Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000216.1 Hibiscus syriacus cultivar Beakdansim tig00000384_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: 227886
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
File 2 of 2
Found at i:173573 original size:21 final size:21
Alignment explanation
Indices: 173543--173590 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
173533 TAATTTTCAA
*
173543 ACATTATTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
173564 ACATTGTTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
173585 ACATTG
1 ACATTG
173591 CAATATTAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (21 bp):
ACATTGTTGCACCTAATTTTG
Found at i:174188 original size:37 final size:37
Alignment explanation
Indices: 174118--174392 Score: 233
Period size: 38 Copynumber: 7.3 Consensus size: 37
174108 AATATATATA
* *
174118 TATATAATATA-A--TTTTGAAAACATTTTTAAAAAC
1 TATATAATATATAGTTTTTTAAAACATTTTTGAAAAC
*
174152 TATATAATATATAGTTTTTTCAAACATTTTTGAAAAC
1 TATATAATATATAGTTTTTTAAAACATTTTTGAAAAC
* * * *
174189 ATAAATAATATATAGTTTTTGAAAATA-TTTTGAATATATA
1 -TATATAATATATAGTTTTTTAAAACATTTTTGAA-A-A-C
* * *
174229 TATATATATATATAATATAATTTTTGAAAACA-TTTTAAAAATA
1 TATATA-ATATAT-A-GT--TTTTT-AAAACATTTTTGAAAA-C
* * *
174272 TATATAATATATCGTTTTTGAAAACATTCTTGAAAAC
1 TATATAATATATAGTTTTTTAAAACATTTTTGAAAAC
* *
174309 ATATATAATATATAGTTTTTGAAAATA-TTTTGAAAA-
1 -TATATAATATATAGTTTTTTAAAACATTTTTGAAAAC
*
174345 TATAT-ATAATATAGTTTTTGAAAACATTTTTGAAAAC
1 TATATAAT-ATATAGTTTTTTAAAACATTTTTGAAAAC
174382 TATATAATATA
1 TATATAATATA
174393 GTTTGGAAAA
Statistics
Matches: 199, Mismatches: 23, Indels: 35
0.77 0.09 0.14
Matches are distributed among these distances:
34 13 0.07
35 23 0.12
36 9 0.05
37 48 0.24
38 60 0.30
39 6 0.03
40 7 0.04
41 1 0.01
42 7 0.04
43 9 0.05
44 5 0.03
45 11 0.06
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (37 bp):
TATATAATATATAGTTTTTTAAAACATTTTTGAAAAC
Found at i:174257 original size:45 final size:46
Alignment explanation
Indices: 174193--174283 Score: 132
Period size: 45 Copynumber: 2.0 Consensus size: 46
174183 GAAAACATAA
* * *
174193 ATAATATATAGTTTTTGAAAATATTTTGAATATATATATATATATAT
1 ATAATATATAGTTTTTGAAAACATTTTAAAAATATATATA-ATATAT
174240 ATAATATA-A-TTTTTGAAAACATTTTAAAAATATATATAATATAT
1 ATAATATATAGTTTTTGAAAACATTTTAAAAATATATATAATATAT
174284 CGTTTTTGAA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
44 6 0.15
45 26 0.63
46 1 0.02
47 8 0.20
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.46
Consensus pattern (46 bp):
ATAATATATAGTTTTTGAAAACATTTTAAAAATATATATAATATAT
Found at i:174280 original size:35 final size:35
Alignment explanation
Indices: 174234--174426 Score: 221
Period size: 35 Copynumber: 5.4 Consensus size: 35
174224 ATATATATAT
*
174234 ATATATATAATATAATTTTTGAAAACATTTTAAAA
1 ATATATATAATATAATTTTTGAAAACATTTTGAAA
*
174269 ATATATATAATATATCGTTTTTGAAAACATTCTTGAAA
1 ATATATATAATATA--ATTTTTGAAAACATT-TTGAAA
* *
174307 ACATATATAATATATAGTTTTTGAAAATATTTTGAAA
1 ATATATATAATATA-A-TTTTTGAAAACATTTTGAAA
*
174344 ATATATATAATATAGTTTTTGAAAACATTTTTGAAA
1 ATATATATAATATAATTTTTGAAAACA-TTTTGAAA
* * * *
174380 A-CTATATAATAT-AGTTTGGAAAACATTTT-AAT
1 ATATATATAATATAATTTTTGAAAACATTTTGAAA
174412 ATATATATATATATA
1 ATATATATA-ATATA
174427 TATATATATA
Statistics
Matches: 135, Mismatches: 15, Indels: 16
0.81 0.09 0.10
Matches are distributed among these distances:
32 3 0.02
33 10 0.07
34 14 0.10
35 35 0.26
36 9 0.07
37 33 0.24
38 31 0.23
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (35 bp):
ATATATATAATATAATTTTTGAAAACATTTTGAAA
Found at i:174298 original size:120 final size:119
Alignment explanation
Indices: 174109--174357 Score: 403
Period size: 120 Copynumber: 2.1 Consensus size: 119
174099 TTTTTTGAAA
* **
174109 ATATATATATATATAATATAATTTTGAAAACATTTTTAAAAACTATATAATATATAGTTTTTTCA
1 ATATATATATATATAATATAATTTTGAAAACATTTTTAAAAAATATATAATATATAGTTTTTGAA
* *
174174 AACATTTTTGAAAACATAAATAATATATAGTTTTTGAAAATATTTTGAATATAT
66 AACATTCTTGAAAACATAAATAATATATAGTTTTTGAAAATATTTTGAAAATAT
*
174228 ATATATATATATATAATATAATTTTTGAAAACA-TTTTAAAAATATATATAATATATCGTTTTTG
1 ATATATATATATATAATATAA-TTTTGAAAACATTTTTAAAAA-ATATATAATATATAGTTTTTG
*
