Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008151.1 Hibiscus syriacus cultivar Beakdansim tig00110717_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: 219606
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:160043 original size:18 final size:17
Alignment explanation
Indices: 160002--160044 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
159992 GGTAAAAGGG
*
160002 AAAAATAAAATAAATAA
1 AAAAATAAAATAAAGAA
*
160019 AATAAATAAGATAAAGGAA
1 AA-AAATAAAATAAA-GAA
160038 AAAAATA
1 AAAAATA
160045 GTAAAGTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 2 0.09
18 16 0.73
19 4 0.18
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.16
Consensus pattern (17 bp):
AAAAATAAAATAAAGAA
Found at i:160090 original size:2 final size:2
Alignment explanation
Indices: 160083--160111 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
160073 GAAAAAGGAA
160083 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
160112 CATCAAAGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:160414 original size:2 final size:2
Alignment explanation
Indices: 160374--160400 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
160364 ATAATTAAGA
160374 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
160401 ATAATAGGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:160514 original size:2 final size:2
Alignment explanation
Indices: 160507--160561 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
160497 TATTAAAGAA
160507 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
160549 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
160562 ATAATAATAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:160580 original size:18 final size:17
Alignment explanation
Indices: 160559--160601 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
160549 ATATATATAT
160559 ATAATAATAATAACATAA
1 ATAATAATAATAA-ATAA
* *
160577 ATAATAAAAATAAATGA
1 ATAATAATAATAAATAA
160594 ATAA-AATA
1 ATAATAATA
160602 TCCATATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 3 0.14
17 7 0.32
18 12 0.55
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATAA
Found at i:160598 original size:14 final size:13
Alignment explanation
Indices: 160561--160599 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
160551 ATATATATAT
160561 AATAATAATAACATA
1 AATAATAA-AA-ATA
160576 AATAATAAAAATA
1 AATAATAAAAATA
160589 AATGAATAAAA
1 AAT-AATAAAA
160600 TATCCATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.26
14 9 0.39
15 8 0.35
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (13 bp):
AATAATAAAAATA
Found at i:161689 original size:23 final size:21
Alignment explanation
Indices: 161654--161697 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
161644 ATAATTATTT
161654 AAAAAATTAAATAAAAATATAA
1 AAAAAATTAAATAAAAA-ATAA
*
161676 AAAAATATTTAATAAAAAATAA
1 AAAAA-ATTAAATAAAAAATAA
161698 TTTTTTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (21 bp):
AAAAAATTAAATAAAAAATAA
Found at i:162744 original size:43 final size:43
Alignment explanation
Indices: 162688--162998 Score: 263
Period size: 43 Copynumber: 7.3 Consensus size: 43
162678 GGTAACAAAA
** **
162688 AAACGCCGCAATAGGTAAAGATATACAGCGGCGTTTGTCCAAC
1 AAACGCCGCAATAGGTATTGATATTTAGCGGCGTTTGTCCAAC
* * * * * *
162731 AAACGCCGTAATAGGTGTTGATATTTAGCGACATTTTTCCCAC
1 AAACGCCGCAATAGGTATTGATATTTAGCGGCGTTTGTCCAAC
* * * *
162774 AAATGCTGCAATAGGTTTTGAGATTTAGCGGCGTTTGTCCAAC
1 AAACGCCGCAATAGGTATTGATATTTAGCGGCGTTTGTCCAAC
* *
162817 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTTCC-AC
1 AAACGCCGCAATAGGTATTGATATTTAGCGGCG-TTTGTCCAAC
* * * *
162860 AAACGGCGCAATAGGTCTTGAGATTTAGCGGCGTTT-T-GACAC
1 AAACGCCGCAATAGGTATTGATATTTAGCGGCGTTTGTCCA-AC
* * ** *
162902 AAACGCCGCAATAGGTCTTGAGATTTAGCGATGTTTTTCTC-AC
1 AAACGCCGCAATAGGTATTGATATTTAGCGGCGTTTGTC-CAAC
* * * * * **
162945 AAACGCCGCAAAAGATCTTG-TATATAGCGGCGTTTTTTAGAAC
1 AAACGCCGCAATAGGTATTGATATTTAGCGGCG-TTTGTCCAAC
162988 AAACGCCGCAA
1 AAACGCCGCAA
162999 AATGTCATAT
Statistics
Matches: 220, Mismatches: 40, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
41 1 0.00
42 46 0.21
43 167 0.76
44 6 0.03
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.28
Consensus pattern (43 bp):
AAACGCCGCAATAGGTATTGATATTTAGCGGCGTTTGTCCAAC
Found at i:162812 original size:86 final size:86
Alignment explanation
Indices: 162714--162998 Score: 344
Period size: 86 Copynumber: 3.3 Consensus size: 86
162704 AAAGATATAC
* * *
