Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008284.1 Hibiscus syriacus cultivar Beakdansim tig00110946_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: 665325
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 4
Found at i:171 original size:24 final size:25
Alignment explanation
Indices: 143--194 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
133 CTTCTTCCTC
143 TCTTTTC-CTTCCTCTTCCTCCACT
1 TCTTTTCTCTTCCTCTTCCTCCACT
**
167 TC-TTTCTCTTCCTCTTTTTCCACT
1 TCTTTTCTCTTCCTCTTCCTCCACT
191 TCTT
1 TCTT
195 CCTCTTTCAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 4 0.17
24 19 0.79
25 1 0.04
ACGTcount: A:0.04, C:0.40, G:0.00, T:0.56
Consensus pattern (25 bp):
TCTTTTCTCTTCCTCTTCCTCCACT
Found at i:195 original size:36 final size:36
Alignment explanation
Indices: 135--219 Score: 93
Period size: 36 Copynumber: 2.3 Consensus size: 36
125 TCCGCTGTCT
*
135 TCTTCCTCTCTTTTCCTTCCTCTTCCTCCACTT-CTTTC
1 TCTTCCTCT-TTTTCCTACCTCTTCCT-C-CTTACTTTC
* *
173 TCTTCCTCTTTTTCC-ACTTCTTCCTCTTTCACTTTC
1 TCTTCCTCTTTTTCCTACCTCTTCCTCCTT-ACTTTC
209 TCTTCCTCTTT
1 TCTTCCTCTTT
220 CTCGTCAACT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
34 2 0.05
35 1 0.02
36 24 0.57
37 6 0.14
38 9 0.21
ACGTcount: A:0.04, C:0.41, G:0.00, T:0.55
Consensus pattern (36 bp):
TCTTCCTCTTTTTCCTACCTCTTCCTCCTTACTTTC
Found at i:199 original size:24 final size:24
Alignment explanation
Indices: 150--200 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
140 CTCTCTTTTC
*
150 CTTCCTCTTCCTCCACTTCTTTCT
1 CTTCCTCTTCCTCCACTTCTTCCT
**
174 CTTCCTCTTTTTCCACTTCTTCCT
1 CTTCCTCTTCCTCCACTTCTTCCT
198 CTT
1 CTT
201 TCACTTTCTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.04, C:0.43, G:0.00, T:0.53
Consensus pattern (24 bp):
CTTCCTCTTCCTCCACTTCTTCCT
Found at i:207 original size:24 final size:24
Alignment explanation
Indices: 161--207 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
151 TTCCTCTTCC
* *
161 TCCACTTCTTTCTCTTCCTCTTTT
1 TCCACTTCTTCCTCTTCCACTTTT
*
185 TCCACTTCTTCCTCTTTCACTTT
1 TCCACTTCTTCCTCTTCCACTTT
208 CTCTTCCTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.06, C:0.38, G:0.00, T:0.55
Consensus pattern (24 bp):
TCCACTTCTTCCTCTTCCACTTTT
Found at i:1281 original size:30 final size:31
Alignment explanation
Indices: 1239--1304 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
1229 ATATTTTAGT
* * *
1239 AATAAAGTATTTT-AGTACTTATTTTGATAA
1 AATAAAGTATTTTAAGCACTTACTTTGACAA
1269 AATAAA-TAATTTTAAGCACTTACTTTGACAA
1 AATAAAGT-ATTTTAAGCACTTACTTTGACAA
1300 AATAA
1 AATAA
1305 CATTATATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 1 0.03
30 11 0.35
31 19 0.61
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (31 bp):
AATAAAGTATTTTAAGCACTTACTTTGACAA
Found at i:16554 original size:2 final size:2
Alignment explanation
Indices: 16547--16580 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
16537 CACAACTGCA
16547 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
16581 TAATGAATCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18231 original size:21 final size:20
Alignment explanation
Indices: 18180--18231 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
18170 TTTTCCCAAT
*
18180 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
* * **
18200 TCGTAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGAAAA
18221 TCGCAATGCGA
1 TCGCAATGCGA
18232 TACTGACTAT
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATAAGAAAA
Found at i:18245 original size:20 final size:20
Alignment explanation
Indices: 18220--18313 Score: 100
Period size: 20 Copynumber: 4.7 Consensus size: 20
18210 AATTGGGAAA
18220 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
18240 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
18260 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
18281 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
18301 TTCGCAACGCGAT
1 ATCGCAATGCGAT
18314 TTACATAGCA
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 2 0.03
20 45 0.73
21 13 0.21
22 2 0.03
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:18878 original size:19 final size:19
Alignment explanation
