAATCCAAAAATATTTTGC
Found at i:407075 original size:2 final size:2
Alignment explanation
Indices: 407068--407123 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
407058 GTATTATGAT
407068 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
407110 TA TA TG TA TA TA TA
1 TA TA TA TA TA TA TA
407124 GATACATTTG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:409419 original size:16 final size:16
Alignment explanation
Indices: 409398--409428 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
409388 ATTGTATGTT
409398 CATTTTGTTTAACAGA
1 CATTTTGTTTAACAGA
*
409414 CATTTTTTTTAACAG
1 CATTTTGTTTAACAG
409429 TTATTGAGTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.13, G:0.10, T:0.48
Consensus pattern (16 bp):
CATTTTGTTTAACAGA
Found at i:411127 original size:18 final size:19
Alignment explanation
Indices: 411091--411130 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
411081 TTGGGACAAA
411091 AATGTTCTAATATGTTTAT
1 AATGTTCTAATATGTTTAT
411110 AATGTT-TAA-ATGGTTTAT
1 AATGTTCTAATAT-GTTTAT
411128 AAT
1 AAT
411131 CATGAACATG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 2 0.10
18 12 0.60
19 6 0.30
ACGTcount: A:0.35, C:0.03, G:0.12, T:0.50
Consensus pattern (19 bp):
AATGTTCTAATATGTTTAT
Found at i:412249 original size:14 final size:15
Alignment explanation
Indices: 412221--412251 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
412211 GCTATATTGA
412221 AAGGATTTAAATTTG
1 AAGGATTTAAATTTG
412236 AAGGATTT-AATTTG
1 AAGGATTTAAATTTG
412250 AA
1 AA
412252 TAAATAGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.39
Consensus pattern (15 bp):
AAGGATTTAAATTTG
Found at i:413761 original size:49 final size:49
Alignment explanation
Indices: 413632--413892 Score: 380
Period size: 49 Copynumber: 5.3 Consensus size: 49
413622 ATATTGAGAG
* *
413632 TAAAAGGTGCCACTAATGAAAGTTAAATGCATAGCGGTGCATTTCGGCA
1 TAAAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTCGACA
* ** *
413681 TAAAAAGATGCCACTAATGAAAGTTAAATGCATAATTGTGTATTTCGACA
1 T-AAAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTCGACA
* * *
413731 CAAAAAGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTT-TAGCA
1 TAAAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTCGA-CA
*
413780 TAAAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTCGGCA
1 TAAAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTCGACA
* *
413829 TAAAAGGTGCCACTAATGAAAGTTAAATGCATACCAGTGCATTTTCGACA
1 TAAAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTGCA-TTTCGACA
413879 TAAAAGGTGCCACT
1 TAAAAGGTGCCACT
413893 CATGGTATTC
Statistics
Matches: 188, Mismatches: 20, Indels: 7
0.87 0.09 0.03
Matches are distributed among these distances:
48 1 0.01
49 124 0.66
50 63 0.34
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (49 bp):
TAAAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTCGACA
Found at i:419835 original size:14 final size:14
Alignment explanation
Indices: 419803--419852 Score: 64
Period size: 14 Copynumber: 3.6 Consensus size: 14
419793 AACCCATATT
* *
419803 GAGTAAACTCGTCC
1 GAGTCAACTCATCC
* *
419817 TAGTCAACTCATCT
1 GAGTCAACTCATCC
419831 GAGTCAACTCATCC
1 GAGTCAACTCATCC
419845 GAGTCAAC
1 GAGTCAAC
419853 CTGTTGACTT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.24
Consensus pattern (14 bp):
GAGTCAACTCATCC
Found at i:445446 original size:11 final size:11
Alignment explanation
Indices: 445432--445487 Score: 51
Period size: 13 Copynumber: 4.7 Consensus size: 11
445422 TCTTTTTGAA
445432 TTCTTTTTCTT
1 TTCTTTTTCTT
445443 TTCTTTTCTTCTT
1 TTC-TTT-TTCTT
*
445456 TTCTTCTTCTTTT
1 TTCTT-TT-TCTT
445469 TGTCTTTTTC-T
1 T-TCTTTTTCTT
445480 TTCTTTTT
1 TTCTTTTT
445488 GCACTCCAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 7 0.18
11 5 0.13
12 7 0.18
13 15 0.39
14 4 0.11
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (11 bp):
TTCTTTTTCTT
Found at i:445456 original size:19 final size:18
Alignment explanation
Indices: 445432--445487 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
445422 TCTTTTTGAA
445432 TTCTTTTTCTTTTCTTTT
1 TTCTTTTTCTTTTCTTTT
445450 CTTC-TTTTCTTCTTCTTTT
1 -TTCTTTTTCTT-TTCTTTT
445469 TGTCTTTTTC-TTTCTTTT
1 T-TCTTTTTCTTTTCTTTT
445487 T
1 T
445488 GCACTCCAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 16 0.47
19 13 0.38
20 5 0.15
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (18 bp):
TTCTTTTTCTTTTCTTTT
Found at i:447355 original size:26 final size:27
Alignment explanation
Indices: 447301--447357 Score: 73
Period size: 26 Copynumber: 2.1 Consensus size: 27
447291 TAACTGAAAC
*
447301 AAATCTACATAATGGAGAAAACGAAAT
1 AAATCTACATAATGGAGAAAACCAAAT
*
447328 AAATCTACAT-ATCGGA-AAAACCATAT
1 AAATCTACATAAT-GGAGAAAACCAAAT
447354 AAAT
1 AAAT
447358 GTAACTTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 14 0.52
27 13 0.48
ACGTcount: A:0.54, C:0.14, G:0.11, T:0.21
Consensus pattern (27 bp):
AAATCTACATAATGGAGAAAACCAAAT
Found at i:448768 original size:41 final size:41
Alignment explanation
Indices: 448713--448807 Score: 129
Period size: 41 Copynumber: 2.3 Consensus size: 41
448703 GTGTTTGTAA
*
448713 ATACAAACGTCACTAAAGTA-CAAGTCTATAGCGGCGTTTGT
1 ATACAAACGCCACTAAAGTATC-AGTCTATAGCGGCGTTTGT
* * *
448754 ATAGAAACGCCACTAAAGTATCAGTCTTTAGTGGCGTTTGT
1 ATACAAACGCCACTAAAGTATCAGTCTATAGCGGCGTTTGT
*
448795 ATACAAACACCAC
1 ATACAAACGCCAC
448808 ATGTACTGAT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
41 46 0.98
42 1 0.02
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (41 bp):
ATACAAACGCCACTAAAGTATCAGTCTATAGCGGCGTTTGT
Found at i:448935 original size:83 final size:83
Alignment explanation
Indices: 448820--448983 Score: 204
Period size: 83 Copynumber: 2.0 Consensus size: 83
448810 GTACTGATAA
* * * * *
448820 ATTGTGGCGTTTGTTGGAAAAAAACCATTATAGATGAACCCTATTATGGTATTTGTATAAAAACA
1 ATTGTGGCATTTGTTGGAAAAAAACCACTATAGATGAACCCTATTACGGCATTTGAATAAAAACA
*
448885 CTGCTAAAGTACTACTCT
66 CAGCTAAAGTACTACTCT
* * * * *
448903 ATTGTGGCATTTGTT-GAAAAAATGCCACTATAGATTAACCCTTTTGCGGCATTTGAATAAAAAT
1 ATTGTGGCATTTGTTGGAAAAAA-ACCACTATAGATGAACCCTATTACGGCATTTGAATAAAAAC
*
448967 ACAGCTAAGGTACTACT
65 ACAGCTAAAGTACTACT
448984 ATGTTATCGA
Statistics
Matches: 68, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
82 7 0.10
83 61 0.90
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (83 bp):
ATTGTGGCATTTGTTGGAAAAAAACCACTATAGATGAACCCTATTACGGCATTTGAATAAAAACA
CAGCTAAAGTACTACTCT
Found at i:448999 original size:83 final size:83
Alignment explanation
Indices: 448828--449004 Score: 187
Period size: 83 Copynumber: 2.1 Consensus size: 83
448818 AAATTGTGGC
* * * * *
448828 GTTTGTTGGAAAAAAACCATTATAGATGAACCCTATTATGGTATTTGTATAAAAACACTGCTAAA
1 GTTTGTT-GAAAAAAACCACTATAGATGAACCCTATTACGGCATTTGAATAAAAACACAGCTAAA
* * *
448893 GTACTACTCTATTGTGGCA
65 GTACTACTATATTATCGCA
* * * * * *
448912 -TTTGTTGAAAAAATGCCACTATAGATTAACCCTTTTGCGGCATTTGAATAAAAATACAGCTAAG
1 GTTTGTTGAAAAAA-ACCACTATAGATGAACCCTATTACGGCATTTGAATAAAAACACAGCTAAA
*
448976 GTACTACTATGTTATCG-A
65 GTACTACTATATTATCGCA
448994 GTTTGTTGAAA
1 GTTTGTTGAAA
449005 CTATAGATGA
Statistics
Matches: 76, Mismatches: 15, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
82 8 0.11
83 68 0.89
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (83 bp):
GTTTGTTGAAAAAAACCACTATAGATGAACCCTATTACGGCATTTGAATAAAAACACAGCTAAAG
TACTACTATATTATCGCA
Found at i:452430 original size:64 final size:63
Alignment explanation
Indices: 452345--452569 Score: 310
Period size: 64 Copynumber: 3.5 Consensus size: 63
452335 TTGTTTAAGG
* * * ** * *
452345 TGCATCGATGCACATGCAGTGCATCGATGCAT-TAATTTAAAAAGAAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCA-TTAAATA-CAAACATCGAATAGGATTTA
452409 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCAT-CCCATTAAATACAAACATCGAATAGGATTTA
452473 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCAT-CCCATTAAATACAAACATCGAATAGGATTTA
*
452537 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
452570 ACCTCCATTA
Statistics
Matches: 149, Mismatches: 8, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
63 1 0.01
64 126 0.85
65 21 0.14
66 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (63 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCCATTAAATACAAACATCGAATAGGATTTA
Found at i:453195 original size:23 final size:22
Alignment explanation
Indices: 453161--453223 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 22
453151 ATTATTATAT
453161 GGCACTACGGTGCAATTCTACGC
1 GGCACTA-GGTGCAATTCTACGC
* *
453184 GGCACTCAGGTGTAATTCTACGT
1 GGCACT-AGGTGCAATTCTACGC
453207 GGCACTTAGGTGCAATT
1 GGCAC-TAGGTGCAATT
453224 ATATGAGTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 33 0.94
24 2 0.06
ACGTcount: A:0.22, C:0.24, G:0.27, T:0.27
Consensus pattern (22 bp):
GGCACTAGGTGCAATTCTACGC
Found at i:459412 original size:64 final size:63
Alignment explanation
Indices: 459327--459551 Score: 292
Period size: 64 Copynumber: 3.5 Consensus size: 63
459317 TTGTTTAAGG
* * * ** * * *
459327 TGCATCGATGCACATGCAGTGCATCGATGCAT-TAATTTAAAAAGAAAACATTGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCA-TTAAATA-CAAACATCGAATAGGATTTA
*
459391 TGCATCGATGCATAAGGAGTGCATCGATGTATCCCCATTAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCAT-CCCATTAAATACAAACATCGAATAGGATTTA
459455 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCAT-CCCATTAAATACAAACATCGAATAGGATTTA
*
459519 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
459552 ACCTCCATTA
Statistics
Matches: 146, Mismatches: 11, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
63 1 0.01
64 123 0.84
65 21 0.14
66 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (63 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCCATTAAATACAAACATCGAATAGGATTTA
Found at i:460169 original size:23 final size:23
Alignment explanation
Indices: 460143--460210 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
460133 ATTATTATAT
460143 GGCACTACGGTGCAATTCTATGC
1 GGCACTACGGTGCAATTCTATGC
* *
460166 GGCACT-CAGGTGCAATTCTACGT