162714 AGCGGCGTTTGTCCAACAAACGCCGTAATAGGTGTTGATATTTAGCGACATTTTTCCCACAAA-T
1 AGCGGCGTTTGTCCAACAAACGCCGCAATAGGTGTTGATATTTAGCGACGTTTTTCCCACAAACG
*
162778 GCTGCAATAGGTTTTGAGATTT
66 GC-GCAATAGGTCTTGAGATTT
* *
162800 AGCGGCGTTTGTCCAACAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTTCCACAAACG
1 AGCGGCGTTTGTCCAACAAACGCCGCAATAGGTGTTGATATTTAGCGACGTTTTTCCCACAAACG
162865 GCGCAATAGGTCTTGAGATTT
66 GCGCAATAGGTCTTGAGATTT
* * * * *
162886 AGCGGCGTTT-T-GACACAAACGCCGCAATAGGTCTTGAGATTTAGCGATGTTTTTCTCACAAAC
1 AGCGGCGTTTGTCCA-ACAAACGCCGCAATAGGTGTTGATATTTAGCGACGTTTTTCCCACAAAC
* * * * *
162949 GCCGCAAAAGATCTTG-TATAT
65 GGCGCAATAGGTCTTGAGATTT
* **
162970 AGCGGCGTTTTTTAGAACAAACGCCGCAA
1 AGCGGCG-TTTGTCCAACAAACGCCGCAA
162999 AATGTCATAT
Statistics
Matches: 176, Mismatches: 18, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
84 11 0.06
85 60 0.34
86 101 0.57
87 4 0.02
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (86 bp):
AGCGGCGTTTGTCCAACAAACGCCGCAATAGGTGTTGATATTTAGCGACGTTTTTCCCACAAACG
GCGCAATAGGTCTTGAGATTT
Found at i:162990 original size:128 final size:129
Alignment explanation
Indices: 162707--162998 Score: 338
Period size: 128 Copynumber: 2.3 Consensus size: 129
162697 AATAGGTAAA
* * * * * * * *
162707 GATATACAGCGGCGTTTGTCCAACAAACGCCGTAATAGGTGTTGATATTTAGCGACATTTTTCCC
1 GATATATAGCGGCGTTTTTTCAACAAACGCCGCAATAGGTCTTGAGATTTAGCGACAGTTTTCAC
* * * * * * *
162772 ACAAATGCTGCAATAGGTTTTGAGATTTAGCGGCGTTTGTCCAACAAACGCCGCAATAGGTGTT
66 ACAAACGCCGCAATAGGTCTTGAGATTTAGCGACGTTTGTCCAACAAACGCCGCAAAAGATCTT
* * * * *
162836 GATATTTAGCGGCGTTTTTTCCACAAACGGCGCAATAGGTCTTGAGATTTAGCGGC-GTTTTGAC
1 GATATATAGCGGCGTTTTTTCAACAAACGCCGCAATAGGTCTTGAGATTTAGCGACAGTTTTCAC
* *
162900 ACAAACGCCGCAATAGGTCTTGAGATTTAGCGATGTTTTTCTC-ACAAACGCCGCAAAAGATCTT
66 ACAAACGCCGCAATAGGTCTTGAGATTTAGCGACGTTTGTC-CAACAAACGCCGCAAAAGATCTT
*
162964 G-TATATAGCGGCGTTTTTTAGAACAAACGCCGCAA
1 GATATATAGCGGCGTTTTTT-CAACAAACGCCGCAA
162999 AATGTCATAT
Statistics
Matches: 135, Mismatches: 26, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
127 17 0.13
128 71 0.53
129 47 0.35
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (129 bp):
GATATATAGCGGCGTTTTTTCAACAAACGCCGCAATAGGTCTTGAGATTTAGCGACAGTTTTCAC
ACAAACGCCGCAATAGGTCTTGAGATTTAGCGACGTTTGTCCAACAAACGCCGCAAAAGATCTT
Found at i:163035 original size:43 final size:43
Alignment explanation
Indices: 162945--163039 Score: 104
Period size: 43 Copynumber: 2.2 Consensus size: 43
162935 TTTTTCTCAC
* * * *
162945 AAACGCCGCAAAAGATCTTGTATATAGCGGCGTTTTTTAGAAC
1 AAACGCCGCAAAAGATCATATATATAGCGGCGTTTTTAAGAAA
* *
162988 AAACGCCGCAAAATG-TCATATCTATATCGGCG-TTTTAAGATAA
1 AAACGCCGCAAAA-GATCATATATATAGCGGCGTTTTTAAGA-AA
163031 AAACGCCGC
1 AAACGCCGC
163040 TAATTACCTC
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
42 7 0.16
43 36 0.82
44 1 0.02
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (43 bp):
AAACGCCGCAAAAGATCATATATATAGCGGCGTTTTTAAGAAA
Found at i:163991 original size:74 final size:74
Alignment explanation
Indices: 163904--164050 Score: 285
Period size: 74 Copynumber: 2.0 Consensus size: 74
163894 GTTTCGAAAG
163904 AAAAAAACACATAATTCATAAACAAGTATAATCCTCGATTTTAAAAGATATAGTAATTTACAGAC
1 AAAAAAACACATAATTCATAAACAAGTATAATCCTCGATTTTAAAAGATATAGTAATTTACAGAC
163969 ATTGTAGAA
66 ATTGTAGAA
*
163978 AAAAAAACACATAATTCATAAACAAGTATAATCCTCGATTTTAAAAGATATAGTAATTTACGGAC
1 AAAAAAACACATAATTCATAAACAAGTATAATCCTCGATTTTAAAAGATATAGTAATTTACAGAC
164043 ATTGTAGA
66 ATTGTAGA
164051 CAGATACATA
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 72 1.00
ACGTcount: A:0.49, C:0.12, G:0.10, T:0.29
Consensus pattern (74 bp):
AAAAAAACACATAATTCATAAACAAGTATAATCCTCGATTTTAAAAGATATAGTAATTTACAGAC
ATTGTAGAA
Found at i:185212 original size:6 final size:6
Alignment explanation
Indices: 185201--185225 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
185191 CTATATTGCA
185201 TTTCCT TTTCCT TTTCCT TTTCCT T
1 TTTCCT TTTCCT TTTCCT TTTCCT T
185226 GCTCTGGGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTCCT
Found at i:185581 original size:21 final size:20
Alignment explanation
Indices: 185543--185581 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
185533 GAAGGAAAAG
* *
185543 ATGAAATGAGGTAGAAGACA
1 ATGAAATGAGGAAAAAGACA
185563 ATGAAGATGAGGAAAAAGA
1 ATGAA-ATGAGGAAAAAGA
185582 AAAGAGTGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.54, C:0.03, G:0.31, T:0.13
Consensus pattern (20 bp):
ATGAAATGAGGAAAAAGACA