Indices: 18833--18880 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
18823 TTCGAGAATG
*
18833 AAAATCGCAACGCGGAAAT
1 AAAATCGCAACGCGGAAAC
*
18852 AACTATCGCAACGC-GAAACC
1 AA-AATCGCAACGCGGAAA-C
18872 AAAATCGCA
1 AAAATCGCA
18881 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.46, C:0.27, G:0.17, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGGAAAC
Found at i:18898 original size:19 final size:19
Alignment explanation
Indices: 18876--19026 Score: 141
Period size: 19 Copynumber: 8.1 Consensus size: 19
18866 GAAACCAAAA
*
18876 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
18895 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
18914 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
18933 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
18947 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
* **
18966 TCGCGTTGCAATAGTCATT
1 TCGCGTTGCGATTTTCATT
* * *
18985 TCCGCATTGTGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
* *
19005 ATCTCATTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
19025 TC
1 TC
19027 AACCAAAAGA
Statistics
Matches: 112, Mismatches: 13, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
14 10 0.09
16 2 0.02
17 3 0.03
19 68 0.61
20 28 0.25
21 1 0.01
ACGTcount: A:0.15, C:0.23, G:0.19, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:18965 original size:52 final size:53
Alignment explanation
Indices: 18898--19001 Score: 138
Period size: 52 Copynumber: 2.0 Consensus size: 53
18888 TTTCATTTCG
** * ** *
18898 CGTTGCGATTTTCATTTCGCGTTGCGATTTTCATTT-CGCGTTGCGATTCTCT
1 CGTTGCGATAGTCATTTCGCGTTGCAATAGTCATTTCCGCATTGCGATTCTCT
*
18950 CGTTGCGATAGTCATTTCGCGTTGCAATAGTCATTTCCGCATTGTGATTCTC
1 CGTTGCGATAGTCATTTCGCGTTGCAATAGTCATTTCCGCATTGCGATTCTC
19002 ATTATCTCAT
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
52 31 0.70
53 13 0.30
ACGTcount: A:0.13, C:0.23, G:0.21, T:0.42
Consensus pattern (53 bp):
CGTTGCGATAGTCATTTCGCGTTGCAATAGTCATTTCCGCATTGCGATTCTCT
Found at i:21200 original size:21 final size:21
Alignment explanation
Indices: 21176--21284 Score: 53
Period size: 21 Copynumber: 5.2 Consensus size: 21
21166 TTATTCCTCG
21176 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** *
21197 AGAGACCACTGTCATCC-CTCA
1 AGAGTCCCCTCCCA-CCGTTCA
* * * *
21218 AGAGTCCACTCCTATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
* ** *
21239 AGAGGCCCCTATCATTCC--TCG
1 AGAGTCCCCTCCCA--CCGTTCA
21260 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
21281 AGAG
1 AGAG
21285 GCCACTGTCA
Statistics
Matches: 58, Mismatches: 24, Indels: 12
0.62 0.26 0.13
Matches are distributed among these distances:
19 2 0.03
20 1 0.02
21 52 0.90
22 2 0.03
23 1 0.02
ACGTcount: A:0.23, C:0.39, G:0.17, T:0.21
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:21222 original size:42 final size:42
Alignment explanation
Indices: 21121--21296 Score: 181
Period size: 42 Copynumber: 4.2 Consensus size: 42
21111 CCCGACTCAC
* * * * *
21121 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAATAGGCCC
1 CTGTCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCA
* * * * * *
21163 CTATTATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGACCA
1 CTGTCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCA
* * * *
21205 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCC
1 CTGTCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCA
* * * *
21247 CTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCA
21289 CTGTCATC
1 CTGTCATC
21297 GTTGAAGAGG
Statistics
Matches: 103, Mismatches: 31, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
42 103 1.00
ACGTcount: A:0.22, C:0.38, G:0.16, T:0.24
Consensus pattern (42 bp):
CTGTCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCA
Found at i:21299 original size:21 final size:21
Alignment explanation
Indices: 21191--21306 Score: 56
Period size: 21 Copynumber: 5.5 Consensus size: 21
21181 CCCCTCCCAC
*
21191 CGTTCAAGAGACCACTGTCAT
1 CGTTCAAGAGGCCACTGTCAT
** * *
21212 CCCTCAAGAGTCCACT-CCTAT
1 CGTTCAAGAGGCCACTGTC-AT
* * *
21233 CGTTGAAGAGGCCCCTATCATT
1 CGTTCAAGAGGCCACTGTCA-T
* * * * ** *
21255 C-CTCGAGAGTCCCCTCCCAC
1 CGTTCAAGAGGCCACTGTCAT