1 GGCACTAC-GGTGCAATTCTATGC
*
460189 GGCACTTA-GGTGCAATTATATG
1 GGCAC-TACGGTGCAATTCTATG
460211 AGCTGTGGTG
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
22 1 0.03
23 36 0.95
24 1 0.03
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.28
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTATGC
Found at i:464559 original size:46 final size:45
Alignment explanation
Indices: 464509--464609 Score: 114
Period size: 45 Copynumber: 2.2 Consensus size: 45
464499 ATTCATACTT
* * * * *
464509 ATAATACACCATTATGAATTTTTATATATGGTATTCTTTCAT-TCCA
1 ATAATGCACCAATATCAATTTTAAT-TATGGTATCCTTTCATGT-CA
* *
464555 ATAATGCACTAATATCCATTTTAATTATGGTATCCTTTCATGTCA
1 ATAATGCACCAATATCAATTTTAATTATGGTATCCTTTCATGTCA
464600 ATAATGCACC
1 ATAATGCACC
464610 CATGCATTTT
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
45 26 0.57
46 20 0.43
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.42
Consensus pattern (45 bp):
ATAATGCACCAATATCAATTTTAATTATGGTATCCTTTCATGTCA
Found at i:464728 original size:45 final size:46
Alignment explanation
Indices: 464614--464867 Score: 316
Period size: 46 Copynumber: 5.6 Consensus size: 46
464604 TGCACCCATG
* * * * * *
464614 CATTTTATTTATGAAATCTTTTCATACCCTTTTATAAGCTATTATA
1 CATTTCATTTATGACATCCTTTCATGCCCTTCTATACGCTATTATA
* * * *
464660 CATTTTATTTACGGCATTCTTTCATGCCCTTCTATACGCTATTATA
1 CATTTCATTTATGACATCCTTTCATGCCCTTCTATACGCTATTATA
* * *
464706 CACTT-ATTTATGACATCCTTTCATGCCCATCTATACGCTATTTTA
1 CATTTCATTTATGACATCCTTTCATGCCCTTCTATACGCTATTATA
*
464751 CA-TTCATTTATGACATCCTTTCAT-ACCTTCTATACGCTATTATA
1 CATTTCATTTATGACATCCTTTCATGCCCTTCTATACGCTATTATA
* * *
464795 CTTTTCATTTATGGCATCCTTTCATGCCCTTCTATACACTATTATA
1 CATTTCATTTATGACATCCTTTCATGCCCTTCTATACGCTATTATA
* *
464841 CATTTCATTTATGGCATCATTTCATGC
1 CATTTCATTTATGACATCCTTTCATGC
464868 TTTTTATACA
Statistics
Matches: 182, Mismatches: 23, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
44 20 0.11
45 77 0.42
46 85 0.47
ACGTcount: A:0.25, C:0.23, G:0.07, T:0.45
Consensus pattern (46 bp):
CATTTCATTTATGACATCCTTTCATGCCCTTCTATACGCTATTATA
Found at i:464820 original size:135 final size:137
Alignment explanation
Indices: 464620--464867 Score: 376
Period size: 135 Copynumber: 1.8 Consensus size: 137
464610 CATGCATTTT
* * *
464620 ATTTATGAAATCTTTTCATACCCTTTTATAAGCTATTATACATTTTATTTACGGCATTCTTTCAT
1 ATTTATGAAATCCTTTCATACCCTTCTATAAGCTATTATACATTTTATTTACGGCATCCTTTCAT
* *
464685 GCCCTTCTATACGCTATTATACACTT-ATTTATGACATCCTTTCATGCCCATCTATACGCTATTT
66 GCCCTTCTATACACTATTATACACTTCATTTATGACATCATTTCATGCCCATCTATACGCTATTT
464749 TACATTC
131 TACATTC
* * *
464756 ATTTATGACATCCTTTCATA-CCTTCTATACGCTATTATAC-TTTTCATTTATGGCATCCTTTCA
1 ATTTATGAAATCCTTTCATACCCTTCTATAAGCTATTATACATTTT-ATTTACGGCATCCTTTCA
* *
464819 TGCCCTTCTATACACTATTATACATTTCATTTATGGCATCATTTCATGC
65 TGCCCTTCTATACACTATTATACACTTCATTTATGACATCATTTCATGC
464868 TTTTTATACA
Statistics
Matches: 100, Mismatches: 10, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
134 4 0.04
135 59 0.59
136 37 0.37
ACGTcount: A:0.25, C:0.23, G:0.07, T:0.45
Consensus pattern (137 bp):
ATTTATGAAATCCTTTCATACCCTTCTATAAGCTATTATACATTTTATTTACGGCATCCTTTCAT
GCCCTTCTATACACTATTATACACTTCATTTATGACATCATTTCATGCCCATCTATACGCTATTT
TACATTC
Found at i:465445 original size:110 final size:110
Alignment explanation
Indices: 465272--465545 Score: 381
Period size: 110 Copynumber: 2.5 Consensus size: 110
465262 GTAGTCCATT
* * * * * *
465272 AACTCATGATAAATTTTGTGG-GTAGCACACAT-CGTGCTTGTACGGTTATTCATCAACTTATGA
1 AACTCATGATGAATTCTGTGGATTTGCACACATAC-TGCTTGTACGATTATTCATCAACTCATGA
* * * *
465335 TGAATTCCGTGGATTTGCACACATAGTGCCTGTACGATTATTCATC
65 TGAATTCCATGGATTTACACACACAGTGCCCGTACGATTATTCATC
*
465381 AACTCATGATGAATTCTGTGGATTTGCACACATACTGCTTGTACGATTACTCATCAACTCATGAT
1 AACTCATGATGAATTCTGTGGATTTGCACACATACTGCTTGTACGATTATTCATCAACTCATGAT
465446 GAATTCCATGGATTTACACACACAGTGCCCGTACGATTATTCATC
66 GAATTCCATGGATTTACACACACAGTGCCCGTACGATTATTCATC
* * * * *
465491 AACTCATGATGAATTCCGTGGATTTCCACACATAGTGCATGTACAATTATTCATC
1 AACTCATGATGAATTCTGTGGATTTGCACACATACTGCTTGTACGATTATTCATC
465546 CACATAGGAT
Statistics
Matches: 146, Mismatches: 17, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
109 19 0.13
110 126 0.86
111 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (110 bp):
AACTCATGATGAATTCTGTGGATTTGCACACATACTGCTTGTACGATTATTCATCAACTCATGAT
GAATTCCATGGATTTACACACACAGTGCCCGTACGATTATTCATC
Found at i:465598 original size:54 final size:54
Alignment explanation
Indices: 465537--466389 Score: 1142
Period size: 54 Copynumber: 15.9 Consensus size: 54
465527 GCATGTACAA
*
465537 TTATTCATCCACATAGGATGAATTCTGTGAAATGCACACTTAGTGCCGAAATGG
1 TTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAATGG
* * * * * *
465591 TTATTCATCAACCTAGAATGAATTCTGTGAAATGCACACTTAGTGCGGAAACGG
1 TTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAATGG
* *
465645 TTATTCATCCACCTAGGATGAATTCCGTGAAATGCACACTTAGTGCTGAAATGG
1 TTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAATGG
* * *
465699 TTATTCATCTACATAGGATGAATTCTGTGAAATGCACACTTAGTGCCGAAACGG
1 TTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAATGG
* * * **
465753 TTATTCATCAACCTAGAATGAATTCCGTGAAATGCACACTTAGTGTGGAAATGG
1 TTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAATGG
* * *
465807 TTATTCATCCACCTAGGATGAATTCCGTGAAATGCACACTTAGTTCTGAAATGG
1 TTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAATGG
* * *
465861 TTATTCATCCACCTAGGATGAATTCCGTGAAATGCACACTTAGTGCTGAAATGC
1 TTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAATGG
* * **
465915 TTATTCATCCACATAGGATGAATTACGTGAAATGCACACTTAGTGCTGAAACAG
1 TTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAATGG
* * *
465969 TTATTCATCCAC--AGGATGAATTCCGTGAAATGCACACGTAGTTCCGAAACGG
1 TTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAATGG
466021 TTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACT-G
1 TTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAA-TGG
* * *
466075 TTATTCATCCACATAGGATGAATTCCGTGAAATGCACACGTAGTTCCGAAACGG
1 TTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAATGG
*
466129 TTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCTGAAATGG
1 TTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAATGG
* * * ** * *
466183 TTATTCATCCACCTATGATTAATTTTGTGAAATGCACACGTAGTGCCG-AATCGA
1 TTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAAT-GG
* * * * * * **
466237 TTTTTCATCCACCTAGGATGAACTCTGTTAAATG--CACGTAGTATCGAAATGG
1 TTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAATGG
* * * * *
466289 TTATTCATCCATATAGGATGAATTCCGTGAAATGCACACGTAGTGTCGAAACGA
1 TTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAATGG
* *
466343 TTATTCATCCACATAGGATGAATTCCGTGAAATGCACATTTAATGCC
1 TTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCC
466390 TATTTGGTCA
Statistics
Matches: 711, Mismatches: 80, Indels: 16
0.88 0.10 0.02
Matches are distributed among these distances:
52 86 0.12
53 6 0.01
54 619 0.87
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.29
Consensus pattern (54 bp):
TTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAATGG
Found at i:482272 original size:25 final size:25
Alignment explanation
Indices: 482235--482298 Score: 121
Period size: 25 Copynumber: 2.6 Consensus size: 25
482225 TTACACCATT
482235 CCATTC-TACATCATGCTTCCATCA
1 CCATTCTTACATCATGCTTCCATCA
482259 CCATTCTTACATCATGCTTCCATCA
1 CCATTCTTACATCATGCTTCCATCA
482284 CCATTCTTACATCAT
1 CCATTCTTACATCAT
482299 CATAACAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
24 6 0.15
25 33 0.85
ACGTcount: A:0.25, C:0.36, G:0.03, T:0.36
Consensus pattern (25 bp):
CCATTCTTACATCATGCTTCCATCA
Found at i:489743 original size:25 final size:25
Alignment explanation
Indices: 489699--489746 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
489689 GTGTTAATAC
* *
489699 ACATAAGGTCTTGCCCACCATATAT
1 ACATAAGGTCATACCCACCATATAT
*
489724 ACATAAGGTCATACCTACCATAT
1 ACATAAGGTCATACCCACCATAT
489747 GCACTAAGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.35, C:0.27, G:0.10, T:0.27
Consensus pattern (25 bp):
ACATAAGGTCATACCCACCATATAT
Found at i:490764 original size:46 final size:44
Alignment explanation
Indices: 490706--490811 Score: 133
Period size: 45 Copynumber: 2.3 Consensus size: 44
490696 TATGCACACC
* *
490706 ATGCACCGATGCACTGAGGAT-TTTATAAGAACATCGAATGCATTTG
1 ATGCATCGATGCACTG-GGATATTT-TAA-AACATCGAATGCACTTG
*
490752 ATGCATCGATGCACTTGGGCTATTTTAAAACATCGAATGCACTTG
1 ATGCATCGATGCAC-TGGGATATTTTAAAACATCGAATGCACTTG
*
490797 ATGCATCGGTGCACT
1 ATGCATCGATGCACT
490812 CTTAGTGCAC
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
44 1 0.02
45 29 0.54
46 19 0.35
47 5 0.09
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (44 bp):
ATGCATCGATGCACTGGGATATTTTAAAACATCGAATGCACTTG
Found at i:498967 original size:19 final size:19
Alignment explanation
Indices: 498943--498980 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
498933 AAAGGGGGAG
*
498943 AAATGTTAAGTTTTGAAAT
1 AAATGTTAAGTGTTGAAAT
498962 AAATGTTAAGTGTTGAAAT
1 AAATGTTAAGTGTTGAAAT
498981 GTTTTTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.00, G:0.18, T:0.39
Consensus pattern (19 bp):
AAATGTTAAGTGTTGAAAT
Found at i:499423 original size:17 final size:17
Alignment explanation
Indices: 499410--499442 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
499400 CGAATGCATT
499410 CCATGCATCGATGCACA
1 CCATGCATCGATGCACA
*
499427 CCATGCACCGATGCAC
1 CCATGCATCGATGCAC
499443 TGAGGATTTT
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:0.27, C:0.39, G:0.18, T:0.15
Consensus pattern (17 bp):
CCATGCATCGATGCACA
Found at i:499508 original size:45 final size:46
Alignment explanation
Indices: 499429--499534 Score: 155
Period size: 45 Copynumber: 2.3 Consensus size: 46
499419 GATGCACACC
* *
499429 ATGCACCGATGCACTGAGGATTTTATAAGAACATCGAATGCATTTG
1 ATGCATCGATGCACTGAGGATTTTATAAGAACATCGAATGCACTTG
499475 ATGCATCGATGCACTCG-GGATATTT-TAA-AACATCGAATGCACTTG
1 ATGCATCGATGCACT-GAGGAT-TTTATAAGAACATCGAATGCACTTG
499520 ATGCATCGATGCACT