Found at i:189654 original size:3 final size:3
Alignment explanation
Indices: 189639--189681 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
189629 AGTTAAAAAA
* *
189639 TAT TAT TA- AAT TAT TAT TAT TAT TAT TAT TAT TAG TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
189682 AGTGTATTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 1 0.03
3 34 0.97
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:191589 original size:2 final size:2
Alignment explanation
Indices: 191582--191618 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
191572 GTTAAACGTG
191582 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
191619 TTATTTATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:191735 original size:97 final size:99
Alignment explanation
Indices: 191607--191825 Score: 356
Period size: 97 Copynumber: 2.2 Consensus size: 99
191597 ATATATATAT
* * **
191607 ATATATATATATTTATTTATTTAATGTGTCTTGGAAACTGATTTTTTGTTC-ATATATATATATT
1 ATATATATATATATATTTGTTTAACATGTCTTGGAAACTGATTTTTTGTTCAATATATATATATT
191671 TGTTTAACATGTCTTGGAAACTGATT-TTTGTTC
66 TGTTTAACATGTCTTGGAAACTGATTCTTTGTTC
191704 ATATATATATATATATTTGTTTAACATGTCTTGGAAACTGATTTTTTGTTCATATATATATATAT
1 ATATATATATATATATTTGTTTAACATGTCTTGGAAACTGATTTTTTGTTCA-ATATATATATAT
191769 TTGTTTAACATGTCTTGGAAACTGATTCTTTGTTC
65 TTGTTTAACATGTCTTGGAAACTGATTCTTTGTTC
*
191804 --ATATACATATATATTTGTTTAA
1 ATATATATATATATATTTGTTTAA
191826 TGTGTCTTAG
Statistics
Matches: 114, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
97 47 0.41
98 21 0.18
99 39 0.34
100 7 0.06
ACGTcount: A:0.30, C:0.08, G:0.11, T:0.51
Consensus pattern (99 bp):
ATATATATATATATATTTGTTTAACATGTCTTGGAAACTGATTTTTTGTTCAATATATATATATT
TGTTTAACATGTCTTGGAAACTGATTCTTTGTTC
Found at i:191833 original size:49 final size:49
Alignment explanation
Indices: 191609--191825 Score: 341
Period size: 49 Copynumber: 4.4 Consensus size: 49
191599 ATATATATAT
* * **
191609 ATATATATATTTATTTATTTAATGTGTCTTGGAAACTGATTTTTTGTTC
1 ATATATATATATATTTGTTTAACATGTCTTGGAAACTGATTTTTTGTTC
191658 --ATATATATATATTTGTTTAACATGTCTTGGAAACTGA-TTTTTGTTC
1 ATATATATATATATTTGTTTAACATGTCTTGGAAACTGATTTTTTGTTC
191704 ATATATATATATATATTTGTTTAACATGTCTTGGAAACTGATTTTTTGTTC
1 --ATATATATATATATTTGTTTAACATGTCTTGGAAACTGATTTTTTGTTC
*
191755 ATATATATATATATTTGTTTAACATGTCTTGGAAACTGATTCTTTGTTC
1 ATATATATATATATTTGTTTAACATGTCTTGGAAACTGATTTTTTGTTC
*
191804 ATATACATATATATTTGTTTAA
1 ATATATATATATATTTGTTTAA
191826 TGTGTCTTAG
Statistics
Matches: 157, Mismatches: 6, Indels: 10
0.91 0.03 0.06
Matches are distributed among these distances:
46 9 0.06
47 33 0.21
49 69 0.44
50 37 0.24
51 9 0.06
ACGTcount: A:0.29, C:0.08, G:0.12, T:0.51
Consensus pattern (49 bp):
ATATATATATATATTTGTTTAACATGTCTTGGAAACTGATTTTTTGTTC
Found at i:191930 original size:181 final size:185
Alignment explanation
Indices: 191709--192060 Score: 525
Period size: 181 Copynumber: 1.9 Consensus size: 185
191699 TGTTCATATA
* *
191709 TATATATATATTTGTTTAACATGTCTTGGAAACTGATTTTTTGTTCATATATATATATATTTGTT
1 TATATATATATTTATTTAACATGTCTTGGAAACTGATTTTTTGTTCATATATATATATATTTATT
**
191774 TAACATGTCTTGGAAACTGA-TTCTTTGTTC-ATATACATATATA-TTTGTTTAATGTGTCTTAG
66 TAACATGTCTTGGAAACTGATTTCTTTGTTCAATATACATATATATTTTGTTTAACATGTCTTAG
*
191836 GAAGAATAGCCAT-TATTTATTTGTTTAATATATAGCTTAGTTTATTTGTTAAACG
131 GAAGAATAGCCATAT-TTTATTTGTTTAACATATAGCTTAGTTTATTTGTTAAACG
**
191891 TATATATAT-TTTATTTAATGTGTCTTGGAAACTGATTTTTTGTTCATATATATATATATTTATT
1 TATATATATATTTATTTAACATGTCTTGGAAACTGATTTTTTGTTCATATATATATATATTTATT
** * * *
191955 TAATGTGTCTTGTAAACTGATTTTTTTGTTCATATATATATATATATTTTGTTTAACATGTCTTA
66 TAACATGTCTTGGAAACTGATTTCTTTGTTCA-ATATACATATATATTTTGTTTAACATGTCTTA
* *
192020 GGAAGAATAGGCATATTTTATTTGTTTAACGTATAGCTTAG
130 GGAAGAATAGCCATATTTTATTTGTTTAACATATAGCTTAG
192061 CTGGATATAT
Statistics
Matches: 151, Mismatches: 14, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
181 68 0.45
182 18 0.12
184 12 0.08
185 52 0.34
186 1 0.01
ACGTcount: A:0.30, C:0.07, G:0.13, T:0.50
Consensus pattern (185 bp):
TATATATATATTTATTTAACATGTCTTGGAAACTGATTTTTTGTTCATATATATATATATTTATT
TAACATGTCTTGGAAACTGATTTCTTTGTTCAATATACATATATATTTTGTTTAACATGTCTTAG
GAAGAATAGCCATATTTTATTTGTTTAACATATAGCTTAGTTTATTTGTTAAACG
Found at i:191980 original size:50 final size:49
Alignment explanation
Indices: 191891--191999 Score: 193
Period size: 49 Copynumber: 2.2 Consensus size: 49
191881 TTGTTAAACG
191891 TATATATAT-TTTATTTAATGTGTCTTGGAAACTGATTTTTTGTTCATA