21275 CGTTCAAGAGGCCACTGTCAT
1 CGTTCAAGAGGCCACTGTCAT
*
21296 CGTTGAAGAGG
1 CGTTCAAGAGG
21307 TCCCTCCCAT
Statistics
Matches: 66, Mismatches: 25, Indels: 8
0.67 0.25 0.08
Matches are distributed among these distances:
20 2 0.03
21 61 0.92
22 3 0.05
ACGTcount: A:0.23, C:0.34, G:0.21, T:0.22
Consensus pattern (21 bp):
CGTTCAAGAGGCCACTGTCAT
Found at i:21305 original size:84 final size:84
Alignment explanation
Indices: 21121--21296 Score: 325
Period size: 84 Copynumber: 2.1 Consensus size: 84
21111 CCCGACTCAC
* *
21121 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAATAGGCCCCTATTATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
21186 CCCACCGTTCAAGAGACCA
66 CCCACCGTTCAAGAGACCA
21205 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
*
21270 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGACCA
21289 CTGTCATC
1 CTGTCATC
21297 GTTGAAGAGG
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
84 89 1.00
ACGTcount: A:0.22, C:0.38, G:0.16, T:0.24
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
CCCACCGTTCAAGAGACCA
Found at i:21312 original size:42 final size:41
Alignment explanation
Indices: 21176--21326 Score: 142
Period size: 42 Copynumber: 3.6 Consensus size: 41
21166 TTATTCCTCG
* * *
21176 AGAGTCCCCTCCCACCGTTCAAGAGACCACTGTCATCCCTCA
1 AGAGT-CCCTCCCACCGTTCAAGAGGCCACTGTCATCCTTGA
* * * * * *
21218 AGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCG-
1 AGAGTCC-CTCCCACCGTTCAAGAGGCCACTGTCA-TCCTTGA
*
21260 AGAGTCCCCTCCCACCGTTCAAGAGGCCACTGTCATCGTTGA
1 AGAGT-CCCTCCCACCGTTCAAGAGGCCACTGTCATCCTTGA
* *
21302 AGAGGTCCCTCCCATCATTCAAGAG
1 AGA-GTCCCTCCCACCGTTCAAGAG
21327 CCCGATTCAC
Statistics
Matches: 86, Mismatches: 18, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
41 6 0.07
42 73 0.85
43 7 0.08
ACGTcount: A:0.23, C:0.36, G:0.19, T:0.22
Consensus pattern (41 bp):
AGAGTCCCTCCCACCGTTCAAGAGGCCACTGTCATCCTTGA
Found at i:21317 original size:21 final size:20
Alignment explanation
Indices: 21266--21326 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
21256 CTCGAGAGTC
*
21266 CCCTCCCACCGTTCAAGAGG
1 CCCTCCCATCGTTCAAGAGG
** *
21286 CCACTGTCATCGTTGAAGAGG
1 CC-CTCCCATCGTTCAAGAGG
*
21307 TCCCTCCCATCATTCAAGAG
1 -CCCTCCCATCGTTCAAGAG
21327 CCCGATTCAC
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.23, C:0.36, G:0.20, T:0.21
Consensus pattern (20 bp):
CCCTCCCATCGTTCAAGAGG
Found at i:21326 original size:84 final size:84
Alignment explanation
Indices: 21121--21326 Score: 288
Period size: 84 Copynumber: 2.5 Consensus size: 84
21111 CCCGACTCAC
* * * * *
21121 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAATAGGCCCCTATTATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCCATCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
21186 CCCACCGTTCAAGAGACCA
66 CCCACCGTTCAAGAGACCA
* * *
21205 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCCATCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
*
21270 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGACCA
** *
21289 CTGTCATCGTTGAAGAGGTCC-CTCCCATCATTCAAGAG
1 CTGTCATCCCTCAAGA-GTCCACTCCCATCATTCAAGAG
21327 CCCGATTCAC
Statistics
Matches: 112, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
84 108 0.96
85 4 0.04
ACGTcount: A:0.22, C:0.36, G:0.17, T:0.24
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAGTCCACTCCCATCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
CCCACCGTTCAAGAGACCA
Found at i:22702 original size:14 final size:14
Alignment explanation
Indices: 22683--22718 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
22673 ATTGTTTAAT
22683 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
22697 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
22711 TGATTTGT
1 TGATTTGT
22719 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:22871 original size:19 final size:19
Alignment explanation
Indices: 22847--22938 Score: 78
Period size: 19 Copynumber: 5.4 Consensus size: 19
22837 GATTCCCTCG
22847 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* * *
22866 TTGCGA-----AATTAGCG
1 TTGCGATTTTCATTTCGCA
22880 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