1 ATGCATCGATGCACT
499535 AAGGTTCAAA
Statistics
Matches: 56, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
45 31 0.55
46 21 0.38
47 4 0.07
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (46 bp):
ATGCATCGATGCACTGAGGATTTTATAAGAACATCGAATGCACTTG
Found at i:500577 original size:20 final size:20
Alignment explanation
Indices: 500537--500578 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
500527 AATTTGATCC
* *
500537 AAATCAACATTATAACCTTA
1 AAATCAACATTACAACATTA
*
500557 AAATCAACATTCCAACATTA
1 AAATCAACATTACAACATTA
500577 AA
1 AA
500579 TTTTAGCATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.26
Consensus pattern (20 bp):
AAATCAACATTACAACATTA
Found at i:500880 original size:21 final size:21
Alignment explanation
Indices: 500839--500884 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
500829 ATTCAACTTC
* *
500839 TCAACATCATTTCCAAGCAAT
1 TCAACATCAATTCCAACCAAT
500860 TCAA-ATCAATTCCATACCAAT
1 TCAACATCAATTCCA-ACCAAT
500881 TCAA
1 TCAA
500885 TCCAAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.41, C:0.28, G:0.02, T:0.28
Consensus pattern (21 bp):
TCAACATCAATTCCAACCAAT
Found at i:501418 original size:20 final size:19
Alignment explanation
Indices: 501393--501432 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
501383 AAATATTATT
501393 TAATATATTTATTATATTAA
1 TAATATATTT-TTATATTAA
*
501413 TAATATATTTTTTTATTAA
1 TAATATATTTTTATATTAA
501432 T
1 T
501433 TTGTAGTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TAATATATTTTTATATTAA
Found at i:503578 original size:31 final size:30
Alignment explanation
Indices: 503543--503638 Score: 115
Period size: 31 Copynumber: 3.1 Consensus size: 30
503533 GTAACTTTTA
*
503543 ATAGTTGGACGACTCAACAAAGCAACATCCT
1 ATAGTTGGA-GACTCAACAAAACAACATCCT
**
503574 ATAGTT-GATGGACTCAACAAATTAACATCCT
1 ATAGTTGGA--GACTCAACAAAACAACATCCT
503605 ATAGTTGAGAGACTCAACAAAACAA-ATCCT
1 ATAGTTG-GAGACTCAACAAAACAACATCCT
503635 ATAG
1 ATAG
503639 CCGGGGAACC
Statistics
Matches: 57, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
30 11 0.19
31 44 0.77
33 2 0.04
ACGTcount: A:0.42, C:0.21, G:0.15, T:0.23
Consensus pattern (30 bp):
ATAGTTGGAGACTCAACAAAACAACATCCT
Found at i:503789 original size:15 final size:15
Alignment explanation
Indices: 503765--503823 Score: 72
Period size: 14 Copynumber: 4.1 Consensus size: 15
503755 GTAATTGGTT
503765 TTCTGG-AAATTGAA
1 TTCTGGAAAATTGAA
503779 TTCTGGAAAATT-AA
1 TTCTGGAAAATTGAA
503793 TTACT-GAAAATTGAA
1 TT-CTGGAAAATTGAA
*
503808 TTATGGAAAA-TGAA
1 TTCTGGAAAATTGAA
503822 TT
1 TT
503824 ACATTTCTGG
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
14 24 0.60
15 16 0.40
ACGTcount: A:0.42, C:0.05, G:0.17, T:0.36
Consensus pattern (15 bp):
TTCTGGAAAATTGAA
Found at i:504199 original size:23 final size:23
Alignment explanation
Indices: 504169--504241 Score: 76
Period size: 23 Copynumber: 3.1 Consensus size: 23
504159 AGTGTTATAT
504169 TATATTTTAAAAATATTAATTAA
1 TATATTTTAAAAATATTAATTAA
* * *
504192 TATATTTTAAATATCTTTATTAA
1 TATATTTTAAAAATATTAATTAA
* *
504215 AATATTATT-AGAATATTATATTAA
1 TATATT-TTAAAAATATTA-ATTAA
504239 TAT
1 TAT
504242 TAAATATATA
Statistics
Matches: 39, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
23 30 0.77
24 9 0.23
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (23 bp):
TATATTTTAAAAATATTAATTAA
Found at i:504222 original size:11 final size:11
Alignment explanation
Indices: 504178--504233 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
504168 TTATATTTTA
504178 AAAATATTAATT
1 AAAATATT-ATT
*
504190 AATATATT-TT
1 AAAATATTATT
*
504200 AAATATCTTTATT
1 AAA-AT-ATTATT
504213 AAAATATTATT
1 AAAATATTATT
*
504224 AGAATATTAT
1 AAAATATTAT
504234 ATTAATATTA
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
10 4 0.11
11 16 0.44
12 11 0.31
13 5 0.14
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (11 bp):
AAAATATTATT
Found at i:504420 original size:30 final size:32
Alignment explanation
Indices: 504386--504445 Score: 88
Period size: 30 Copynumber: 1.9 Consensus size: 32
504376 AACATAATTG
*
504386 ATTATTTTATCATAA-TATTAA-AAATATAAT
1 ATTATATTATCATAACTATTAATAAATATAAT
*
504416 ATTATATTATTATAACTATTAATAAATATA
1 ATTATATTATCATAACTATTAATAAATATA
504446 TTTTAAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 13 0.50
31 6 0.23
32 7 0.27
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (32 bp):
ATTATATTATCATAACTATTAATAAATATAAT
Found at i:504469 original size:53 final size:53
Alignment explanation
Indices: 504353--504471 Score: 127
Period size: 53 Copynumber: 2.2 Consensus size: 53
504343 TTAAAATAAC
** *
504353 AATATAATATCTTATATTATTATAACATAATTGATTATTTTATCATAATATTAAA
1 AATATAATA--TTATATTATTATAACATAATAAATTATTTTATAATAATATTAAA
* *
504408 AATATAATATTATATTATTATAACTATTAATAAATATATTTTA-AAT-ATTTTAAT
1 AATATAATATTATATTATTATAAC-A-TAATAAAT-TATTTTATAATAATATTAAA
504462 AAT-TAATATT
1 AATATAATATT
504472 TTGATTAAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
53 22 0.39
54 10 0.18
55 17 0.30
56 7 0.12
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (53 bp):
AATATAATATTATATTATTATAACATAATAAATTATTTTATAATAATATTAAA
Found at i:504683 original size:42 final size:42
Alignment explanation
Indices: 504635--504724 Score: 119
Period size: 42 Copynumber: 2.1 Consensus size: 42
504625 TTCCTCCAAC
* * *
504635 CAAACAT-TGAAAAACATTTTCTGGAAAACGAATTACGTGAAA
1 CAAACATGTG-AAAACATTTTCCGAAAAACAAATTACGTGAAA
* *
504677 TAAACATGTGAAAATATTTTCCGAAAAACAAATTACGTGAAA
1 CAAACATGTGAAAACATTTTCCGAAAAACAAATTACGTGAAA
504719 CAAACA
1 CAAACA
504725 CGAGATTTCA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
42 39 0.95
43 2 0.05
ACGTcount: A:0.50, C:0.14, G:0.12, T:0.23
Consensus pattern (42 bp):
CAAACATGTGAAAACATTTTCCGAAAAACAAATTACGTGAAA
Found at i:507814 original size:28 final size:27
Alignment explanation
Indices: 507773--507848 Score: 118
Period size: 28 Copynumber: 2.8 Consensus size: 27
507763 ATTTAAATAC
507773 TTATTTTTTTAACACAATTTAGCTCTT
1 TTATTTTTTTAACACAATTTAGCTCTT
*
507800 TTATTTTTTTTAACACAATTTAGTTCTT
1 TTA-TTTTTTTAACACAATTTAGCTCTT
*
507828 TTA-TTTTTTAACATAATTTAG
1 TTATTTTTTTAACACAATTTAG
507849 AGTGATTACA
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
26 17 0.37
27 3 0.07
28 26 0.57
ACGTcount: A:0.28, C:0.11, G:0.04, T:0.58
Consensus pattern (27 bp):
TTATTTTTTTAACACAATTTAGCTCTT
Found at i:515181 original size:20 final size:21
Alignment explanation
Indices: 515144--515186 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
515134 CCGTTAGACA
515144 GGGGGAATCGGTACCCCCTGG
1 GGGGGAATCGGTACCCCCTGG
*
515165 GGGGGAATCTGTACCCCCTGG
1 GGGGGAATCGGTACCCCCTGG
515186 G
1 G
515187 CAATCTGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.14, C:0.28, G:0.42, T:0.16
Consensus pattern (21 bp):
GGGGGAATCGGTACCCCCTGG
Found at i:515562 original size:24 final size:24
Alignment explanation
Indices: 515533--515598 Score: 123
Period size: 24 Copynumber: 2.8 Consensus size: 24
515523 CCCCCTTACT
*
515533 TTAACACTTCTCCCCTTTAACACC
1 TTAACACTTCTCCCCCTTAACACC
515557 TTAACACTTCTCCCCCTTAACACC
1 TTAACACTTCTCCCCCTTAACACC
515581 TTAACACTTCTCCCCCTT
1 TTAACACTTCTCCCCCTT
515599 TTTGTTAAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.23, C:0.44, G:0.00, T:0.33
Consensus pattern (24 bp):
TTAACACTTCTCCCCCTTAACACC
Found at i:516671 original size:19 final size:20
Alignment explanation
Indices: 516628--516675 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
516618 TCTAAATCCT
*
516628 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
516648 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
516667 TTTTCAAAA
1 TTTTCAAAA
516676 GAAATTCGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:517960 original size:21 final size:21
Alignment explanation
Indices: 517921--518019 Score: 141
Period size: 21 Copynumber: 4.9 Consensus size: 21
517911 TAGACAGGGA
*
517921 GAATCGGTACCCCCT-GGGGG
1 GAATCTGTACCCCCTGGGGGG
*
517941 GAATCTGTTCCCCCTGGGGGG
1 GAATCTGTACCCCCTGGGGGG
*
517962 GAATCGGTACCCCCTGGGGGG
1 GAATCTGTACCCCCTGGGGGG
517983 GAATCTGTACCCCCT--GGGG
1 GAATCTGTACCCCCTGGGGGG
*
518002 GAATCTATACCCCCTGGG
1 GAATCTGTACCCCCTGGG
518020 CAATCTGATT
Statistics
Matches: 70, Mismatches: 6, Indels: 5
0.86 0.07 0.06
Matches are distributed among these distances:
19 18 0.26
20 13 0.19
21 39 0.56
ACGTcount: A:0.15, C:0.30, G:0.35, T:0.19
Consensus pattern (21 bp):
GAATCTGTACCCCCTGGGGGG
Found at i:518560 original size:16 final size:16
Alignment explanation
Indices: 518539--518569 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
518529 TAACATATGA
*
518539 CTAGTTTTAATTAGTT
1 CTAGTTTGAATTAGTT
518555 CTAGTTTGAATTAGT
1 CTAGTTTGAATTAGT
518570 AATCGGGCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.06, G:0.16, T:0.52
Consensus pattern (16 bp):
CTAGTTTGAATTAGTT
Found at i:518710 original size:20 final size:21
Alignment explanation
Indices: 518674--518716 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
518664 AAAAAAATGA
518674 TTTTATTTTAAATTGTTG-TT
1 TTTTATTTTAAATTGTTGCTT
*
518694 TTTTA-TTTAATTATGTTGCTT
1 TTTTATTTTAAAT-TGTTGCTT
518715 TT
1 TT
518717 AATGAAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 6 0.30
20 10 0.50
21 4 0.20
ACGTcount: A:0.19, C:0.02, G:0.09, T:0.70
Consensus pattern (21 bp):
TTTTATTTTAAATTGTTGCTT
Found at i:524131 original size:24 final size:23
Alignment explanation
Indices: 524103--524162 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
524093 ACTTTTCTTT
*
524103 CTTTCTTTTTCTTCTTTTTGAGTG
1 CTTTCATTTTCTTC-TTTTGAGTG
*
524127 CTTTCAATTTCTTCTTTTGAGTG
1 CTTTCATTTTCTTCTTTTGAGTG
*
524150 CTTTGATTTTCTT
1 CTTTCATTTTCTT
524163 TGCTGGATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 20 0.62
24 12 0.38
ACGTcount: A:0.08, C:0.17, G:0.12, T:0.63
Consensus pattern (23 bp):
CTTTCATTTTCTTCTTTTGAGTG
Found at i:528297 original size:54 final size:54
Alignment explanation
Indices: 528186--528463 Score: 443
Period size: 54 Copynumber: 5.2 Consensus size: 54
528176 ACACATCTAC
* *