1 TATATATATATTTATTTAATGTGTCTTGGAAACTGATTTTTTGTTCATA
*
191939 TATATATATATTTATTTAATGTGTCTTGTAAACTGATTTTTTTGTTCATA
1 TATATATATATTTATTTAATGTGTCTTGGAAACTGA-TTTTTTGTTCATA
191989 TATATATATAT
1 TATATATATAT
192000 ATTTTGTTTA
Statistics
Matches: 58, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
48 9 0.16
49 25 0.43
50 24 0.41
ACGTcount: A:0.29, C:0.06, G:0.10, T:0.55
Consensus pattern (49 bp):
TATATATATATTTATTTAATGTGTCTTGGAAACTGATTTTTTGTTCATA
Found at i:192208 original size:24 final size:24
Alignment explanation
Indices: 192181--192226 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
192171 ATATTCTTTA
192181 TATCATTTATTTAATAAGTATAGT
1 TATCATTTATTTAATAAGTATAGT
192205 TATCATTTATTTAATAAGTATA
1 TATCATTTATTTAATAAGTATA
192227 ATGTTCCATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.50
Consensus pattern (24 bp):
TATCATTTATTTAATAAGTATAGT
Found at i:203992 original size:33 final size:32
Alignment explanation
Indices: 203951--204047 Score: 117
Period size: 31 Copynumber: 3.0 Consensus size: 32
203941 TATGCTTGAA
203951 GAAAAAAAAATAACAAATAAAAAGATGAAAAAT
1 GAAAAAAAAATAA-AAATAAAAAGATGAAAAAT
* * *
203984 G-AAAAAAAATGAAAAGAAAAAAATGAAAAAT
1 GAAAAAAAAATAAAAATAAAAAGATGAAAAAT
204015 GAAAAAAGAAATGAAAAAATAAAAAGA-GAAAAA
1 GAAAAAA-AAAT--AAAAATAAAAAGATGAAAAA
204048 GGAGGGTTTG
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
31 18 0.33
32 15 0.28
33 5 0.09
34 6 0.11
35 10 0.19
ACGTcount: A:0.77, C:0.01, G:0.12, T:0.09
Consensus pattern (32 bp):
GAAAAAAAAATAAAAATAAAAAGATGAAAAAT
Found at i:205163 original size:136 final size:136
Alignment explanation
Indices: 204918--205255 Score: 544
Period size: 136 Copynumber: 2.5 Consensus size: 136
204908 GGTGAACCAG
204918 CATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATG
1 CATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATG
* *
204983 AGAAGAGCTTGTTCGACCTATCACTCGATTCACTACATTTTGAATCAGTGACAGCTTGCTTGAAG
66 AGAAGAGCTTGTTCGACCTATCACTCGATTCACTACATTTTGAATCAGTGACACCTCGCTTGAAG
*
205048 GATCAG
131 GATCAA
*
205054 TATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATG
1 CATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATG
*
205119 AGAAGAGCTTGTTCGACCTATCACTCGATTCA-TAACATTTTGAATCAGTGACACCTCGCTTGAG
66 AGAAGAGCTTGTTCGACCTATCACTCGATTCACT-ACATTTTGAATCAGTGACACCTCGCTTGAA
205183 GGATCAA
130 GGATCAA
* * * *
205190 CATTTCCAGTGAAGAGTTCATAATGAGAAGAACTCGTCCTA-A-A-GGAG-A-AAGTTCATAATG
1 CATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATG
205250 AGAAGA
66 AGAAGA
205256 ACTCGTCCTA
Statistics
Matches: 191, Mismatches: 10, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
131 18 0.09
132 1 0.01
133 4 0.02
134 1 0.01
135 2 0.01
136 165 0.86
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.25
Consensus pattern (136 bp):
CATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATG
AGAAGAGCTTGTTCGACCTATCACTCGATTCACTACATTTTGAATCAGTGACACCTCGCTTGAAG
GATCAA
Found at i:205250 original size:35 final size:35
Alignment explanation
Indices: 205204--205288 Score: 170
Period size: 35 Copynumber: 2.4 Consensus size: 35
205194 TCCAGTGAAG
205204 AGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAA
1 AGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAA
205239 AGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAA
1 AGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAA
205274 AGTTCATAATGAGAA
1 AGTTCATAATGAGAA
205289 AAACATGTTC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 50 1.00
ACGTcount: A:0.44, C:0.13, G:0.22, T:0.21
Consensus pattern (35 bp):
AGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAA
Found at i:205421 original size:105 final size:105
Alignment explanation
Indices: 205235--205469 Score: 445
Period size: 105 Copynumber: 2.2 Consensus size: 105
205225 GTCCTAAAGG
205235 AGAA-AGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCATAATGAGAAAAACATGTTC
1 AGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCATAATGAGAAAAACATGTTC
205299 TTTCTAAGTCCACCGCAAAAGGATTTGGATCAACATTTCC
66 TTTCTAAGTCCACCGCAAAAGGATTTGGATCAACATTTCC
205339 AGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCATAATGAGAAAAACATGTTC
1 AGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCATAATGAGAAAAACATGTTC
*
205404 TTTCTAAGTCCACCGCAAAAGGATTTGGATCAACGTTTCC
66 TTTCTAAGTCCACCGCAAAAGGATTTGGATCAACATTTCC
*
205444 AAAAGAGTTCATAATGAGAAGAACTC
1 AGAAGAGTTCATAATGAGAAGAACTC
205470 ATCCACGAGA
Statistics
Matches: 128, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