174292 AAAACATTCTTGAAAACATATATAATATATAGTTTTTGAAAATATTTTGAAAATAT
64 AAAACATTCTTGAAAACATAAATAATATATAGTTTTTGAAAATATTTTGAAAATAT
174348 ATATA-ATATA
1 ATATATATATA
174358 GTTTTTGAAA
Statistics
Matches: 121, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
119 35 0.29
120 86 0.71
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (119 bp):
ATATATATATATATAATATAATTTTGAAAACATTTTTAAAAAATATATAATATATAGTTTTTGAA
AACATTCTTGAAAACATAAATAATATATAGTTTTTGAAAATATTTTGAAAATAT
Found at i:174481 original size:2 final size:2
Alignment explanation
Indices: 174410--174466 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
174400 AAACATTTTA
174410 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
174452 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
174467 GTTTTAAAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:174487 original size:3 final size:3
Alignment explanation
Indices: 174479--174538 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
174469 TTTAAAAATA
174479 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
174527 TAT TAT TAT TAT
1 TAT TAT TAT TAT
174539 ATGCTTTATT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:175806 original size:10 final size:10
Alignment explanation
Indices: 175793--175827 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
175783 TTTCCCACCT
175793 TTTTATTCTA
1 TTTTATTCTA
175803 TTTTATTCTA
1 TTTTATTCTA
175813 TTTTA-T-TA
1 TTTTATTCTA
175821 TTTTATT
1 TTTTATT
175828 TTTTTCTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 7 0.29
9 2 0.08
10 15 0.62
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTTATTCTA
Found at i:179441 original size:33 final size:33
Alignment explanation
Indices: 179404--179469 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
179394 TTGCCTCTGT
*
179404 TGTGGATGTAGCCATAACTGACTGCAATTTTGA
1 TGTGGATGTAGCCACAACTGACTGCAATTTTGA
*
179437 TGTGGATGTAGCCACAACTGACTGTAATTTTGA
1 TGTGGATGTAGCCACAACTGACTGCAATTTTGA
179470 AACCCAGCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.33
Consensus pattern (33 bp):
TGTGGATGTAGCCACAACTGACTGCAATTTTGA
Found at i:184130 original size:20 final size:21
Alignment explanation
Indices: 184105--184197 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
184095 TTTTCCCAAT
*
184105 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
184125 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
184146 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
184166 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
184187 TCGCAATGCGA
1 TCGCAATGCGA
184198 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:184150 original size:41 final size:41
Alignment explanation
Indices: 184105--184197 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
184095 TTTTCCCAAT
184105 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
184146 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
184187 TCGCAATGCGA
1 TCGCAATGCGA
184198 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:184210 original size:41 final size:41
Alignment explanation
Indices: 184124--184258 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
184114 GAATAAGTAA
* *
184124 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
184165 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
184206 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
184247 TTCGCAACGCGA
1 ATCGCAACGCGA
184259 TACTGACTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:184211 original size:20 final size:20
Alignment explanation
Indices: 184186--184279 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
184176 AATTGGGAAA
*
184186 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
184206 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
184227 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
184247 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
184267 TTCGCAACGCGAT
1 ATCGCAACGCGAT
184280 TTACATAGCG
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 46 0.77
21 14 0.23
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:184826 original size:20 final size:19
Alignment explanation
Indices: 184793--184863 Score: 72
Period size: 18 Copynumber: 3.7 Consensus size: 19
184783 ATAGTTTCGA
*
184793 GAATGAAAATCGCAACGCG