22899 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
22913 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
22932 TTGCGAT
1 TTGCGAT
22939 AGTAATTTCC
Statistics
Matches: 55, Mismatches: 8, Indels: 20
0.66 0.10 0.24
Matches are distributed among these distances:
14 17 0.31
16 7 0.13
17 7 0.13
19 24 0.44
ACGTcount: A:0.16, C:0.21, G:0.20, T:0.43
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:22938 original size:33 final size:33
Alignment explanation
Indices: 22828--22938 Score: 161
Period size: 33 Copynumber: 3.4 Consensus size: 33
22818 AAAAGTACTA
* *
22828 TCGCTTTGCGATTCCCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATT
* **
22861 TCGCATTGCGAAAT-TAGCGTTGCGATTTTCATT
1 TCGCATTGCG-ATTCTCTCGTTGCGATTTTCATT
22894 TCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATT
22927 TCGCATTGCGAT
1 TCGCATTGCGAT
22939 AGTAATTTCC
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
32 2 0.03
33 64 0.94
34 2 0.03
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.42
Consensus pattern (33 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:25245 original size:12 final size:12
Alignment explanation
Indices: 25228--25264 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
25218 TCTTCGGGGA
25228 CTTTTTCTTCTT
1 CTTTTTCTTCTT
25240 CTTTTTCTTCTT
1 CTTTTTCTTCTT
25252 CTTTTTCTTCTT
1 CTTTTTCTTCTT
25264 C
1 C
25265 AGGATTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:25473 original size:24 final size:24
Alignment explanation
Indices: 25439--25492 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
25429 CTGAAACATC
*
25439 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
25463 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
25487 ATCAAA
1 ATCAAA
25493 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:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:26315 original size:35 final size:36
Alignment explanation
Indices: 26275--26343 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
26265 GATTTTCCTA
*
26275 ATTCGCAATGCGAA-TAAGTAAATCGCAATGCGAAT
1 ATTCGCAATGCGAATTAAGAAAATCGCAATGCGAAT
**
26310 ATTCGCAATGCGAATTTGGAAAATCGCAATGCGA
1 ATTCGCAATGCGAATTAAGAAAATCGCAATGCGA
26344 TACTGACTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 14 0.47
36 16 0.53
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (36 bp):
ATTCGCAATGCGAATTAAGAAAATCGCAATGCGAAT
Found at i:26417 original size:20 final size:20
Alignment explanation
Indices: 26328--26419 Score: 67
Period size: 20 Copynumber: 4.5 Consensus size: 20
26318 TGCGAATTTG
* *
26328 GAAAATCGCAATGCGATACT
1 GAAAATCGCAACGAGATACT
** *
26348 GACTATCGCAACGAGATAAT
1 GAAAATCGCAACGAGATACT
* * *
26368 ACAAAATCGCAATGAGATTCT
1 -GAAAATCGCAACGAGATACT
*** *
26389 GACTTTCGCAACGAGATTCT
1 GAAAATCGCAACGAGATACT
26409 GAAAATCGCAA
1 GAAAATCGCAA
26420 TCATCTTCAA
Statistics
Matches: 52, Mismatches: 19, Indels: 2
0.71 0.26 0.03
Matches are distributed among these distances:
20 38 0.73
21 14 0.27
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.22
Consensus pattern (20 bp):
GAAAATCGCAACGAGATACT
Found at i:26658 original size:20 final size:20
Alignment explanation
Indices: 26633--26719 Score: 104
Period size: 20 Copynumber: 4.3 Consensus size: 20
26623 CAGCTGGGAA
26633 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
26653 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
** ***
26673 ATCGCAATTCG-AAATGAAAA
1 ATCGCAACGCGAAAATG-GCT
26693 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
*
26713 ATTGCAA
1 ATCGCAA
26720 ATAGAAAATC
Statistics
Matches: 54, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
19 5 0.09
20 44 0.81
21 5 0.09
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:26732 original size:34 final size:37
Alignment explanation
Indices: 26653--26740 Score: 101
Period size: 40 Copynumber: 2.4 Consensus size: 37
26643 GAAAATGGCT
26653 ATCGCAACGCGAAAATGGCTATCGCAATTCGAAATGAAAA
1 ATCGCAACGCGAAAATGGCTATCGCAA-T--AAATGAAAA
* *
26693 ATCGCAACGCGAAAATGGCTATTGCAA-ATA-G-AAA
1 ATCGCAACGCGAAAATGGCTATCGCAATAAATGAAAA
*
26727 ATCGCAATGCGAAA
1 ATCGCAACGCGAAA
26741 TGAAAATCGC
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