104 4 0.03
105 124 0.97
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.24
Consensus pattern (105 bp):
AGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCATAATGAGAAAAACATGTTC
TTTCTAAGTCCACCGCAAAAGGATTTGGATCAACATTTCC
Found at i:205655 original size:3 final size:3
Alignment explanation
Indices: 205640--205682 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
205630 AGTTAAAAAA
* *
205640 TAT TAT TA- AAT TAT TAT TAT TAT TAT TAT TAT TAG TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
205683 AGTGTATTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 1 0.03
3 34 0.97
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:207042 original size:14 final size:16
Alignment explanation
Indices: 207018--207050 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
207008 GTTTATTTTG
207018 TTTTAAGTATTT-TAT
1 TTTTAAGTATTTATAT
207033 TTTTAA-TATTTATAT
1 TTTTAAGTATTTATAT
207048 TTT
1 TTT
207051 AGTCACACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (16 bp):
TTTTAAGTATTTATAT
Found at i:207605 original size:2 final size:2
Alignment explanation
Indices: 207598--207626 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
207588 GTTAAACGTG
207598 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
207627 TTATTTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:207738 original size:100 final size:100
Alignment explanation
Indices: 207615--207849 Score: 393
Period size: 100 Copynumber: 2.4 Consensus size: 100
207605 ATATATATAT
* *
207615 ATATATATATATTTATTTATTTAATGTGTCTTGGAAACTGATTTTTTGTTCATATATATATATAT
1 ATATATATATATATATTTGTTTAATGTGTCTTGGAAACTGATTTTTTGTTCATATATATATATAT
*
207680 TTGTTTAACATGTCTTGGAAACTGATTTTTTGTTC
66 TTGTTTAACATGTCTTGGAAACTGATTCTTTGTTC
**
207715 ATATATATATATATATTTGTTTAACATGTCTTGGAAACTGATTTTTTGTTCATATATATATATAT
1 ATATATATATATATATTTGTTTAATGTGTCTTGGAAACTGATTTTTTGTTCATATATATATATAT
207780 TTGTTTAACATGTCTTGGAAACTGATTCTTTGTTC
66 TTGTTTAACATGTCTTGGAAACTGATTCTTTGTTC
*
207815 --ATATACATATATATTTGTTTAATGTGTCTTAGGAA
1 ATATATATATATATATTTGTTTAATGTGTCTT-GGAA
207850 GAATAGCCAT
Statistics
Matches: 126, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
98 27 0.21
99 4 0.03
100 95 0.75
ACGTcount: A:0.29, C:0.08, G:0.12, T:0.51
Consensus pattern (100 bp):
ATATATATATATATATTTGTTTAATGTGTCTTGGAAACTGATTTTTTGTTCATATATATATATAT
TTGTTTAACATGTCTTGGAAACTGATTCTTTGTTC
Found at i:207844 original size:49 final size:49
Alignment explanation
Indices: 207617--207836 Score: 368
Period size: 49 Copynumber: 4.4 Consensus size: 49
207607 ATATATATAT
* * **
207617 ATATATATATTTATTTATTTAATGTGTCTTGGAAACTGATTTTTTGTTC
1 ATATATATATATATTTGTTTAACATGTCTTGGAAACTGATTTTTTGTTC
207666 ATATATATATATATTTGTTTAACATGTCTTGGAAACTGATTTTTTGTTC
1 ATATATATATATATTTGTTTAACATGTCTTGGAAACTGATTTTTTGTTC
207715 ATATATATATATATATTTGTTTAACATGTCTTGGAAACTGATTTTTTGTTC
1 --ATATATATATATATTTGTTTAACATGTCTTGGAAACTGATTTTTTGTTC
*
207766 ATATATATATATATTTGTTTAACATGTCTTGGAAACTGATTCTTTGTTC
1 ATATATATATATATTTGTTTAACATGTCTTGGAAACTGATTTTTTGTTC
*
207815 ATATACATATATATTTGTTTAA
1 ATATATATATATATTTGTTTAA
207837 TGTGTCTTAG
Statistics
Matches: 163, Mismatches: 6, Indels: 4
0.94 0.03 0.02
Matches are distributed among these distances:
49 114 0.70
51 49 0.30
ACGTcount: A:0.30, C:0.08, G:0.11, T:0.51
Consensus pattern (49 bp):
ATATATATATATATTTGTTTAACATGTCTTGGAAACTGATTTTTTGTTC
Found at i:207969 original size:55 final size:56
Alignment explanation
Indices: 207902--208024 Score: 207
Period size: 55 Copynumber: 2.2 Consensus size: 56
207892 TTGTTAAACG
207902 TATATATATATTTTTATTTAATGTGTCTTGGAAACTGA-TTTTTTGTTCATATATA
1 TATATATATATTTTTATTTAATGTGTCTTGGAAACTGATTTTTTTGTTCATATATA
*
207957 TATATATATA--TTTATTTAATGTGTCTTGTAAACTGATTTTTTTTGTTCATATATA
1 TATATATATATTTTTATTTAATGTGTCTTGGAAACTGA-TTTTTTTGTTCATATATA
208012 TATATATATATTT
1 TATATATATATTT
208025 GTTTAACATG
Statistics
Matches: 63, Mismatches: 1, Indels: 6
0.90 0.01 0.09
Matches are distributed among these distances:
53 25 0.40
55 37 0.59
57 1 0.02
ACGTcount: A:0.30, C:0.05, G:0.09, T:0.56
Consensus pattern (56 bp):
TATATATATATTTTTATTTAATGTGTCTTGGAAACTGATTTTTTTGTTCATATATA
Found at i:207972 original size:53 final size:54
Alignment explanation
Indices: 207902--208030 Score: 215
Period size: 53 Copynumber: 2.4 Consensus size: 54
207892 TTGTTAAACG
*
207902 TATATATATATTTTTATTTAATGTGTCTTGGAAACTGA-TTTTTTGTTCATATA
1 TATATATATATATTTATTTAATGTGTCTTGGAAACTGATTTTTTTGTTCATATA
*