528186 TGCCAATA-GAGAAATTCATAAACTCATTAT-AATTTCTTAGGTTGCACACATAG
1 TGCCAATACGA-AAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACACAG
* * *
528239 TGCCAATAGGGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAG
1 TGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACACAG
*
528293 TGCCAATACGTAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACACAG
1 TGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACACAG
* *
528347 TGCCAATACGAAAATTCATAAACTTATAATGAATTTCTTAGGTTGTACACACAG
1 TGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACACAG
* *
528401 TACCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACACAC
1 TGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACACAG
528455 TGCCAATAC
1 TGCCAATAC
528464 ATACATTAAG
Statistics
Matches: 210, Mismatches: 13, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
53 26 0.12
54 184 0.88
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (54 bp):
TGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACACAG
Found at i:528695 original size:25 final size:25
Alignment explanation
Indices: 528661--528711 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
528651 ATACTATACC
528661 AATGTTAGTATATTCCCTAACATTT
1 AATGTTAGTATATTCCCTAACATTT
528686 AATGTTAGTATATTCCCTAACATTT
1 AATGTTAGTATATTCCCTAACATTT
528711 A
1 A
528712 TACTTTAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.43
Consensus pattern (25 bp):
AATGTTAGTATATTCCCTAACATTT
Found at i:528940 original size:94 final size:95
Alignment explanation
Indices: 528815--529002 Score: 290
Period size: 94 Copynumber: 2.0 Consensus size: 95
528805 ACCATGGTAT
* * *
528815 CGATACTTCTATACTATAGTACTGATTCTCCCTTTCAGTATTGATACCATTTCTACATTCTGGAT
1 CGATACTTCTATACTATAGTACCGATACTCCCTTTCAGTATCGATACCATTTCTACATTCTGGAT
*
528880 -CCATGGTATCGATA-CTACTCTCCTAGTAC
66 CCCAAGGTATCGATACCT-CTCTCCTAGTAC
*
528909 CGATACTTCTATACTATGGTACCGATACTCCCTTTCAGTATCGATACCATTTCTACATTCTGGAT
1 CGATACTTCTATACTATAGTACCGATACTCCCTTTCAGTATCGATACCATTTCTACATTCTGGAT
* *
528974 CCCAAGGTATTGATACCTCTCTCTTAGTA
66 CCCAAGGTATCGATACCTCTCTCCTAGTA
529003 TAGATACTCA
Statistics
Matches: 85, Mismatches: 7, Indels: 3
0.89 0.07 0.03
Matches are distributed among these distances:
94 61 0.72
95 22 0.26
96 2 0.02
ACGTcount: A:0.24, C:0.26, G:0.12, T:0.37
Consensus pattern (95 bp):
CGATACTTCTATACTATAGTACCGATACTCCCTTTCAGTATCGATACCATTTCTACATTCTGGAT
CCCAAGGTATCGATACCTCTCTCCTAGTAC
Found at i:531527 original size:96 final size:96
Alignment explanation
Indices: 531419--531600 Score: 244
Period size: 96 Copynumber: 1.9 Consensus size: 96
531409 CATGATGAAG
* * * *
531419 GTATCGATACCATTGATTTATAGAAT-GCAGAAATGGTATCGATACCGTAATA-G-AGTATCGAT
1 GTATCAATACCATTAATTTACAGAATACCA-AAATGGTATCGATA-CGTAA-AGGTAGTATCGAT
*
531481 ACCATAATATAGAAGTATCAATACTGAGAGGAAT
63 ACCATAATATAAAAGTATCAATACTGAGAGGAAT
* *
531515 GTATCAATACCATTAATTTACAGAATACCAAAATGGTATCGATACTTAAAGGTAGTATCGGTACC
1 GTATCAATACCATTAATTTACAGAATACCAAAATGGTATCGATACGTAAAGGTAGTATCGATACC
*
531580 ATAATATAAAAGTATCGATAC
66 ATAATATAAAAGTATCAATAC
531601 CATGGTATTG
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
94 1 0.01
95 5 0.07
96 67 0.89
97 2 0.03
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.29
Consensus pattern (96 bp):
GTATCAATACCATTAATTTACAGAATACCAAAATGGTATCGATACGTAAAGGTAGTATCGATACC
ATAATATAAAAGTATCAATACTGAGAGGAAT
Found at i:532029 original size:45 final size:45
Alignment explanation
Indices: 531975--532368 Score: 590
Period size: 45 Copynumber: 8.8 Consensus size: 45
531965 TATAAATAGA
*
531975 GCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGT
1 GCATTAAAGGCATGAAAGGATGCCATAAATAAAATGCATAACGGT
*
532020 GCATTAAAGGCATGAAAGGATGTCATAAATAAAATGCATAACGGT
1 GCATTAAAGGCATGAAAGGATGCCATAAATAAAATGCATAACGGT
* * * *
532065 GCATTAAAGGCATGAAAGAATGACATAAATGAAATGCATAACAGT
1 GCATTAAAGGCATGAAAGGATGCCATAAATAAAATGCATAACGGT
532110 GCATTAAAGGCATGAAAGGATGCCATAAATAAAATGCATAACGGT
1 GCATTAAAGGCATGAAAGGATGCCATAAATAAAATGCATAACGGT
* * * *
532155 GTATTAAAGGCATGAAATGATGCCATAAATGAAATGCATAATGGT
1 GCATTAAAGGCATGAAAGGATGCCATAAATAAAATGCATAACGGT
* * *
532200 GCATTAAAGGAATGAAAGGATGCCATAAATAAAATGCATAATGTT
1 GCATTAAAGGCATGAAAGGATGCCATAAATAAAATGCATAACGGT
* * *
532245 GCATTAAAGGCATGAATGGATGCCATAAATGAAATACATAACGGT
1 GCATTAAAGGCATGAAAGGATGCCATAAATAAAATGCATAACGGT
* * *
532290 GCATTACATGCATGAAAGGATGACATAAATAAAATGCATAACGGT
1 GCATTAAAGGCATGAAAGGATGCCATAAATAAAATGCATAACGGT
* * *
532335 GCATTAATGGCATGAAAGAATTCCATAAATAAAA
1 GCATTAAAGGCATGAAAGGATGCCATAAATAAAA
532369 ATAATGAATA
Statistics
Matches: 312, Mismatches: 37, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 312 1.00
ACGTcount: A:0.45, C:0.12, G:0.21, T:0.22
Consensus pattern (45 bp):
GCATTAAAGGCATGAAAGGATGCCATAAATAAAATGCATAACGGT
Found at i:532183 original size:21 final size:21
Alignment explanation
Indices: 532159--532228 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
532149 AACGGTGTAT
*
532159 TAAAGGCATGAAATGATGCCA
1 TAAAGGAATGAAATGATGCCA
* *
532180 TAAATGAAATGCATAATGGTG-CA
1 TAAA-GGAATG-A-AATGATGCCA
*
532203 TTAAAGGAATGAAAGGATGCCA
1 -TAAAGGAATGAAATGATGCCA
532225 TAAA
1 TAAA
532229 TAAAATGCAT
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
21 13 0.34
22 7 0.18
23 8 0.21
24 10 0.26
ACGTcount: A:0.46, C:0.10, G:0.23, T:0.21
Consensus pattern (21 bp):
TAAAGGAATGAAATGATGCCA
Found at i:536660 original size:96 final size:96
Alignment explanation
Indices: 536500--536684 Score: 259
Period size: 96 Copynumber: 1.9 Consensus size: 96
536490 TCGATACCAT
* *
536500 GAGGAAGGTGTCGATACCATTGATTTACAAAATGTAGAAATGGTATCAATACCATAATAGAGTAT
1 GAGGAAGGTATCGATACCATTAATTTACAAAATGTAGAAATGGTATCAATACCATAATAGAGTAT
*
536565 CGATACCATAATACAGAAGTATCGGTACTGA
66 CGATACCATAATACAAAAGTATCGGTACTGA
* *
536596 GAGGAAGGTATCGATACCATTAATTTACAAAATGTCGAAATGGTATCGATA-C-TGAA-AGGTAG
1 GAGGAAGGTATCGATACCATTAATTTACAAAATGTAGAAATGGTATCAATACCAT-AATA-G-AG
* *
536658 TATCGATACCATAGTATAAAAGTATCG
63 TATCGATACCATAATACAAAAGTATCG
536685 ATACCATGGT
Statistics
Matches: 79, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
94 2 0.03
95 4 0.05
96 73 0.92
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.26
Consensus pattern (96 bp):
GAGGAAGGTATCGATACCATTAATTTACAAAATGTAGAAATGGTATCAATACCATAATAGAGTAT
CGATACCATAATACAAAAGTATCGGTACTGA
Found at i:537111 original size:45 final size:45
Alignment explanation
Indices: 537062--537365 Score: 441
Period size: 45 Copynumber: 6.8 Consensus size: 45
537052 TATAAATAGG
* * *
537062 GCATTAAAGGTATGAAAAGATACCATAAATGAAATGCATAACGAT
1 GCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGAT
*
537107 GCATTAAAGGCATGAAAGGATGCCATAAATAAAATGCATAAC-AGT
1 GCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGA-T
* * *
537152 ACATTAAAGGCATGAAAGGATTCCATAAATAAAATGCATAAC-AGT
1 GCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGA-T
*
537197 GCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGT
1 GCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGAT
*
537242 GCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGGT
1 GCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGAT
* * * * *
537287 GCTTTACAGGTATGAAAAGATGCCATAAATAAAATGCATAACGAT
1 GCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGAT
*
537332 GCATTAATGGCATGAAAGGATGCCATAAATGAAA
1 GCATTAAAGGCATGAAAGGATGCCATAAATGAAA
537366 ATAATAAATA
Statistics
Matches: 235, Mismatches: 22, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
44 1 0.00
45 234 1.00
ACGTcount: A:0.45, C:0.13, G:0.20, T:0.21
Consensus pattern (45 bp):
GCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGAT
Found at i:542310 original size:32 final size:33
Alignment explanation
Indices: 542244--542311 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
542234 GATATTAAAA
*
542244 AATAAAAATAAATATTTAAATTTTAATAATTTT
1 AATAAAAATAAATATATAAATTTTAATAATTTT
* *
542277 AATAAAACTAAAT-TAT-AATTTTTATAATGTTT
1 AATAAAAATAAATATATAAATTTTAATAAT-TTT
542309 AAT
1 AAT
542312 TATTTAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 11 0.35
32 8 0.26
33 12 0.39
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (33 bp):
AATAAAAATAAATATATAAATTTTAATAATTTT
Found at i:543828 original size:25 final size:24
Alignment explanation
Indices: 543778--543850 Score: 76
Period size: 25 Copynumber: 2.8 Consensus size: 24
543768 ATGTAATTTG
*
543778 TAATATATATATATATATAATAAATAA
1 TAATATA-ATATAT-TAT-ATTAATAA
543805 TAATAATAATATATTATATTAATAA
1 TAAT-ATAATATATTATATTAATAA
543830 TAATTATAAT-TATTACTATTA
1 TAA-TATAATATATTA-TATTA
543851 TTATGAAAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
24 5 0.12
25 20 0.48
26 4 0.10
27 10 0.24
28 3 0.07
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.45
Consensus pattern (24 bp):
TAATATAATATATTATATTAATAA
Found at i:543841 original size:16 final size:16
Alignment explanation
Indices: 543794--543841 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
543784 ATATATATAT
*
543794 ATAATAAATAATAA-TA
1 ATAAT-AATTATAATTA
543810 ATAATATATTAT-ATTA
1 ATAATA-ATTATAATTA
543826 ATAATAATTATAATTA
1 ATAATAATTATAATTA
543842 TTACTATTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
15 7 0.25
16 21 0.75
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATAATAATTATAATTA
Found at i:543843 original size:19 final size:19
Alignment explanation
Indices: 543778--543844 Score: 61
Period size: 19 Copynumber: 3.5 Consensus size: 19
543768 ATGTAATTTG
543778 TAATATATATATATATATAATA
1 TAATATAT-TA-ATA-ATAATA
543800 -AATA-A-TAATAATAATA
1 TAATATATTAATAATAATA
*
543816 TATTATATTAATAATAATTA
1 TAATATATTAATAATAA-TA
543836 TAAT-TATTA
1 TAATATATTA
543845 CTATTATTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
16 6 0.15
17 6 0.15
18 3 0.08
19 14 0.36
20 6 0.15
21 4 0.10
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TAATATATTAATAATAATA
Found at i:544067 original size:76 final size:76
Alignment explanation
Indices: 543974--544871 Score: 1617
Period size: 76 Copynumber: 11.9 Consensus size: 76
543964 GATGAAAATG
* * *