1 GAATAAAAATCGCAACGCG
**
184812 GAAATAACTATCGCAACGC-
1 G-AATAAAAATCGCAACGCG
184831 GAATAAAAATCGCAACGCG
1 GAATAAAAATCGCAACGCG
* **
184850 AAACCAAAATCGCA
1 GAATAAAAATCGCA
184864 TTGCGATTTT
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
18 15 0.36
19 13 0.31
20 14 0.33
ACGTcount: A:0.46, C:0.24, G:0.18, T:0.11
Consensus pattern (19 bp):
GAATAAAAATCGCAACGCG
Found at i:184842 original size:18 final size:18
Alignment explanation
Indices: 184793--184851 Score: 73
Period size: 18 Copynumber: 3.2 Consensus size: 18
184783 ATAGTTTCGA
*
184793 GAATGAAAATCGCAACGC
1 GAATAAAAATCGCAACGC
**
184811 GGAAATAACTATCGCAACGC
1 -G-AATAAAAATCGCAACGC
184831 GAATAAAAATCGCAACGC
1 GAATAAAAATCGCAACGC
184849 GAA
1 GAA
184852 ACCAAAATCG
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
18 18 0.53
19 2 0.06
20 14 0.41
ACGTcount: A:0.46, C:0.22, G:0.20, T:0.12
Consensus pattern (18 bp):
GAATAAAAATCGCAACGC
Found at i:184881 original size:19 final size:19
Alignment explanation
Indices: 184859--185043 Score: 165
Period size: 19 Copynumber: 10.1 Consensus size: 19
184849 GAAACCAAAA
*
184859 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
184878 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
184897 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
184916 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
* *
184936 TCGCTTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
184952 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
184969 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
184983 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
185002 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
185022 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
185042 TC
1 TC
185044 AACCAAAAGA
Statistics
Matches: 136, Mismatches: 17, Indels: 26
0.76 0.09 0.15
Matches are distributed among these distances:
14 19 0.14
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 59 0.43
20 49 0.36
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:184936 original size:39 final size:38
Alignment explanation
Indices: 184859--185043 Score: 147
Period size: 33 Copynumber: 5.1 Consensus size: 38
184849 GAAACCAAAA
184859 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* *
184897 TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGC-GTTGCGATTTTCATT
* * * **
184936 TCGCTTTGCGATTGTC---T-G-GTCGCGATAGTCATT
1 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* * **
184969 TCGCGTTGCGA--TTC---TCTCGTTGCGATAGTCATT
1 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* * *
185002 TCCGCGTTGCGATTCTCATTATCTCGTTGCGATTTTCATT
1 T-CGCATTGCGATTTTCATT-TCGCGTTGCGATTTTCATT
185042 TC
1 TC
185044 AACCAAAAGA
Statistics
Matches: 122, Mismatches: 15, Indels: 19
0.78 0.10 0.12
Matches are distributed among these distances:
31 3 0.02
33 37 0.30
34 10 0.08
35 1 0.01
36 3 0.02
38 21 0.17
39 29 0.24
40 18 0.15
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (38 bp):
TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
Found at i:185020 original size:20 final size:20
Alignment explanation
Indices: 184986--185043 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
184976 GCGATTCTCT
**
184986 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
185006 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
185026 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
185044 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:187106 original size:42 final size:42
Alignment explanation
Indices: 187046--187168 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
187036 GCCCGACTCG
* * *
187046 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
187088 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
187130 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
187169 CCGATTCACA
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:187126 original size:21 final size:21
Alignment explanation
Indices: 187102--187168 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
187092 TCATTCCTCG
187102 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
187123 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
187144 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