207955 TATATATATATATTTATTTAATGTGTCTTGTAAACTGATTTTTTTTGTTCATATA
1 TATATATATATATTTATTTAATGTGTCTTGGAAACTGA-TTTTTTTGTTCATATA
*
208010 TATATATATATATTTGTTTAA
1 TATATATATATATTTATTTAA
208031 CATGTCTTAG
Statistics
Matches: 71, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
53 36 0.51
55 35 0.49
ACGTcount: A:0.30, C:0.05, G:0.09, T:0.56
Consensus pattern (54 bp):
TATATATATATATTTATTTAATGTGTCTTGGAAACTGATTTTTTTGTTCATATA
Found at i:208228 original size:24 final size:24
Alignment explanation
Indices: 208201--208246 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
208191 ATATTCTTTA
208201 TATCATTTATTTAATAAGTATAGT
1 TATCATTTATTTAATAAGTATAGT
208225 TATCATTTATTTAATAAGTATA
1 TATCATTTATTTAATAAGTATA
208247 ATGTTCCATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.50
Consensus pattern (24 bp):
TATCATTTATTTAATAAGTATAGT
Found at i:213297 original size:2 final size:2
Alignment explanation
Indices: 213290--213318 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
213280 TGTTTTTGTT
213290 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
213319 TTACTAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:213392 original size:28 final size:29
Alignment explanation
Indices: 213331--213392 Score: 67
Period size: 28 Copynumber: 2.2 Consensus size: 29
213321 ACTAAATTTC
*
213331 ATTTATTTATTTTTTATCTATTTTCTTATT
1 ATTT-TTTATTTTTTATCTATTTACTTATT
*
213361 -TTTTTTCTTTTTTA-CATATTTACTT-TT
1 ATTTTTTATTTTTTATC-TATTTACTTATT
213388 ATTTT
1 ATTTT
213393 ATCTAACATA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
27 3 0.11
28 22 0.79
29 3 0.11
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.74
Consensus pattern (29 bp):
ATTTTTTATTTTTTATCTATTTACTTATT
Found at i:217253 original size:105 final size:106
Alignment explanation
Indices: 217096--218370 Score: 1941
Period size: 105 Copynumber: 12.2 Consensus size: 106
217086 AAAAGTTGTA
* * * * * * * *
217096 TGTCAACAAACAACTTTCCATTTCATCAGAGTCTATTTCAACTTCGCAGCGAAGAAAATTGGACT
1 TGTCAATAAACAACTTCCCAATT--TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACT
*
217161 CCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGT
64 CCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
* * * * *
217204 TGTCAATAAACAATTTTCCACTTTTAGAGCCAA-TTCAATTTCACAGCGAAGGATATTGGACTCC
1 TGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
217268 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
*
217309 TGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCA-AGCGAAGGATATTAGACTCC
1 TGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
* *
217373 AGACAACCCATGTTCAACTTCACGAC---GGGACCGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
217411 TGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
1 TGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
* * *
217476 AGACAATGCATGTTCAACATCACGACGAAGGGACCGCT-GT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
* * * * *
217516 TGTTAACAAACAACTTCTCAATTTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCC
1 TGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
217581 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
* *
217622 TGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACGGCGAAGGATA-TGGACTCC
1 TGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
*
217686 AGACAACGCAAGTTCAACTTCACGACGAATGGACCGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
* *
217727 TGTC-ATAAACAACTTCCCAATTTTAGAGCCAATTTCAACTTCACATCGAAGGATATTGGACTCC
1 TGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
217791 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCT-GT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
* * * **
217831 TGTTAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAATGAAGGATATTGGACTCC
1 TGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
217896 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
* * *
217937 TGTCAATAAACAATTTCCCAATTTCA-AGCCAATTTCAACTTCACAGCGAAGGATAATGGACTCA
1 TGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
218001 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
* *
218042 TGTCAATAAAC-ACTTCCCAATTTTAGAGCCAATTTCAACTTCACAACGAA-GATATTGGACTCC
1 TGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
* *
218105 AGAC-ACACAAGTTCAACTTCACGACAAAGGGACCGCTGG-
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
* * * *
218144 TGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAAATTGGACTCC
1 TGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