543974 TTTGAAAACATAAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCATTGTAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
544039 GACCCTAAGGCT
66 GACCCTAAGG-T
* *
544051 TTT-AAAACATCAAAAAGCTCCCTAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
* *
544115 TACCCTAAGGC
66 GACCCTAAGGT
* *
544126 TTTAAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTACAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
*
544191 GACCCTAAGGC
66 GACCCTAAGGT
*
544202 TTTGAAAACATC-AAAAGCTCCCGAAGGC-TTTTGGAAACATCATGCACTGCAGGACTTACAAAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
544265 GACCCTAAGGT
66 GACCCTAAGGT
*
544276 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAAAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
544341 GACCCTAAGGT
66 GACCCTAAGGT
544352 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
544417 GACCCTAAGGT
66 GACCCTAAGGT
544428 TTTGAAAACATCAAAAAGCTCCCGAAGGC-TTTTGGAAACATCATGCACTGCAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
*
544492 GACCCTAATGT
66 GACCCTAAGGT
544503 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
544568 GACCCTAAGGT
66 GACCCTAAGGT
*
544579 TTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
544644 GACCCTAAGGT
66 GACCCTAAGGT
544655 TTTGAAAACATC-AAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
544719 GACCCTAAGGT
66 GACCCTAAGGT
544730 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
544795 GACCCTAAGGT
66 GACCCTAAGGT
*
544806 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
544871 G
66 G
544872 TGGGAAATAG
Statistics
Matches: 797, Mismatches: 19, Indels: 11
0.96 0.02 0.01
Matches are distributed among these distances:
74 55 0.07
75 183 0.23
76 556 0.70
77 3 0.00
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (76 bp):
TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
GACCCTAAGGT
Found at i:544505 original size:151 final size:152
Alignment explanation
Indices: 543974--544871 Score: 1617
Period size: 151 Copynumber: 5.9 Consensus size: 152
543964 GATGAAAATG
* * *
543974 TTTGAAAACATAAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCATTGTAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
* *
544039 GACCCTAAGGCTTTT-AAAACATCAAAAAGCTCCCTAAGGCTTTTTGGAAACATCATGCACTGTA
66 GACCCTAAGG-TTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCA
* *
544103 GGACTTACAGATTACCCTAAGGC
130 GGACTTACAGATGACCCTAAGGT
* *
544126 TTTAAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTACAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
*
544191 GACCCTAAGGCTTTGAAAACATC-AAAAGCTCCCGAAGGC-TTTTGGAAACATCATGCACTGCAG
66 GACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAG
*
544254 GACTTACAAATGACCCTAAGGT
131 GACTTACAGATGACCCTAAGGT
*
544276 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAAAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
544341 GACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAG
66 GACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAG
544406 GACTTACAGATGACCCTAAGGT
131 GACTTACAGATGACCCTAAGGT
544428 TTTGAAAACATCAAAAAGCTCCCGAAGGC-TTTTGGAAACATCATGCACTGCAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
*
544492 GACCCTAATGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAG
66 GACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAG
544557 GACTTACAGATGACCCTAAGGT
131 GACTTACAGATGACCCTAAGGT
*
544579 TTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
544644 GACCCTAAGGTTTTGAAAACATC-AAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAG
66 GACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAG
544708 GACTTACAGATGACCCTAAGGT
131 GACTTACAGATGACCCTAAGGT
544730 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
*
544795 GACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAG
66 GACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAG
544860 GACTTACAGATG
131 GACTTACAGATG
544872 TGGGAAATAG
Statistics
Matches: 719, Mismatches: 22, Indels: 10
0.96 0.03 0.01
Matches are distributed among these distances:
150 126 0.18
151 332 0.46
152 261 0.36
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (152 bp):
TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
GACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAG
GACTTACAGATGACCCTAAGGT
Found at i:544552 original size:227 final size:227
Alignment explanation
Indices: 543974--544871 Score: 1613
Period size: 227 Copynumber: 4.0 Consensus size: 227
543964 GATGAAAATG
* * *
543974 TTTGAAAACATAAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCATTGTAGGACTTACAGAT
1 TTTGAAAACAT-CAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
* *
544039 GACCCTAAGGCTTTT-AAAACATCAAAAAGCTCCCTAAGGCTTTTTGGAAACATCATGCACTGTA
65 GACCCTAAGG-TTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCA
* * *
544103 GGACTTACAGATTACCCTAAGGCTTTAAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACAT
129 GGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACAT
* *
544168 CATGCACTACAGGACTTACAGATGACCCTAAGGC
194 CATGCACTGCAGGACTTACAGATGACCCTAAGGT
*
544202 TTTGAAAACATCAAAAGCTCCCGAAGGC-TTTTGGAAACATCATGCACTGCAGGACTTACAAATG
1 TTTGAAAACATCAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
544266 ACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGG
66 ACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGG
*
544331 ACTTACAAATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCA
131 ACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCA
544396 TGCACTGCAGGACTTACAGATGACCCTAAGGT
196 TGCACTGCAGGACTTACAGATGACCCTAAGGT
544428 TTTGAAAACATCAAAAAGCTCCCGAAGGC-TTTTGGAAACATCATGCACTGCAGGACTTACAGAT
1 TTTGAAAACATC-AAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
*
544492 GACCCTAATGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAG
65 GACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAG
*
544557 GACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAAACATC
130 GACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATC
544622 ATGCACTGCAGGACTTACAGATGACCCTAAGGT
195 ATGCACTGCAGGACTTACAGATGACCCTAAGGT
544655 TTTGAAAACATCAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
1 TTTGAAAACATCAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
544720 ACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGG
66 ACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGG
544785 ACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCA
131 ACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCA
*
544850 TGCACTGTAGGACTTACAGATG
196 TGCACTGCAGGACTTACAGATG
544872 TGGGAAATAG
Statistics
Matches: 648, Mismatches: 19, Indels: 7
0.96 0.03 0.01
Matches are distributed among these distances:
225 4 0.01
226 210 0.32
227 423 0.65
228 11 0.02
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (227 bp):
TTTGAAAACATCAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
ACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGG
ACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCA
TGCACTGCAGGACTTACAGATGACCCTAAGGT
Found at i:545740 original size:22 final size:22
Alignment explanation
Indices: 545715--545769 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
545705 CATAAAGCTT
545715 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
545737 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
545759 TCATCTTTGAA
1 TCATCTTTGAA
545770 GAGTGTAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:547182 original size:78 final size:77
Alignment explanation
Indices: 547009--547182 Score: 210
Period size: 77 Copynumber: 2.3 Consensus size: 77
546999 GATGTGGGCC
* * * *
547009 TTCAGCATGCCCCAACA-ATTGCTGATACGAATGTTCAAAATACATCAACCTTCTTCATTCTGAT
1 TTCAGCATGCCCCAACATTTTGCTGATACAAATGTTCAAAATACATCAACATTCCTCATTCTGAT
547073 TGAAAAAGGCAT
66 TGAAAAAGGCAT
* * * *
547085 TTCAGCATGCCCCAGCATTTTGCTGATATAAACT-TTCAAGATACATCAACATTCCTGATTCATG
1 TTCAGCATGCCCCAACATTTTGCTGATACAAA-TGTTCAAAATACATCAACATTCCTCATTC-TG
*
547149 ATTGAAAAAAGG-TT
64 ATTG-AAAAAGGCAT
*
547163 TTTAGCATGCCCCAACATTT
1 TTCAGCATGCCCCAACATTT
547183 GATTCTTGTT
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
76 16 0.19
77 34 0.41
78 26 0.31
79 7 0.08
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.31
Consensus pattern (77 bp):
TTCAGCATGCCCCAACATTTTGCTGATACAAATGTTCAAAATACATCAACATTCCTCATTCTGAT
TGAAAAAGGCAT
Found at i:553417 original size:36 final size:36
Alignment explanation
Indices: 553340--553429 Score: 94
Period size: 36 Copynumber: 2.5 Consensus size: 36
553330 GTAAATGCTA
* *
553340 AAATGCATAA-ATGCAAAAATAAGAATGCAAACTGTG
1 AAATGCA-AAGATGCAAAAATAAGAATACAAAATGTG
* *
553376 TAATGCAAAGATGTAAAAAGTAAGAATACAAAATG-G
1 AAATGCAAAGATGCAAAAA-TAAGAATACAAAATGTG
* *
553412 AAATGCACAGATACAAAA
1 AAATGCAAAGATGCAAAA
553430 TGTAAATGCA
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
35 2 0.05
36 29 0.66
37 13 0.30
ACGTcount: A:0.56, C:0.10, G:0.17, T:0.18
Consensus pattern (36 bp):
AAATGCAAAGATGCAAAAATAAGAATACAAAATGTG
Found at i:555784 original size:14 final size:13
Alignment explanation
Indices: 555752--555808 Score: 52
Period size: 11 Copynumber: 4.5 Consensus size: 13
555742 TTAATACCTG
555752 AATAAAATAA-AT
1 AATAAAATAATAT
555764 -A-AAAATAATATT
1 AATAAAATAATA-T
555776 AATAAAATAATAT
1 AATAAAATAATAT
555789 -A-AAAATAATAAGT
1 AATAAAATAAT-A-T
555802 AATAAAA
1 AATAAAA
555809 AATTTGAAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 13
0.74 0.00 0.26
Matches are distributed among these distances:
10 7 0.19
11 10 0.27
12 3 0.08
13 3 0.08
14 10 0.27
15 4 0.11
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (13 bp):
AATAAAATAATAT
Found at i:555793 original size:11 final size:11
Alignment explanation
Indices: 555755--555798 Score: 54
Period size: 11 Copynumber: 3.8 Consensus size: 11
555745 ATACCTGAAT
555755 AAAATAA-ATA
1 AAAATAATATA
555765 AAAATAATATTAA
1 AAAATAATA-T-A
555778 TAAAATAATATA
1 -AAAATAATATA
555790 AAAATAATA
1 AAAATAATA
555799 AGTAATAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 7 0.23
11 10 0.33
12 2 0.07