187165 AGAG
1 AGAG
187169 CCGATTCACA
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:188542 original size:14 final size:14
Alignment explanation
Indices: 188523--188558 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
188513 ATTGTTTAAT
188523 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
188537 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
188551 TGATTTGT
1 TGATTTGT
188559 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:188783 original size:33 final size:32
Alignment explanation
Indices: 188741--188867 Score: 166
Period size: 33 Copynumber: 3.9 Consensus size: 32
188731 ATTAAATTCG
188741 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
188774 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
*
188807 CGTTGCGATTTTCATTTCGCATTGAGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
* *
188840 CGTTGTGATTTTCATTTCGTATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
188868 AGTAATTTCC
Statistics
Matches: 82, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
31 3 0.04
33 76 0.93
35 3 0.04
ACGTcount: A:0.16, C:0.20, G:0.20, T:0.44
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:188830 original size:66 final size:66
Alignment explanation
Indices: 188734--188866 Score: 221
Period size: 66 Copynumber: 2.0 Consensus size: 66
188724 ACGCGAAATT
* *
188734 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGAGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
188799 G
66 G
* * *
188800 AAATTAGCGTTGCGATTTTCATTTCGCATTGAGATTCTCTCGTTGTGATTTTCATTTCGTATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGAGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
188865 G
66 G
188866 A
1 A
188867 TAGTAATTTC
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 62 1.00
ACGTcount: A:0.17, C:0.20, G:0.20, T:0.43
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGAGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:191176 original size:12 final size:12
Alignment explanation
Indices: 191159--191183 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
191149 TCTTCGGGGA
191159 CTTTTTCTTCTT
1 CTTTTTCTTCTT
191171 CTTTTTCTTCTT
1 CTTTTTCTTCTT
191183 C
1 C
191184 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:191392 original size:24 final size:24
Alignment explanation
Indices: 191358--191411 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
191348 CTGAAACATC
* *
191358 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
191382 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
191406 ATCAAA
1 ATCAAA
191412 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:192494 original size:20 final size:20
Alignment explanation
Indices: 192469--192525 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
192459 TTCATTTGAC
192469 TATCGCAACGCGAAAATGGA
1 TATCGCAACGCGAAAATGGA
*
192489 TATCGCAACGCGAAAATGGT
1 TATCGCAACGCGAAAATGGA
*
192509 TATCGCAACGAGAAAAT
1 TATCGCAACGCGAAAAT
192526 CGCAATGCGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.18
Consensus pattern (20 bp):
TATCGCAACGCGAAAATGGA
Found at i:192581 original size:33 final size:35
Alignment explanation
Indices: 192544--192682 Score: 130
Period size: 33 Copynumber: 3.9 Consensus size: 35
192534 GAAATGAAAA
192544 TCGCATTGCGATTTTC-TCG-TTGCGATTTTCATT
1 TCGCATTGCGATTTTCTTCGATTGCGATTTTCATT
*
192577 TCGCATTGCGATTTTCATTTCGCATTGCGA-TTTC--C
1 TCGCATTGCGATTTTC--TTCG-ATTGCGATTTTCATT
192612 TCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTC--TTCG-ATTGCGATTTTCATT
*
192648 TCGCATTGCGATTTTCATTTCGCATTACGATTTTC
1 TCGCATTGCGATTTTC--TTCG-ATTGCGATTTTC
192683 GCGTTGCGAT
Statistics
Matches: 93, Mismatches: 3, Indels: 15
0.84 0.03 0.14
Matches are distributed among these distances:
33 41 0.44
34 4 0.04
35 3 0.03
36 6 0.06
37 4 0.04
38 35 0.38
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.47
Consensus pattern (35 bp):
TCGCATTGCGATTTTCTTCGATTGCGATTTTCATT
Found at i:192585 original size:19 final size:19
Alignment explanation
Indices: 192544--192682 Score: 190
Period size: 19 Copynumber: 7.8 Consensus size: 19
192534 GAAATGAAAA
192544 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