*
218209 AGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
* * * * *
218250 TGTCAATAAACAATTTCCCAATTTCAGAGTCAATTTCAACTTCATAGCGAAGGATATCGGACTCA
1 TGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
* *
218315 AGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCCGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
218356 TGTCAAT-AACAACTT
1 TGTCAATAAACAACTT
218371 TCAACTTCAC
Statistics
Matches: 1070, Mismatches: 83, Indels: 31
0.90 0.07 0.03
Matches are distributed among these distances:
102 66 0.06
103 112 0.10
104 95 0.09
105 574 0.54
106 203 0.19
108 20 0.02
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
TGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
Found at i:217703 original size:313 final size:314
Alignment explanation
Indices: 217096--218370 Score: 1958
Period size: 313 Copynumber: 4.1 Consensus size: 314
217086 AAAAGTTGTA
* * * * * * * *
217096 TGTCAACAAACAACTTTCCATTTCATCAGAGTCTATTTCAACTTCGCAGCGAAGAAAATTGGACT
1 TGTCAATAAACAACTTCCCAATT--TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACT
* * * *
217161 CCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAA-TTTTCCAC
64 CCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCT-GTTGTCAACAAACAACTTCT-CAA
* * *
217225 TTTTAGAGCCAA-TTCAATTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTC
127 TTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTC
217289 ACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCA-
192 ACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCAC
* * * *
217353 AGCGAAGGATATTAGACTCCAGACAACCCATGTTCAACTTCACGAC-GGGACCGCTGGT
257 AGCGAAGGATA-TGGACTCAAGACAACGCAAGTTCAACTTCACGACAGGGACCGCTGGT
217411 TGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
1 TGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
* * * *
217476 AGACAATGCATGTTCAACATCACGACGAAGGGACCGCTGTTGTTAACAAACAACTTCTCAATTTC
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGTTGTCAACAAACAACTTCTCAATTTC
*
217541 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
131 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* *
217606 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACGGCG
196 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCG
* *
217671 AAGGATATGGACTCCAGACAACGCAAGTTCAACTTCACGACGAATGGACCGCTGGT
261 AAGGATATGGACTCAAGACAACGCAAGTTCAACTTCACGAC--AGGGACCGCTGGT
* *
217727 TGTC-ATAAACAACTTCCCAATTTTAGAGCCAATTTCAACTTCACATCGAAGGATATTGGACTCC
1 TGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
*
217791 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGTTGTTAACAAACAACTTCTCAATTTC
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGTTGTCAACAAACAACTTCTCAATTTC
*
217856 AGAGCCAATTTCAACTTCACAATGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
131 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
217921 CGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCA-AGCCAATTTCAACTTCACAGCG
196 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCG
217985 AAGGATAATGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
261 AAGGAT-ATGGACTCAAGACAACGCAAGTTCAACTTCACGAC--AGGGACCGCTGGT
* *
218042 TGTCAATAAAC-ACTTCCCAATTTTAGAGCCAATTTCAACTTCACAACGAA-GATATTGGACTCC
1 TGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
* * *
218105 AGAC-ACACAAGTTCAACTTCACGACAAAGGGACCGCTGGTGTCAACAAACAACTTCTCAATTTC
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGTTGTCAACAAACAACTTCTCAATTTC
*
218169 AGAGCCAATTTCAACTTCACAACGAAGGAAATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
131 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* * * *
218234 TGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGTCAATTTCAACTTCATAGCG
196 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCG
* *
218299 AAGGATATCGGACTCAAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCCGGT
261 AAGGATAT-GGACTCAAGACAACGCAAGTTCAACTTCACGAC--AGGGACCGCTGGT
218356 TGTCAAT-AACAACTT
1 TGTCAATAAACAACTT
218371 TCAACTTCAC
Statistics
Matches: 899, Mismatches: 50, Indels: 23
0.92 0.05 0.02
Matches are distributed among these distances:
312 25 0.03
313 383 0.43
314 137 0.15
315 333 0.37
316 21 0.02
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (314 bp):
TGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGTTGTCAACAAACAACTTCTCAATTTC
AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
CGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCG
AAGGATATGGACTCAAGACAACGCAAGTTCAACTTCACGACAGGGACCGCTGGT