34 16 0.36
35 1 0.02
36 2 0.04
40 26 0.58
ACGTcount: A:0.43, C:0.19, G:0.20, T:0.17
Consensus pattern (37 bp):
ATCGCAACGCGAAAATGGCTATCGCAATAAATGAAAA
Found at i:26747 original size:19 final size:20
Alignment explanation
Indices: 26718--26757 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
26708 TGGCTATTGC
26718 AAATAGAAAATCGCAATGCG
1 AAATAGAAAATCGCAATGCG
*
26738 AAAT-GAAAATCGCATTGCG
1 AAATAGAAAATCGCAATGCG
26757 A
1 A
26758 TTTTCTCGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.47, C:0.15, G:0.20, T:0.17
Consensus pattern (20 bp):
AAATAGAAAATCGCAATGCG
Found at i:26792 original size:19 final size:19
Alignment explanation
Indices: 26770--26814 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
26760 TTCTCGTTGC
26770 GATTTTCATTTCGCATTGT
1 GATTTTCATTTCGCATTGT
26789 GATTTTCATTTCGCATTGT
1 GATTTTCATTTCGCATTGT
26808 GATTTTC
1 GATTTTC
26815 TCGTTGCGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.53
Consensus pattern (19 bp):
GATTTTCATTTCGCATTGT
Found at i:26970 original size:14 final size:14
Alignment explanation
Indices: 26951--26987 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
26941 CATCAATTAA
26951 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
26965 ACAAATCATCTTTT
1 ACAAATCAACATTT
26979 ACAAATCAA
1 ACAAATCAA
26988 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:28003 original size:19 final size:19
Alignment explanation
Indices: 27979--28089 Score: 73
Period size: 19 Copynumber: 6.4 Consensus size: 19
27969 TGTCCGTATA
27979 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
27998 TTGCGA-TTT--TGT--CG
1 TTGCGATTTTCATTTCGCG
*
28012 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCG
*
28030 TTGCGA-TTT--TGT--CG
1 TTGCGATTTTCATTTCGCG
*
28044 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCG
***
28063 TTGCGATAGCCATTTCCGCG
1 TTGCGATTTTCATTT-CGCG
28083 TTGCGAT
1 TTGCGAT
28090 AGTCATTTTC
Statistics
Matches: 71, Mismatches: 11, Indels: 19
0.70 0.11 0.19
Matches are distributed among these distances:
14 18 0.25
15 3 0.04
16 6 0.08
17 2 0.03
18 13 0.18
19 19 0.27
20 10 0.14
ACGTcount: A:0.13, C:0.21, G:0.23, T:0.44
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:28015 original size:14 final size:14
Alignment explanation
Indices: 27996--28053 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
27986 TTTCATTTCG
27996 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
28010 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
28026 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
28042 CGTTGCGATTTT
1 CGTTGCGATTTT
28054 CATTTCGCAT
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:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:28060 original size:33 final size:33
Alignment explanation
Indices: 27979--28069 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
27969 TGTCCGTATA
*
27979 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
28012 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
28044 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
28070 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:28106 original size:20 final size:20
Alignment explanation
Indices: 28054--28097 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
28044 TTGCGATTTT
*
28054 CATTT-CGCATTGCGATAGC
1 CATTTCCGCGTTGCGATAGC
*
28073 CATTTCCGCGTTGCGATAGT
1 CATTTCCGCGTTGCGATAGC
28093 CATTT
1 CATTT
28098 TCGTGTTGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.36
Consensus pattern (20 bp):
CATTTCCGCGTTGCGATAGC
Found at i:29908 original size:20 final size:20
Alignment explanation
Indices: 29860--29918 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
29850 AATAGTTTCT
** *
29860 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
29880 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
29900 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
29919 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:30190 original size:22 final size:22
Alignment explanation
Indices: 30163--30206 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
30153 GATGGAGATA
30163 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