192560 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
192577 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
192596 TCGCATTGCGA-TTTC--C
1 TCGCATTGCGATTTTCATT
192612 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
192629 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
192648 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
192667 TCGCATTACGATTTTC
1 TCGCATTGCGATTTTC
192683 GCGTTGCGAT
Statistics
Matches: 110, Mismatches: 3, Indels: 17
0.85 0.02 0.13
Matches are distributed among these distances:
14 17 0.15
15 4 0.04
16 6 0.05
17 6 0.05
18 4 0.04
19 73 0.66
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:192600 original size:52 final size:52
Alignment explanation
Indices: 192544--192663 Score: 231
Period size: 52 Copynumber: 2.3 Consensus size: 52
192534 GAAATGAAAA
192544 TCGCATTGCGATTTTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
*
192596 TCGCATTGCGATTTCCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
192648 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
192664 ATTTCGCATT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 66 1.00
ACGTcount: A:0.13, C:0.23, G:0.17, T:0.47
Consensus pattern (52 bp):
TCGCATTGCGATTTTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
Found at i:192639 original size:71 final size:71
Alignment explanation
Indices: 192563--192711 Score: 235
Period size: 71 Copynumber: 2.1 Consensus size: 71
192553 GATTTTCTCG
* * ***
192563 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTCCTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTACGATTTCCGCGTTGCGATAGCCAT
192628 TTCGCA
66 TTCGCA
*
192634 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTACGATTTTCGCGTTGCGATAGCCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTACGATTTCCGCGTTGCGATAGCCAT
*
192699 TTCGCG
66 TTCGCA
192705 TTGCGAT
1 TTGCGAT
192712 AGTCTGTTTT
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.15, C:0.22, G:0.19, T:0.44
Consensus pattern (71 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTACGATTTCCGCGTTGCGATAGCCAT
TTCGCA
Found at i:192683 original size:52 final size:51
Alignment explanation
Indices: 192544--192711 Score: 187
Period size: 52 Copynumber: 3.2 Consensus size: 51
192534 GAAATGAAAA
* *
192544 TCGCATTGCGATTTTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGA-TTTCTCATTGCGATTTACATTTCGCATTGCGATTTTCATT
* *
192596 TCGCATTGCGATTTCCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTT-CTCATTGCGATTTACATTTCGCATTGCGATTTTCATT
* * ***
192648 TCGCATTGCGATTT-TCATTTCGCA-TTACGATTTTCGCGTTGCGATAGCCATT
1 TCGCATTGCGATTTCTCATTGCG-ATTTAC-A-TTTCGCATTGCGATTTTCATT
*
192700 TCGCGTTGCGAT
1 TCGCATTGCGAT
192712 AGTCTGTTTT
Statistics
Matches: 104, Mismatches: 8, Indels: 8
0.87 0.07 0.07
Matches are distributed among these distances:
50 9 0.09
51 5 0.05
52 90 0.87
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (51 bp):
TCGCATTGCGATTTCTCATTGCGATTTACATTTCGCATTGCGATTTTCATT
Found at i:194723 original size:19 final size:19
Alignment explanation
Indices: 194699--194765 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
194689 GAAACTTAAA
194699 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
* *
194718 ATCGCAATGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
194738 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
194757 ATCGCAACG
1 ATCGCAACG
194766 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 23 0.56
20 18 0.44
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.16
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:194734 original size:20 final size:19
Alignment explanation
Indices: 194699--194754 Score: 85
Period size: 20 Copynumber: 2.9 Consensus size: 19
194689 GAAACTTAAA
*
194699 ATCGCAACGCGAAATGACT
1 ATCGCAATGCGAAATGACT
*
194718 ATCGCAATGCGGAAATGGCT
1 ATCGCAATGC-GAAATGACT
194738 ATCGCAATGCGAAATGA
1 ATCGCAATGCGAAATGA
194755 AAATCGCAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 15 0.45
20 18 0.55
ACGTcount: A:0.36, C:0.21, G:0.25, T:0.18
Consensus pattern (19 bp):
ATCGCAATGCGAAATGACT
Found at i:194773 original size:14 final size:14
Alignment explanation
Indices: 194754--194811 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
194744 ATGCGAAATG