13 2 0.07
14 9 0.30
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
AAAATAATATA
Found at i:555796 original size:25 final size:25
Alignment explanation
Indices: 555752--555808 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
555742 TTAATACCTG
*
555752 AATAAAATAAATAAAAATAAT-ATT
1 AATAAAATAAATAAAAATAATAAGT
555776 AATAAAATAATATAAAAATAATAAGT
1 AATAAAATAA-ATAAAAATAATAAGT
555802 AATAAAA
1 AATAAAA
555809 AATTTGAAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 10 0.33
25 11 0.37
26 9 0.30
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (25 bp):
AATAAAATAAATAAAAATAATAAGT
Found at i:556467 original size:31 final size:33
Alignment explanation
Indices: 556406--556467 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
556396 CGATATTAAA
*
556406 AAATAAAAATAAATATTTAAATTTTAATAATTT
1 AAATAAAAATAAATATATAAATTTTAATAATTT
* *
556439 AAATAAAACTAAAT-TAT-AATTTTTATAAT
1 AAATAAAAATAAATATATAAATTTTAATAAT
556468 GTCTAATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 11 0.42
32 2 0.08
33 13 0.50
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (33 bp):
AAATAAAAATAAATATATAAATTTTAATAATTT
Found at i:557992 original size:16 final size:16
Alignment explanation
Indices: 557937--558002 Score: 62
Period size: 16 Copynumber: 3.9 Consensus size: 16
557927 ATGTAATTTG
557937 TAATATATATATATATAT
1 TAATA-ATATAT-TATAT
* * *
557955 ATATATAATAAATAATAA
1 -TA-ATAATATATTATAT
557973 TAATAATATATTATAT
1 TAATAATATATTATAT
557989 TAATAATA-ATTATA
1 TAATAATATATTATA
558003 ATTATTATTA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
15 6 0.15
16 19 0.47
17 2 0.05
18 3 0.08
19 7 0.17
20 3 0.08
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TAATAATATATTATAT
Found at i:557995 original size:22 final size:22
Alignment explanation
Indices: 557967--558012 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
557957 ATATAATAAA
557967 TAATAATAATAATATATTA-TAT
1 TAATAATAATAATA-ATTATTAT
*
557989 TAATAATAATTATAATTATTAT
1 TAATAATAATAATAATTATTAT
558011 TA
1 TA
558013 TGAAAATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TAATAATAATAATAATTATTAT
Found at i:558026 original size:22 final size:23
Alignment explanation
Indices: 557968--558026 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 23
557958 TATAATAAAT
*
557968 AATAATAA-TAATATATTATATT
1 AATAATAATTAATATATTATATG
557990 AATAATAATT-ATAATTATTATTATG
1 AATAATAATTAAT-A-TATTA-TATG
558015 AA-AATAATTAAT
1 AATAATAATTAAT
558027 GTCTACATTC
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
22 10 0.32
23 2 0.06
24 12 0.39
25 7 0.23
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
AATAATAATTAATATATTATATG
Found at i:559074 original size:3 final size:3
Alignment explanation
Indices: 559060--559094 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
559050 GTTTTCTAAG
559060 TCT TCAT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TC-T TCT TCT TCT TCT TCT TCT TCT TCT TCT T
559095 ATCCTCATCC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.03, C:0.31, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:560263 original size:22 final size:22
Alignment explanation
Indices: 560189--560263 Score: 93
Period size: 22 Copynumber: 3.5 Consensus size: 22
560179 TGCGATCTCC
*
560189 ACTATCGCAACAACAACTGTAG
1 ACTATCGCAACGACAACTGTAG
*
560211 ACTATCGCAACG--AA-TTTAG
1 ACTATCGCAACGACAACTGTAG
**
560230 AAAATCGCAACGACAACTGTAG
1 ACTATCGCAACGACAACTGTAG
560252 ACTATCGCAACG
1 ACTATCGCAACG
560264 CGAAATGGAA
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
19 14 0.33
20 2 0.05
21 2 0.05
22 25 0.58
ACGTcount: A:0.40, C:0.25, G:0.16, T:0.19
Consensus pattern (22 bp):
ACTATCGCAACGACAACTGTAG
Found at i:560315 original size:21 final size:21
Alignment explanation
Indices: 560252--560315 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
560242 ACAACTGTAG
*
560252 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* * ** *
560273 A-AATCGTAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
560293 ACTATCGCAACGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
560314 AC
1 AC
560316 GCGAATTTGC
Statistics
Matches: 31, Mismatches: 11, Indels: 2
0.70 0.25 0.05
Matches are distributed among these distances:
20 14 0.45
21 17 0.55
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.19
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:561153 original size:17 final size:17
Alignment explanation
Indices: 561131--561164 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
561121 CGAAATTACT
561131 TTCCTTTGACAAATTTA
1 TTCCTTTGACAAATTTA
561148 TTCCTTTGACAAATTTA
1 TTCCTTTGACAAATTTA
561165 GAGTAGCCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.18, G:0.06, T:0.47
Consensus pattern (17 bp):
TTCCTTTGACAAATTTA
Found at i:567490 original size:2 final size:2
Alignment explanation
Indices: 567452--567578 Score: 57
Period size: 2 Copynumber: 67.5 Consensus size: 2
567442 ATTAATAATA
* *
567452 AT AT A- AT AT A- AT AT AT CAT AA AT AG AT ACT A- AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT -AT AT AT AT AT A-T AT AT AT AT AT AT
* * *
567493 AT AT AT A- AT AT A- AT AA AT AT AT AT ACT GT A- AC AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
567532 AT A- AGT AT AT A- AT A- AT AT AGT AT -T AT ACT AT A- AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT A-T AT AT AT A-T AT AT AT AT AT
567570 A- AT A- AT AT A
1 AT AT AT AT AT A
567579 CTATCCCAGA
Statistics
Matches: 96, Mismatches: 9, Indels: 40
0.66 0.06 0.28
Matches are distributed among these distances:
1 14 0.15
2 72 0.75
3 10 0.10
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.39
Consensus pattern (2 bp):
AT
Found at i:567514 original size:18 final size:18
Alignment explanation
Indices: 567446--567578 Score: 78
Period size: 18 Copynumber: 7.2 Consensus size: 18
567436 AATAATATTA
567446 ATAAT-AATATAATATAAT
1 ATAATAAATAT-ATATAAT
*
567464 ATATCATAAATAGATACTAAT
1 ATA--ATAAATATATA-TAAT
*
567485 AT-ATATATATATATAAT
1 ATAATAAATATATATAAT
*
567502 ATAATAAATATATATACT
1 ATAATAAATATATATAAT
* * *
567520 GTAACATATA-ATATAAGT
1 ATAATAAATATATATAA-T
*
567538 AT-AT-AATAATATAGTATT
1 ATAATAAAT-ATATA-TAAT
*
567556 ATACTATAATATATAATAAT
1 ATAATA-AATATAT-ATAAT
567576 ATA
1 ATA
567579 CTATCCCAGA
Statistics
Matches: 87, Mismatches: 15, Indels: 24
0.69 0.12 0.19
Matches are distributed among these distances:
16 2 0.02
17 13 0.15
18 40 0.46
19 3 0.03
20 15 0.17
21 14 0.16
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.39
Consensus pattern (18 bp):
ATAATAAATATATATAAT
Found at i:570428 original size:81 final size:80
Alignment explanation
Indices: 570195--570432 Score: 334
Period size: 81 Copynumber: 3.0 Consensus size: 80
570185 TATTCTAAAA
* * *
570195 TAAAAGATTAATGGTCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCTAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAA-GTGTCAATTATGCAAGTTAGATGAAAG
*
570260 ATTAAATACCTTTGAG
65 GTTAAATACCTTTGAG
* * *
570276 TAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGATGTCAATTATACCAGTCAGATGAAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAG-TGTCAATTATGCAAGTTAGATGAAAG
570341 GTTAAATACCTTTGAG
65 GTTAAATACCTTTGAG
* * * *
570357 TAAAAGATTAATGGCCTAGTTATGTATTTGGCAAGAAAGTGTCAATCATGCAAGTTAGATGGAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGGC-AGAAAGTGTCAATTATGCAAGTTAGATGAAAG
*
570422 GCTAAAT-CCTT
65 GTTAAATACCTT
570433 AACAGTGCAA
Statistics
Matches: 141, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
80 5 0.04
81 130 0.92
82 6 0.04
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.31
Consensus pattern (80 bp):
TAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGTGTCAATTATGCAAGTTAGATGAAAGG
TTAAATACCTTTGAG
Found at i:572156 original size:18 final size:18
Alignment explanation
Indices: 572135--572172 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
572125 TTTCATGCTT
572135 ATTTGGATTGTCATTACC
1 ATTTGGATTGTCATTACC
*
572153 ATTTGGGTTGTCATTACC
1 ATTTGGATTGTCATTACC
572171 AT
1 AT
572173 CAGTGCTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.21, C:0.16, G:0.18, T:0.45
Consensus pattern (18 bp):
ATTTGGATTGTCATTACC
Found at i:579956 original size:5 final size:5
Alignment explanation
Indices: 579934--580107 Score: 83
Period size: 5 Copynumber: 35.6 Consensus size: 5
579924 AAAACCGAAA
579934 ATAAT ATTAAT AATAAT ATAAT AT-AT AATAA- A-AAT A-AAT AT-AT
1 ATAAT A-TAAT -ATAAT ATAAT ATAAT -ATAAT ATAAT ATAAT ATAAT
*
579977 AT-AT ATACT ATAACAT ATAAT ATAAGT AT-AT ACTAAT ATAAT ATAAT
1 ATAAT ATAAT AT-A-AT ATAAT ATAA-T ATAAT A-TAAT ATAAT ATAAT
* *
580024 ACT-AT AATAAT AT-AT AT-AT ATAAT AT-GT CATGAT ATAAT AT-AT
1 A-TAAT -ATAAT ATAAT ATAAT ATAAT ATAAT -ATAAT ATAAT ATAAT
* *
580067 A-ATAT ATAAT AT--T ATATT ATACT ATAAT AT-AT AATAAT ATA
1 ATA-AT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT -ATAAT ATA
580108 CTATCCCGGA
Statistics
Matches: 137, Mismatches: 7, Indels: 50
0.71 0.04 0.26
Matches are distributed among these distances:
3 5 0.04
4 32 0.23
5 71 0.52
6 25 0.18
7 4 0.03
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:579976 original size:2 final size:2
Alignment explanation
Indices: 579949--580107 Score: 77
Period size: 2 Copynumber: 85.5 Consensus size: 2
579939 ATTAATAATA
* * *
579949 AT AT A- AT AT AT A- AT AA AA AT AA AT AT AT AT AT AT ACT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
*
579989 AC AT AT A- AT AT A- AGT AT AT ACT A- AT AT A- AT AT A- AT ACT
1 AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT A-T
*
580027 AT A- AT A- AT AT AT AT AT AT A- AT AT GT CAT GAT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT -AT AT AT AT AT AT
580067 A- AT AT AT A- AT AT -T AT AT -T AT ACT AT A- AT AT AT A- AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
580103 AT AT A
1 AT AT A
580108 CTATCCCGGA
Statistics
Matches: 124, Mismatches: 8, Indels: 50
0.68 0.04 0.27
Matches are distributed among these distances:
1 19 0.15
2 93 0.75
3 12 0.10
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (2 bp):