30185 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
30207 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:30420 original size:20 final size:20
Alignment explanation
Indices: 30395--30446 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
30385 CTTATGTATT
30395 ATCGCGTTGCGAAAGTCAGA
1 ATCGCGTTGCGAAAGTCAGA
*
30415 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTCAGA
*
30435 ATCTCGTTGCGA
1 ATCGCGTTGCGA
30447 TTTTGTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTCAGA
Found at i:30480 original size:20 final size:20
Alignment explanation
Indices: 30455--30508 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
30445 GATTTTGTAT
30455 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
30475 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
30495 TATCGCATTGCGAT
1 TATCGCATTGCGAT
30509 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:30480 original size:61 final size:61
Alignment explanation
Indices: 30374--30511 Score: 186
Period size: 61 Copynumber: 2.3 Consensus size: 61
30364 CGCTTTGAAA
* * * * *
30374 ATCGCATTGCGCTTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
* * * * *
30435 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
30496 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
30512 CCCAATTCGC
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:30527 original size:61 final size:61
Alignment explanation
Indices: 30394--30529 Score: 157
Period size: 61 Copynumber: 2.2 Consensus size: 61
30384 GCTTATGTAT
* * * * * ** *
30394 TATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTAT
1 TATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAA
* * *
30455 TATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAA
1 TATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAA
30517 T-TCGCGTTGCGAT
1 TATCGCGTTGCGAT
30530 TACTTATTCG
Statistics
Matches: 62, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
61 60 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (61 bp):
TATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAA
Found at i:30618 original size:21 final size:21
Alignment explanation
Indices: 30578--30618 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
30568 ACTGTAGACC
** *
30578 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAACT
30599 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATGCAAC
30619 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAACT
Found at i:37665 original size:15 final size:15
Alignment explanation
Indices: 37629--37668 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
37619 ATATTTTCTG
* *
37629 ATTATTTTTATTTTT
1 ATTATTTTTAATTAT
37644 ATT-TTTTTAATTAT
1 ATTATTTTTAATTAT
37658 ATTATTTTTAA
1 ATTATTTTTAA
37669 AATCTATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
ATTATTTTTAATTAT
Found at i:40908 original size:28 final size:27
Alignment explanation
Indices: 40841--40941 Score: 103
Period size: 27 Copynumber: 3.7 Consensus size: 27
40831 ATCATAGTTG
* * *
40841 TACATCAAATAAATGTCACACAAATTA
1 TACATCAAATAAATATCACTCAAATCA
* *
40868 TATATCAAATAAATATCACTCAAGATCG
1 TACATCAAATAAATATCACTCAA-ATCA
* ** *
40896 TACATTAAATAAATGCCACTCAATTCA
1 TACATCAAATAAATATCACTCAAATCA
*
40923 TACATCGAATAAATATCAC
1 TACATCAAATAAATATCAC
40942 ATTAATCGTA
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
27 37 0.64
28 21 0.36
ACGTcount: A:0.48, C:0.20, G:0.05, T:0.28
Consensus pattern (27 bp):
TACATCAAATAAATATCACTCAAATCA
Found at i:45903 original size:28 final size:29
Alignment explanation
Indices: 45848--45903 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
45838 TGATTAATTG
* * *
45848 AGTGATTTATTTGTAAATTTTTGAAATAT
1 AGTGACTTATTTATAAATTTTAGAAATAT
*
45877 AGTGACTTATTTAT-AATTTTAGTAATA
1 AGTGACTTATTTATAAATTTTAGAAATA
45904 ATTGAACGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 11 0.48
29 12 0.52
ACGTcount: A:0.36, C:0.02, G:0.12, T:0.50
Consensus pattern (29 bp):
AGTGACTTATTTATAAATTTTAGAAATAT
Found at i:48324 original size:22 final size:23
Alignment explanation
Indices: 48290--48333 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
48280 TCAAAAAAAT
48290 TATAGTTGCTCTC-CCTCTTTTA