Found at i:218731 original size:81 final size:83
Alignment explanation
Indices: 218592--218966 Score: 307
Period size: 81 Copynumber: 4.5 Consensus size: 83
218582 AAAGACATTT
* * * * *
218592 GAGTTCGACTACGCTCAGC-TCAACGGCATATCATTTGCAGCATAGCTTAAATCGAGAAGGATTG
1 GAGTTCGACTACGCTCAGCTTCAA-GGCACATCATTTGCAGCATAACTTAAGTCAAGAAGGATTA
218656 TCTG-C-C-AAAGACCCCC
65 TCTGCCACTAAAGACCCCC
* * * *
218672 GAGTTCGATTACACTCAGCTTCAAGGGCACGTCATTTGCAGCATAACTTAAGTCAAGAAGGGTTA
1 GAGTTCGACTACGCTCAGCTTCAA-GGCACATCATTTGCAGCATAACTTAAGTCAAGAAGGATTA
**
218737 TCTGCCAACTAAAGACCTTC
65 TCTGCC-ACTAAAGACCCCC
* * * * *
218757 GAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTTAAGGCTAGAAGGGTTTA
1 GAGTTCGACTACGCTCAGCTTCAAGGCACATCATTTGCAGCATAACTTAAGTCAAGAA-GGATTA
* * **
218822 TCTGTCACCAAAAGACCTTC
65 TCTGCCA-CTAAAGACCCCC
* * * *** * * *
218842 GAGTTCGACTACGTTCA-CTCCAAGGCACATCATTTGCGGCATAACGCCAG-CTAGGAGGGTTAT
1 GAGTTCGACTACGCTCAGCTTCAAGGCACATCATTTGCAGCATAACTTAAGTCAAGAAGGATTAT
* **
218905 CTGCCAAC-AAAGATCTTC
66 CTGCC-ACTAAAGACCCCC
* * * *
218923 AAGTTCGACTACGCTCATC-TCTTAGGCACATCATTTACAGCATA
1 GAGTTCGACTACGCTCAGCTTC-AAGGCACATCATTTGCAGCATA
218967 GCCCCAGGCA
Statistics
Matches: 247, Mismatches: 38, Indels: 18
0.82 0.13 0.06
Matches are distributed among these distances:
80 17 0.07
81 66 0.27
82 32 0.13
83 6 0.02
84 60 0.24
85 66 0.27
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.25
Consensus pattern (83 bp):
GAGTTCGACTACGCTCAGCTTCAAGGCACATCATTTGCAGCATAACTTAAGTCAAGAAGGATTAT
CTGCCACTAAAGACCCCC
Found at i:218823 original size:85 final size:83
Alignment explanation
Indices: 218582--218966 Score: 395
Period size: 85 Copynumber: 4.7 Consensus size: 83
218572 CCAAAAAAAA
* * * * ** *
218582 AAAGACATTTGAGTTCGACTACGCTCAGCT-CAACGGCATATCATTTGCAGCATAGCTTAAATCG
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTGCAGCATAACTTAAGGCT
* *
218646 AGAAGGATTGTCTG-C--C
65 AGAAGGGTTATCTGCCAAC
** * * * * * *
218662 AAAGACCCCCGAGTTCGATTACACTCAGCTTCAAGGGCACGTCATTTGCAGCATAACTTAAGTCA
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTGCAGCATAACTTAAGGCT
218727 AGAAGGGTTATCTGCCAAC
65 AGAAGGGTTATCTGCCAAC
*
218746 TAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTTAAGGCT
1 -AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGGCT
* *
218811 AGAAGGGTTTATCTGTCACC
65 AGAAGGG-TTATCTGCCAAC
* * ***
218831 AAAAGACCTTCGAGTTCGACTACGTTCA-CTCCAAGGCACATCATTTGCGGCATAACGCCA-GCT
1 -AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGGCT
*
218894 AGGAGGGTTATCTGCCAAC
65 AGAAGGGTTATCTGCCAAC
* * * ** *
218913 AAAGATCTTCAAGTTCGACTACGCTCATCTCTTAGGCACATCATTTACAGCATA
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATA
218967 GCCCCAGGCA
Statistics
Matches: 256, Mismatches: 42, Indels: 12
0.83 0.14 0.04
Matches are distributed among these distances:
80 24 0.09
81 64 0.25
82 33 0.13
83 9 0.04
84 61 0.24
85 65 0.25
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (83 bp):
AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGGCTA
GAAGGGTTATCTGCCAAC
Found at i:219010 original size:82 final size:80
Alignment explanation
Indices: 218671--219012 Score: 290
Period size: 84 Copynumber: 4.1 Consensus size: 80
218661 CAAAGACCCC
* * * * * *** * *
218671 CGAGTTCGATTACACTCAGCTTCAAGGGCACGTCATTTGCAGCATAACTTAAGTCAAGAAGGGTT
1 CGAGTTCGACTACGCTCA-CTCCAA-GGCACATCATTTACAGCATAACCCCAGGCTAGAAGGGTT
* *
218736 ATCTGCCAACTAAAGACCTT
64 ATCTGTCAA--AAAGA-TTT
***
218756 CGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTTAAGGCTAGAAGGGTTT
1 CGAGTTCGACTACGCTCA-CTCCAAGGCACATCATTTACAGCATAACCCCAGGCTAGAAGGG-TT
*
218821 ATCTGTCACCAAAAGACCTT
64 ATCTGTCA--AAAAGA-TTT
* * * * *
218841 CGAGTTCGACTACGTTCACTCCAAGGCACATCATTTGCGGCATAACGCCA-GCTAGGAGGGTTAT
1 CGAGTTCGACTACGCTCACTCCAAGGCACATCATTTACAGCATAACCCCAGGCTAGAAGGGTTAT
*
218905 CTGCCAACAAAGATCTT
66 CTGTCAA-AAAGAT-TT
* ** * * *
218922 CAAGTTCGACTACGCTCATCTCTTAGGCACATCATTTACAGCATAGCCCCAGGCAAGAAGGGCTA
1 CGAGTTCGACTACGCTCA-CTCCAAGGCACATCATTTACAGCATAACCCCAGGCTAGAAGGGTTA
*
218987 TCTGTCAAGAAGATTGT
65 TCTGTCAAAAAGATT-T
219004 CGAGTTCGA
1 CGAGTTCGA
219013 TTTCAGTCAG
Statistics
Matches: 218, Mismatches: 31, Indels: 19
0.81 0.12 0.07
Matches are distributed among these distances:
80 1 0.00
81 24 0.11
82 49 0.22
83 26 0.12
84 60 0.28
85 57 0.26
87 1 0.00
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (80 bp):
CGAGTTCGACTACGCTCACTCCAAGGCACATCATTTACAGCATAACCCCAGGCTAGAAGGGTTAT
CTGTCAAAAAGATTT
Done.