AT
Found at i:581402 original size:2 final size:2
Alignment explanation
Indices: 581395--581419 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
581385 GGGGTAAGAT
581395 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
581420 GCGTGCGTGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:581735 original size:53 final size:56
Alignment explanation
Indices: 581642--581751 Score: 172
Period size: 53 Copynumber: 2.0 Consensus size: 56
581632 TTATACGGTT
581642 AACGTGGTCTGATTTGTCTTTTAATATGATATGATATATAATATATTATATTATAGACG
1 AACGTGGTCTGATTTGTC-TTT-ATA-GATATGATATATAATATATTATATTATAGACG
581701 AACGTGGTCTGATTTGTC-TT-TA-ATATGATATATAATATATTATATTATAGA
1 AACGTGGTCTGATTTGTCTTTATAGATATGATATATAATATATTATATTATAGA
581752 TAATAAAGGT
Statistics
Matches: 51, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
53 29 0.57
55 2 0.04
57 2 0.04
59 18 0.35
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.45
Consensus pattern (56 bp):
AACGTGGTCTGATTTGTCTTTATAGATATGATATATAATATATTATATTATAGACG
Found at i:582522 original size:29 final size:29
Alignment explanation
Indices: 582486--582558 Score: 110
Period size: 29 Copynumber: 2.5 Consensus size: 29
582476 TGTCCACCCT
*
582486 AAAATTTTATTTATGCTCATTTCATTAGA
1 AAAATTTTATTTATGCTCATCTCATTAGA
*
582515 AAAATTTTATTTATGCTCATCTCATTAGT
1 AAAATTTTATTTATGCTCATCTCATTAGA
*
582544 AAATTTTTATGTTAT
1 AAAATTTTAT-TTAT
582559 TAATAAACAT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 36 0.90
30 4 0.10
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.51
Consensus pattern (29 bp):
AAAATTTTATTTATGCTCATCTCATTAGA
Found at i:584007 original size:17 final size:17
Alignment explanation
Indices: 583985--584033 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
583975 TAAATTTTTA
583985 TTTTTTGAAACATATAG
1 TTTTTTGAAACATATAG
* * *
584002 TTTTTT-AAAAAAATTG
1 TTTTTTGAAACATATAG
*
584018 GTTTTTGAAACATATA
1 TTTTTTGAAACATATA
584034 TAATATATAG
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
16 12 0.50
17 12 0.50
ACGTcount: A:0.39, C:0.04, G:0.10, T:0.47
Consensus pattern (17 bp):
TTTTTTGAAACATATAG
Found at i:584107 original size:39 final size:38
Alignment explanation
Indices: 584020--584304 Score: 315
Period size: 37 Copynumber: 7.6 Consensus size: 38
584010 AAAAATTGGT
584020 TTTTGAAAC--ATATATAATATATAGTTTTTGAAAACA
1 TTTTGAAACATATATATAATATATAGTTTTTGAAAACA
*
584056 TTTTGAAA-ATATATATATTATATAGTTTTTGAAAACA
1 TTTTGAAACATATATATAATATATAGTTTTTGAAAACA
584093 TTTTGAAAACATATATATAATATATAGTTTTTGAAAACA
1 TTTTG-AAACATATATATAATATATAGTTTTTGAAAACA
584132 TTTTGAAAACATATATATAATATATAGGTTTTTGAAAACA
1 TTTTG-AAACATATATATAATATATA-GTTTTTGAAAACA
* * * **
584172 TTTTTG-AAGATAAATATATTATATAG-TTTTGAAATTA
1 -TTTTGAAACATATATATAATATATAGTTTTTGAAAACA
* *
584209 TTTTTGAAA-ATGTATATAATATATA-TTTTTGAAAATAA
1 -TTTTGAAACATATATATAATATATAGTTTTTGAAAA-CA
* *
584247 TTTTGAAA-AGATATAT--TATATAG-TTTTAAAAACAA
1 TTTTGAAACATATATATAATATATAGTTTTTGAAAAC-A
584282 TTTTTGAAA-ATATAATATAATAT
1 -TTTTGAAACATAT-ATATAATAT
584305 TAATATTATT
Statistics
Matches: 217, Mismatches: 17, Indels: 27
0.83 0.07 0.10
Matches are distributed among these distances:
35 15 0.07
36 19 0.09
37 85 0.39
38 7 0.03
39 73 0.34
40 13 0.06
41 5 0.02
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (38 bp):
TTTTGAAACATATATATAATATATAGTTTTTGAAAACA
Found at i:584125 original size:76 final size:74
Alignment explanation
Indices: 584020--584304 Score: 330
Period size: 76 Copynumber: 3.8 Consensus size: 74
584010 AAAAATTGGT
* *
584020 TTTTG-AAACATATATAATATATAGTTTTTGAAAACA-TTTTGAAAATATATATATTATATAGTT
1 TTTTGAAAATATATATAATATATAG-TTTTGAAAACATTTTTGAAAATATATATAATATATAGTT
584083 TTTGAAAACA
65 TTTGAAAACA
584093 TTTTGAAAACATATATATAATATATAGTTTTTGAAAACA-TTTTGAAAACATATATATAATATAT
1 TTTTG-AAA-ATATATATAATATATAG-TTTTGAAAACATTTTTG-AAA-ATATATATAATATAT
584157 AGGTTTTTGAAAACA
61 A-GTTTTTGAAAACA
* * * ** *
584172 TTTTTGAAGATAAATATATTATATAGTTTTGAAATTATTTTTGAAAATGTATATAATATATA-TT
1 -TTTTGAAAATATATATAATATATAGTTTTGAAAACATTTTTGAAAATATATATAATATATAGTT
*
584236 TTTGAAAATAA
65 TTTGAAAA-CA
* *
584247 TTTTGAAAAGATATAT--TATATAGTTTTAAAAACAATTTTTGAAAATATAATATAATAT
1 TTTTGAAAATATATATAATATATAGTTTTGAAAAC-ATTTTTGAAAATAT-ATATAATAT
584305 TAATATTATT
Statistics
Matches: 185, Mismatches: 16, Indels: 21
0.83 0.07 0.09
Matches are distributed among these distances:
72 14 0.08
73 18 0.10
74 32 0.17
75 3 0.02
76 48 0.26
77 15 0.08
78 35 0.19
79 15 0.08
80 5 0.03
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (74 bp):
TTTTGAAAATATATATAATATATAGTTTTGAAAACATTTTTGAAAATATATATAATATATAGTTT
TTGAAAACA
Found at i:584342 original size:18 final size:18
Alignment explanation
Indices: 584321--584366 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
584311 TATTTTAACT
*
584321 TATATTATTTTTTTATTA
1 TATATTATTTATTTATTA
* *
584339 TATATTATATATTTATTT
1 TATATTATTTATTTATTA
*
584357 TATTTTATTT
1 TATATTATTT
584367 GATTCAGATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (18 bp):
TATATTATTTATTTATTA
Found at i:584344 original size:15 final size:16
Alignment explanation
Indices: 584302--584366 Score: 53
Period size: 18 Copynumber: 3.9 Consensus size: 16
584292 TATAATATAA
584302 TATTA-ATATTATTTT
1 TATTATATATTATTTT
*
584317 AACTTATATTATT-TTTT
1 TA-TTATA-TATTATTTT
584334 TATTATATATTATATATT
1 TATTATATATTAT-T-TT
* *
584352 TATTTTATTTTATTT
1 TATTATATATTATTT
584367 GATTCAGATC
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
15 5 0.12
16 10 0.25
17 8 0.20
18 17 0.43
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.68
Consensus pattern (16 bp):
TATTATATATTATTTT
Found at i:585714 original size:13 final size:12
Alignment explanation
Indices: 585688--585736 Score: 55
Period size: 12 Copynumber: 3.9 Consensus size: 12
585678 CTTTTTATTA
*
585688 TTTATTTATTTC
1 TTTATTTTTTTC
585700 TTTATTTATTTTC
1 TTTATTT-TTTTC
585713 TTTAATTTTTTAT-
1 TTT-ATTTTTT-TC
585726 TTTATTTTTTT
1 TTTATTTTTTT
585737 AAATTATTCT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
11 1 0.03
12 14 0.42
13 13 0.39
14 5 0.15
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTATTTTTTTC
Found at i:585716 original size:21 final size:20
Alignment explanation
Indices: 585685--585737 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 20
585675 ACTCTTTTTA
*
585685 TTATTTATTTATTTCTTTA-T
1 TTATTTTTTTATTT-TTTATT
585705 TTATTTTCTTTAATTTTTTATT
1 TTATTTT-TTT-ATTTTTTATT
585727 TTATTTTTTTA
1 TTATTTTTTTA
585738 AATTATTCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
20 7 0.24
21 10 0.34
22 12 0.41
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.77
Consensus pattern (20 bp):
TTATTTTTTTATTTTTTATT
Found at i:585729 original size:22 final size:21
Alignment explanation
Indices: 585681--585738 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
585671 TTCCACTCTT
*
585681 TTTA-TTATTTATTT-ATTTC
1 TTTATTTATTTTTTTAATTTC
585700 TTTATTTATTTTCTTTAATTT-
1 TTTATTTATTTT-TTTAATTTC
585721 TTTATTTTATTTTTTTAA
1 TTTA-TTTATTTTTTTAA
585739 ATTATTCTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
19 4 0.12
20 6 0.18
21 12 0.35
22 12 0.35
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTATTTATTTTTTTAATTTC
Found at i:585741 original size:22 final size:22
Alignment explanation
Indices: 585695--585738 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
585685 TTATTTATTT
585695 ATTTCTTTATTTATTTTCTTTA
1 ATTTCTTTATTTATTTTCTTTA
585717 ATTT-TTTATTTTATTTT-TTTA
1 ATTTCTTTA-TTTATTTTCTTTA
585738 A
1 A
585739 ATTATTCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (22 bp):
ATTTCTTTATTTATTTTCTTTA
Found at i:592619 original size:17 final size:17
Alignment explanation
Indices: 592599--592647 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
592589 AAGAATTTTT
592599 GTTTTTTGAAACATATA
1 GTTTTTTGAAACATATA
*
592616 GTTTTTT-AAA-AAATCA
1 GTTTTTTGAAACATAT-A
592632 G-TTTTTGAAACATATA
1 GTTTTTTGAAACATATA
592648 TATTATATAG
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
15 8 0.30
16 9 0.33
17 10 0.37
ACGTcount: A:0.39, C:0.06, G:0.10, T:0.45
Consensus pattern (17 bp):
GTTTTTTGAAACATATA
Found at i:592721 original size:39 final size:39
Alignment explanation
Indices: 592634--592962 Score: 425
Period size: 39 Copynumber: 8.8 Consensus size: 39
592624 AAAAATCAGT
592634 TTTTG-AAACATATATAT--TATATAGTTTTTGAAAACA
1 TTTTGAAAACATATATATAATATATAGTTTTTGAAAACA
* *
592670 TTTTG-AAA-ATATATATATTATATTGTTTTTGAAAACA
1 TTTTGAAAACATATATATAATATATAGTTTTTGAAAACA
592707 TTTTGAAAACATATATATAATATATAGTTTTTGAAAACA
1 TTTTGAAAACATATATATAATATATAGTTTTTGAAAACA
* *
592746 TTTT-AAAA-ATATATATAATATATAGTTTTCGAAAAAA
1 TTTTGAAAACATATATATAATATATAGTTTTTGAAAACA
* * *
592783 ATTTGAAAACATATATATAATATATAGTTTTTCAAAA-T
1 TTTTGAAAACATATATATAATATATAGTTTTTGAAAACA
*
592821 TTTTGAAAACATATTTATAATATATAGTTTTTGAAAACA
1 TTTTGAAAACATATATATAATATATAGTTTTTGAAAACA
592860 TTTTGAAAACATATATATAATATATAGTTTTTGAAAACA
1 TTTTGAAAACATATATATAATATATAGTTTTTGAAAACA
* * * * * *
592899 TTTT-TAAAGATAAATATATTATACAG-TTTTGAAAATA
1 TTTTGAAAACATATATATAATATATAGTTTTTGAAAACA
592936 TTTTTG-AAA-ATATATAT--TATATAGTTT
1 -TTTTGAAAACATATATATAATATATAGTTT
592963 GAAATACAAT
Statistics
Matches: 261, Mismatches: 22, Indels: 20
0.86 0.07 0.07
Matches are distributed among these distances:
35 14 0.05
36 10 0.04
37 70 0.27
38 69 0.26
39 98 0.38
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (39 bp):
TTTTGAAAACATATATATAATATATAGTTTTTGAAAACA
Found at i:592723 original size:76 final size:76
Alignment explanation
Indices: 592634--592994 Score: 440
Period size: 76 Copynumber: 4.8 Consensus size: 76
592624 AAAAATCAGT
*
592634 TTTTG-AAACATATATAT--TATATAGTTTTTGAAAACATTTTGAAAATATATATATTATATTGT
1 TTTTGAAAACATATATATAATATATAGTTTTTGAAAACATTTTGAAAATATATATATTATATAGT
592696 TTTTGAAAACA
66 TTTTGAAAACA
* *
592707 TTTTGAAAACATATATATAATATATAGTTTTTGAAAACATTTTAAAAATATATATAATATATAGT
1 TTTTGAAAACATATATATAATATATAGTTTTTGAAAACATTTTGAAAATATATATATTATATAGT
* *
592772 TTTCGAAAAAA
66 TTTTGAAAACA
* * * * *