1 TATAGTTGCTCTCTCCTCTTTTA
*
48312 TATAGTT-CTTCTCTCTTCTTTT
1 TATAGTTGC-TCTCTCCTCTTTT
48334 TAATTATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 1 0.05
22 11 0.58
23 7 0.37
ACGTcount: A:0.11, C:0.25, G:0.07, T:0.57
Consensus pattern (23 bp):
TATAGTTGCTCTCTCCTCTTTTA
Found at i:48662 original size:21 final size:22
Alignment explanation
Indices: 48619--48665 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
48609 TTAATAAAAA
*
48619 TTATCTAAAATATTATTATTTTT
1 TTATCTAAAATATCA-TATTTTT
48642 TTATCTAAAATATCA-ATTTTT
1 TTATCTAAAATATCATATTTTT
48663 TTA
1 TTA
48666 ACATTTCCGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.39
23 14 0.61
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.57
Consensus pattern (22 bp):
TTATCTAAAATATCATATTTTT
Found at i:49663 original size:20 final size:20
Alignment explanation
Indices: 49607--49663 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 20
49597 TGGTACCGAA
* *
49607 ACTCTTATATGGGTATCGAT
1 ACTCTTATATGTGTATTGAT
* * *
49627 ACTATCATAAT-TATATTGAT
1 ACTCTTAT-ATGTGTATTGAT
49647 ACTCTTATATGTGTATT
1 ACTCTTATATGTGTATT
49664 AATATCAAAA
Statistics
Matches: 27, Mismatches: 8, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
19 2 0.07
20 23 0.85
21 2 0.07
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.46
Consensus pattern (20 bp):
ACTCTTATATGTGTATTGAT
Found at i:52958 original size:31 final size:31
Alignment explanation
Indices: 52915--52986 Score: 117
Period size: 31 Copynumber: 2.3 Consensus size: 31
52905 TGTTATGTTT
* *
52915 TCTCCAGGTGATTCAGGTTCGAGTAATTTAC
1 TCTCTAGGTGATTCAGGTTCAAGTAATTTAC
*
52946 TCTCTAGGTGATTCAGGTTTAAGTAATTTAC
1 TCTCTAGGTGATTCAGGTTCAAGTAATTTAC
52977 TCTCTAGGTG
1 TCTCTAGGTG
52987 TGGGTAAGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.39
Consensus pattern (31 bp):
TCTCTAGGTGATTCAGGTTCAAGTAATTTAC
Found at i:62159 original size:29 final size:29
Alignment explanation
Indices: 62126--62192 Score: 134
Period size: 29 Copynumber: 2.3 Consensus size: 29
62116 GAACATAATG
62126 AATAGTCGGATGATAATTTTGTAAATTTT
1 AATAGTCGGATGATAATTTTGTAAATTTT
62155 AATAGTCGGATGATAATTTTGTAAATTTT
1 AATAGTCGGATGATAATTTTGTAAATTTT
62184 AATAGTCGG
1 AATAGTCGG
62193 GGGTCCAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.34, C:0.04, G:0.19, T:0.42
Consensus pattern (29 bp):
AATAGTCGGATGATAATTTTGTAAATTTT
Found at i:62478 original size:2 final size:2
Alignment explanation
Indices: 62471--62508 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
62461 TTGAAAATTC
62471 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
62509 GGGTGAATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:66117 original size:24 final size:24
Alignment explanation
Indices: 66069--66117 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
66059 TGGAAACAAG
* **
66069 AAAGACTAAAACAATATTTTCATT
1 AAAGACTAAAACAATAATTGAATT
*
66093 AAAGATTAAAACAATAATTGAATT
1 AAAGACTAAAACAATAATTGAATT
66117 A
1 A
66118 GGTAGTGGTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.55, C:0.08, G:0.06, T:0.31
Consensus pattern (24 bp):
AAAGACTAAAACAATAATTGAATT
Found at i:80317 original size:18 final size:18
Alignment explanation
Indices: 80283--80318 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
80273 GGCAATTGGA
*
80283 CTAAGGAGGATAACTGGG
1 CTAAGGAGGACAACTGGG
*
80301 CTAAGGAGGACATCTGGG
1 CTAAGGAGGACAACTGGG
80319 TTGAAGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.14, G:0.39, T:0.17
Consensus pattern (18 bp):
CTAAGGAGGACAACTGGG
Found at i:83934 original size:19 final size:19
Alignment explanation
Indices: 83910--83948 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
83900 TGGGTTCAAG
83910 AGGTTGAACAAAGTTATCA
1 AGGTTGAACAAAGTTATCA
83929 AGGTTGAACAAAGTTATCA
1 AGGTTGAACAAAGTTATCA
83948 A
1 A
83949 TGTTTGGAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.44, C:0.10, G:0.21, T:0.26
Consensus pattern (19 bp):
AGGTTGAACAAAGTTATCA
Found at i:85956 original size:18 final size:18
Alignment explanation
Indices: 85933--85976 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
85923 GGCAATTGGA
*
85933 CTAAGGAGGATAACTGGG
1 CTAAGGAGGACAACTGGG
*
85951 CTAAGGAGGACATCTGGG