194754 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
194768 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
194784 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
194800 AAAATCGCAACG
1 AAAATCGCAACG
194812 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:194796 original size:32 final size:33
Alignment explanation
Indices: 194738--194816 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
194728 GGAAATGGCT
*
194738 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
194771 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
194803 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
194817 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:194845 original size:19 final size:18
Alignment explanation
Indices: 194823--194885 Score: 71
Period size: 18 Copynumber: 3.7 Consensus size: 18
194813 GAAACACAAA
194823 TCGCATTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
* *
194842 TCGCGTTGCGATTT--TG
1 TCGCATTGCGATTTCATT
194858 TCG--TTGCGATTTCATT
1 TCGCATTGCGATTTCATT
194874 TCGCATTGCGAT
1 TCGCATTGCGAT
194886 AGCCATTTCC
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
14 9 0.24
16 8 0.22
18 10 0.27
19 10 0.27
ACGTcount: A:0.13, C:0.21, G:0.22, T:0.44
Consensus pattern (18 bp):
TCGCATTGCGATTTCATT
Found at i:194904 original size:20 final size:19
Alignment explanation
Indices: 194870--194924 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
194860 GTTGCGATTT
*
194870 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
194889 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
194909 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
194925 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:195423 original size:18 final size:18
Alignment explanation
Indices: 195397--195441 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
195387 GTCGATCAGA
*
195397 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
195415 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
195433 TGATGGCTC
1 TGATGGCTC
195442 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:196784 original size:20 final size:20
Alignment explanation
Indices: 196759--196796 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
196749 AATAGTTTCT
196759 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
196779 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
196797 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:197084 original size:22 final size:22
Alignment explanation
Indices: 197059--197102 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
197049 GATTTAGATA
197059 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
197081 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
197103 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:197314 original size:20 final size:20
Alignment explanation
Indices: 197289--197382 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
197279 GATTATGTAT
197289 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
197309 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
197329 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
197350 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
197370 TATCGCATTGCGA
1 TATCGCGTTGCGA
197383 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:197383 original size:20 final size:20
Alignment explanation
Indices: 197269--197383 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
197259 CGCTTTGAAA
*
197269 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
197290 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
197310 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
197330 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
197351 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
197371 ATCGCATTGCGAT
1 ATCGCATTGCGAT
197384 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:197401 original size:21 final size:21
Alignment explanation
Indices: 197372--197464 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
197362 ATAGTCAGTA
197372 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
197393 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
197413 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