592783 ATTTGAAAACATATATATAATATATAGTTTTTCAAAA-TTTTTGAAAACATATTTATAATATATA
1 TTTTGAAAACATATATATAATATATAGTTTTTGAAAACATTTTG-AAA-ATATATATATTATATA
592847 GTTTTTGAAAACA
64 GTTTTTGAAAACA
* * *
592860 TTTTGAAAACATATATATAATATATAGTTTTTGAAAACATTTTTAAAGATAAATATATTATACAG
1 TTTTGAAAACATATATATAATATATAGTTTTTGAAAACATTTTGAAA-ATATATATATTATATAG
*
592925 -TTTTGAAAATA
65 TTTTTGAAAACA
*
592936 TTTTTG-AAA-ATATATAT--TATATAG--TTTGAAATACAATTTTTTAAAATATA-ATATTATA
1 -TTTTGAAAACATATATATAATATATAGTTTTTGAAA-AC-A-TTTTGAAAATATATATATTATA
592994 T
62 T
592995 TAATATTATT
Statistics
Matches: 254, Mismatches: 24, Indels: 21
0.85 0.08 0.07
Matches are distributed among these distances:
71 7 0.03
72 10 0.04
73 17 0.07
74 20 0.08
75 12 0.05
76 102 0.40
77 82 0.32
78 4 0.02
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (76 bp):
TTTTGAAAACATATATATAATATATAGTTTTTGAAAACATTTTGAAAATATATATATTATATAGT
TTTTGAAAACA
Found at i:592756 original size:28 final size:28
Alignment explanation
Indices: 592707--592760 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
592697 TTTGAAAACA
*
592707 TTTTGAAAACATATATATAATATATAGT
1 TTTTGAAAACATATATAAAATATATAGT
*
592735 TTTTGAAAACAT-TTTAAAAATATATA
1 TTTTGAAAACATATAT-AAAATATATA
592761 TAATATATAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 2 0.09
28 21 0.91
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.43
Consensus pattern (28 bp):
TTTTGAAAACATATATAAAATATATAGT
Found at i:592873 original size:28 final size:28
Alignment explanation
Indices: 592820--592874 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
592810 TTTTTCAAAA
* *
592820 TTTTTGAAAACATATTTATAATATATAG
1 TTTTTGAAAACATATTTAAAACATATAG
592848 TTTTTGAAAACAT-TTTGAAAACATATA
1 TTTTTGAAAACATATTT-AAAACATATA
592875 TATAATATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 3 0.12
28 21 0.88
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (28 bp):
TTTTTGAAAACATATTTAAAACATATAG
Found at i:592985 original size:34 final size:34
Alignment explanation
Indices: 592633--592993 Score: 106
Period size: 37 Copynumber: 9.6 Consensus size: 34
592623 AAAAAATCAG
* *
592633 TTTTTGAAACATATATATTATATAGTTTTTGAAAACA
1 TTTTTGAAA-A-ATATATTATACAG-TTTTGAAAAAA
** *
592670 -TTTTGAAAATATATATATTATATTGTTTTTGAAAACA
1 TTTTTG-AAA-A-ATATATTATACAG-TTTTGAAAAAA
* *
592707 -TTTTGAAAACATATATATAATATATAGTTTTTGAAAACA
1 TTTTTG-AAA-A-ATATAT--TATACAG-TTTTGAAAAAA
* *
592746 -TTTTAAAAATATATATAATATATAGTTTTCGAAAAAA
1 TTTTTGAAAA-ATATAT--TATACAGTTTT-GAAAAAA
* * **
592783 -ATTTGAAAACATATATATAATATATAGTTTT-TCAAAA
1 TTTTTG-AAA-A-ATATAT--TATACAGTTTTGAAAAAA
* *
592820 TTTTTGAAAACATATTTATAATATATAGTTTTTGAAAACA
1 TTTTTGAAAA-ATA--TAT--TATACAG-TTTTGAAAAAA
* *
592860 -TTTTGAAAACATATATATAATATATAGTTTTTGAAAACA
1 TTTTTG-AAA-A-ATATAT--TATACAG-TTTTGAAAAAA
* *
592899 TTTTTAAAGATAAATATATTATACAGTTTTGAAAATA
1 TTTTT---GAAAAATATATTATACAGTTTTGAAAAAA
*
592936 TTTTTGAAAATATATATTATATAG-TTTGAAATACAA
1 TTTTTGAAAA-ATATATTATACAGTTTTGAAA-A-AA
*
592972 TTTTTTAAAATATAATATTATA
1 TTTTTGAAAA-AT-ATATTATA
592994 TTAATATTAT
Statistics
Matches: 280, Mismatches: 23, Indels: 42
0.81 0.07 0.12
Matches are distributed among these distances:
34 11 0.04
35 13 0.05
36 26 0.09
37 102 0.36
38 28 0.10
39 76 0.27
40 16 0.06
41 5 0.02
42 2 0.01
43 1 0.00
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (34 bp):
TTTTTGAAAAATATATTATACAGTTTTGAAAAAA
Found at i:599092 original size:46 final size:46
Alignment explanation
Indices: 599040--599337 Score: 362
Period size: 46 Copynumber: 6.5 Consensus size: 46
599030 TCAGTTATGT
* *
599040 CGTTCATACATTTTAGTTATGGCATCCTTTCATGTCTTAATGCATC
1 CGTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATC
* * ** * *
599086 TGTTCATGCCTTTTAGTTATATCATCCTTTCATGCCTTAGTGCATT
1 CGTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATC
* * * * *
599132 CGTTCATGCACTTTAATCAAGGCATCCTTTCATGCCTTAATGAATC
1 CGTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATC
* * * ** *
599178 CATTCATGCATTTTAGTTATGGCATCCTTTAATTCCTTGGTACATC
1 CGTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATC
* *
599224 CGTTCATGCACTTTAATTATGGCATCCTTTCATGCCTTAATGCATC
1 CGTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATC
* *
599270 CATTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAGTGCATC
1 CGTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATC
* * *
599316 TGTTCATGCACTTTAATTATGG
1 CGTTCATGCATTTTAGTTATGG
599338 ATTCGATTTA
Statistics
Matches: 206, Mismatches: 46, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
46 206 1.00
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.42
Consensus pattern (46 bp):
CGTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATC
Found at i:599204 original size:26 final size:25
Alignment explanation
Indices: 599175--599304 Score: 82
Period size: 26 Copynumber: 5.5 Consensus size: 25
599165 GCCTTAATGA
*
599175 ATCCATTCATGCATTTTAGTTATGGC
1 ATCCTTTCATGCA-TTTAGTTATGGC
* * * *
599201 ATCCTTTAATTC-CTT-GGTA---C
1 ATCCTTTCATGCATTTAGTTATGGC
* *
599221 ATCCGTTCATGCACTTTAATTATGGC
1 ATCCTTTCATGCA-TTTAGTTATGGC
*
599247 ATCCTTTCATGC-CTTA---AT-GC
1 ATCCTTTCATGCATTTAGTTATGGC
*
599267 ATCCATTCATGCATTTTAGTTATGGC
1 ATCCTTTCATGCA-TTTAGTTATGGC
599293 ATCCTTTCATGC
1 ATCCTTTCATGC
599305 CTTAGTGCAT
Statistics
Matches: 76, Mismatches: 16, Indels: 24
0.66 0.14 0.21
Matches are distributed among these distances:
20 23 0.30
21 2 0.03
22 5 0.07
23 5 0.07
24 5 0.07
25 2 0.03
26 34 0.45
ACGTcount: A:0.22, C:0.24, G:0.13, T:0.42
Consensus pattern (25 bp):
ATCCTTTCATGCATTTAGTTATGGC
Found at i:599270 original size:20 final size:20
Alignment explanation
Indices: 599245--599324 Score: 63
Period size: 20 Copynumber: 3.7 Consensus size: 20
599235 TTTAATTATG
599245 GCATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
* *
599265 GCATCCATTCATGCATTTTAGTTAT
1 GCATCCTTTCATGC--CTTA---AT
*
599290 GGCATCCTTTCATGCCTTAGT
1 -GCATCCTTTCATGCCTTAAT
599311 GCAT-CTGTTCATGC
1 GCATCCT-TTCATGC
599325 ACTTTAATTA
Statistics
Matches: 48, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
19 2 0.04
20 24 0.50
21 1 0.02
22 3 0.06
24 3 0.06
25 2 0.04
26 13 0.27
ACGTcount: A:0.19, C:0.26, G:0.15, T:0.40
Consensus pattern (20 bp):
GCATCCTTTCATGCCTTAAT
Found at i:599333 original size:92 final size:92
Alignment explanation
Indices: 599041--599337 Score: 425
Period size: 92 Copynumber: 3.2 Consensus size: 92
599031 CAGTTATGTC
* * * * ** *
599041 GTTCATACATTTTAGTTATGGCATCCTTTCATGTCTTAATGCATCTGTTCATGCCTTTTAGTTAT
1 GTTCATGCACTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCATTCATGCATTTTAGTTAT
**
599106 ATCATCCTTTCATGCCTTAGTGCAT-T
66 GGCATCCTTTCATGCCTTAGTGCATCT
* * *
599132 CGTTCATGCACTTTAATCAAGGCATCCTTTCATGCCTTAATGAATCCATTCATGCATTTTAGTTA
1 -GTTCATGCACTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCATTCATGCATTTTAGTTA
* * * * *
599197 TGGCATCCTTTAATTCCTTGGTACATCC
65 TGGCATCCTTTCATGCCTTAGTGCATCT
599225 GTTCATGCACTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCATTCATGCATTTTAGTTAT
1 GTTCATGCACTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCATTCATGCATTTTAGTTAT
599290 GGCATCCTTTCATGCCTTAGTGCATCT
66 GGCATCCTTTCATGCCTTAGTGCATCT
599317 GTTCATGCACTTTAATTATGG
1 GTTCATGCACTTTAATTATGG
599338 ATTCGATTTA
Statistics
Matches: 179, Mismatches: 25, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
92 179 1.00
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.42
Consensus pattern (92 bp):
GTTCATGCACTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCATTCATGCATTTTAGTTAT
GGCATCCTTTCATGCCTTAGTGCATCT
Found at i:608110 original size:22 final size:23
Alignment explanation
Indices: 608061--608111 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
608051 ATTCCCCTGT
*
608061 GGGGGGAATCGGTTCCCCTTTAA
1 GGGGGGAATCGGTTCCCCTTCAA
*
608084 AGGGGGAATCGGTT-CCC-TCAA
1 GGGGGGAATCGGTTCCCCTTCAA
608105 GGGGGGA
1 GGGGGGA
608112 TCAATTCCCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 9 0.36
22 3 0.12
23 13 0.52
ACGTcount: A:0.20, C:0.20, G:0.41, T:0.20
Consensus pattern (23 bp):
GGGGGGAATCGGTTCCCCTTCAA
Found at i:614506 original size:22 final size:22
Alignment explanation
Indices: 614479--614525 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
614469 ATTAATAACT
*
614479 ATTCATTA-ATTTCAGTTATGTC
1 ATTCA-TACATTTCAGTTATGAC
*
614501 ATTCATACATTTTAGTTATGAC
1 ATTCATACATTTCAGTTATGAC
614523 ATT
1 ATT
614526 ATTTCATGCC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 2 0.09
22 20 0.91
ACGTcount: A:0.30, C:0.13, G:0.09, T:0.49
Consensus pattern (22 bp):
ATTCATACATTTCAGTTATGAC
Found at i:614558 original size:46 final size:46
Alignment explanation
Indices: 614502--614836 Score: 393
Period size: 46 Copynumber: 7.3 Consensus size: 46
614492 AGTTATGTCA
* * * ** *
614502 TTCATACATTTTAGTTATGACATTATTTCATGCCTTAATGCATTCG
1 TTCATGCACTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCG
* * *
614548 TTCATGCATTTTAGTTATGGAATCCTTTCATGCC-TAAGTGCATCCA
1 TTCATGCACTTTAGTTATGGCATCCTTTCATGCCTTAA-TGCATCCG
* * *
614594 TTCATGCACTTTAATTATGGCATCCTTTCATACCTTATTGCATCCG
1 TTCATGCACTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCG
* * *
614640 TTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAGTGCATCTG
1 TTCATGCACTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCG
* * * * *
614686 TTCATGCACATTAATTATGGCATCATTTCATGCCTTAATGCATGCA
1 TTCATGCACTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCG
* * * * *
614732 TTCATGCATTTTAGTTATTGTATCCTTTCATGCTTTAGTGCATCCG
1 TTCATGCACTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCG
* * * *
614778 TTCATGCACTTTGGTTATGGCATCCTTTCATGACTTAGTGCATCAG
1 TTCATGCACTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCG
614824 TTCATGCACTTTA
1 TTCATGCACTTTA
614837 ATTCTGGATT
Statistics
Matches: 243, Mismatches: 44, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
45 3 0.01
46 238 0.98
47 2 0.01
ACGTcount: A:0.22, C:0.21, G:0.14, T:0.42
Consensus pattern (46 bp):
TTCATGCACTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCG
Done.