197434 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
197454 TCGCATTGCGA
1 TCGCATTGCGA
197465 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:197402 original size:41 final size:41
Alignment explanation
Indices: 197311--197445 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
197301 AAAGTCAGTA
* * * ** *
197311 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
197351 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
197393 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
197434 TCGCGTTGCGAT
1 TCGCGTTGCGAT
197446 TTACTTATTC
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
40 3 0.04
41 74 0.94
42 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:197446 original size:41 final size:41
Alignment explanation
Indices: 197372--197464 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
197362 ATAGTCAGTA
197372 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
197413 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
197454 TCGCATTGCGA
1 TCGCATTGCGA
197465 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:208243 original size:39 final size:39
Alignment explanation
Indices: 208199--208297 Score: 128
Period size: 39 Copynumber: 2.5 Consensus size: 39
208189 CAATTGCCTA
*
208199 AATCCCTAATTCCCCATTTTCATTTC-CCTCTTGCACCTC
1 AATCCCTAATTCCCCATTTTCATTTCTCCT-TCGCACCTC
* * * *
208238 GATCCCTAATTCCCCTTTTTTATTTCTCCTTCGCATCTC
1 AATCCCTAATTCCCCATTTTCATTTCTCCTTCGCACCTC
*
208277 AATCCCTAATTCACCATTTTC
1 AATCCCTAATTCCCCATTTTC
208298 CTCTTCGTTT
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
39 47 0.94
40 3 0.06
ACGTcount: A:0.18, C:0.37, G:0.03, T:0.41
Consensus pattern (39 bp):
AATCCCTAATTCCCCATTTTCATTTCTCCTTCGCACCTC
Found at i:213369 original size:39 final size:39
Alignment explanation
Indices: 213325--213423 Score: 121
Period size: 39 Copynumber: 2.5 Consensus size: 39
213315 CAATTGCCTG
213325 AATCCCTAATTTCCCATTTTCATTTC-CCTCTCGCACCCC
1 AATCCCTAATTTCCCATTTTCATTTCTCCT-TCGCACCCC
* * * * *
213364 GATCCCTAATTCCCCTTTTTCATTTCTCCTTCGCATCTC
1 AATCCCTAATTTCCCATTTTCATTTCTCCTTCGCACCCC
213403 AATCCCTAA-TTCACCATTTTC
1 AATCCCTAATTTC-CCATTTTC
213424 CTCTTTGTTT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
38 2 0.04
39 45 0.90
40 3 0.06
ACGTcount: A:0.18, C:0.39, G:0.03, T:0.39
Consensus pattern (39 bp):
AATCCCTAATTTCCCATTTTCATTTCTCCTTCGCACCCC
Found at i:214323 original size:17 final size:16
Alignment explanation
Indices: 214296--214330 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
214286 AACTTTCCTG
214296 TTCTTTTTTTTTTCTT
1 TTCTTTTTTTTTTCTT
214312 TTCTTTTCTTTTTTCTT
1 TTCTTTT-TTTTTTCTT
214329 TT
1 TT
214331 AGTTCGTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (16 bp):
TTCTTTTTTTTTTCTT
Found at i:219314 original size:21 final size:21
Alignment explanation
Indices: 219267--219335 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 21
219257 GTGGTCATGC
* *
219267 GGGACATATATGTGTTCCTTC
1 GGGACATATATGTGGTCCTTA
* * *
219288 GAGACATCTATGTGGTCTTTA
1 GGGACATATATGTGGTCCTTA
* * *
219309 GGGACATATAAGTGGTTCTTC
1 GGGACATATATGTGGTCCTTA
219330 GGGACA
1 GGGACA
219336 AATTCTATGT
Statistics
Matches: 37, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.33
Consensus pattern (21 bp):
GGGACATATATGTGGTCCTTA
Found at i:219901 original size:18 final size:17
Alignment explanation
Indices: 219878--219914 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 17
219868 AATTTTCTAA
219878 GTTTTTATAAAAGTCAAT
1 GTTTTTA-AAAAGTCAAT
219896 GTTTTTAAAAAGTCAAT
1 GTTTTTAAAAAGTCAAT
219913 GT
1 GT
219915 GACACCTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.38, C:0.05, G:0.14, T:0.43
Consensus pattern (17 bp):
GTTTTTAAAAAGTCAAT
Found at i:226147 original size:21 final size:21
Alignment explanation
Indices: 226117--226174 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
226107 TCCTTAAGGA
226117 GTGGTCCTTCGAGACATATAT
1 GTGGTCCTTCGAGACATATAT
*
226138 GTGGTTCTTC-AGGACATATAT
1 GTGGTCCTTCGA-GACATATAT
226159 GTGGTCCTTCGAGACA
1 GTGGTCCTTCGAGACA
226175 AATTTATATG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.03
21 31 0.94
22 1 0.03
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (21 bp):
GTGGTCCTTCGAGACATATAT
Done.