1 CTAAGGAGGACAACTGGG
85969 CTGAAGGA
1 CT-AAGGA
85977 AGTTAGAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 18 0.78
19 5 0.22
ACGTcount: A:0.32, C:0.14, G:0.39, T:0.16
Consensus pattern (18 bp):
CTAAGGAGGACAACTGGG
Found at i:96726 original size:20 final size:21
Alignment explanation
Indices: 96690--96728 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
96680 ATAACTGTAG
96690 ACAAAAAATAATATAATTAGT
1 ACAAAAAATAATATAATTAGT
96711 ACAAAAAATAAT-TAATTA
1 ACAAAAAATAATATAATTA
96729 ATAAATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.64, C:0.05, G:0.03, T:0.28
Consensus pattern (21 bp):
ACAAAAAATAATATAATTAGT
Found at i:96759 original size:15 final size:15
Alignment explanation
Indices: 96702--96787 Score: 52
Period size: 15 Copynumber: 5.8 Consensus size: 15
96692 AAAAAATAAT
* *
96702 ATAATTAGTACAAAAA
1 ATAATTA-TATAAATA
*
96718 ATAATTA-ATTAATA
1 ATAATTATATAAATA
* *
96732 A-ATTTAAATAAATA
1 ATAATTATATAAATA
96746 ATAATTATATAAAT-
1 ATAATTATATAAATA
* * *
96760 ATTATTTTAATAAAAA
1 ATAATTAT-ATAAATA
*
96776 ATATTTATATAA
1 ATAATTATATAA
96788 TTGTATTAAT
Statistics
Matches: 53, Mismatches: 13, Indels: 9
0.71 0.17 0.12
Matches are distributed among these distances:
13 4 0.08
14 18 0.34
15 19 0.36
16 12 0.23
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (15 bp):
ATAATTATATAAATA
Found at i:103867 original size:2 final size:2
Alignment explanation
Indices: 103862--103899 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
103852 ATGCATATCC
103862 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
103900 TAGGACAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:110546 original size:6 final size:6
Alignment explanation
Indices: 110535--110567 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
110525 TCCCGTCCCG
110535 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
110568 TCATCTAACG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:111701 original size:56 final size:57
Alignment explanation
Indices: 111615--111728 Score: 221
Period size: 56 Copynumber: 2.0 Consensus size: 57
111605 TCCAGGTTTC
111615 TCCATTTCTGGAGATCAAACAACTAGAGTTTTATTTATGTGACTATTCC-TTTTCCT
1 TCCATTTCTGGAGATCAAACAACTAGAGTTTTATTTATGTGACTATTCCTTTTTCCT
111671 TCCATTTCTGGAGATCAAACAACTAGAGTTTTATTTATGTGACTATTCCTTTTTCCT
1 TCCATTTCTGGAGATCAAACAACTAGAGTTTTATTTATGTGACTATTCCTTTTTCCT
111728 T
1 T
111729 TTTCCACCTT
Statistics
Matches: 57, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
56 49 0.86
57 8 0.14
ACGTcount: A:0.25, C:0.19, G:0.12, T:0.44
Consensus pattern (57 bp):
TCCATTTCTGGAGATCAAACAACTAGAGTTTTATTTATGTGACTATTCCTTTTTCCT
Found at i:117748 original size:5 final size:5
Alignment explanation
Indices: 117738--117775 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
117728 CATATATTAT
*
117738 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTC TTTT- TTTT
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTT
117776 CCTTAATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
4 4 0.12
5 28 0.88
ACGTcount: A:0.00, C:0.03, G:0.13, T:0.84
Consensus pattern (5 bp):
TTTTG
Found at i:118298 original size:2 final size:2
Alignment explanation
Indices: 118291--118321 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
118281 ATAAGACTCG
118291 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 T
118322 GCATTTATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:121403 original size:18 final size:18
Alignment explanation
Indices: 121382--121437 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 18
121372 ATTTCATTAA
121382 AATATGTTATAAATGATT
1 AATATGTTATAAATGATT
* *
121400 AATATTTTATTAAA--ATA
1 AATATGTTA-TAAATGATT
121417 AATATGTTATAAATGATT
1 AATATGTTATAAATGATT
121435 AAT
1 AAT
121438 TTATTTTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
16 4 0.13
17 10 0.32
18 13 0.42
19 4 0.13
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (18 bp):
AATATGTTATAAATGATT
Found at i:121406 original size:31 final size:33
Alignment explanation
Indices: 121371--121437 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 33
121361 TTTAATACAT
121371 TATTTCATT-A-AAATATGTTATAAATGATTAA
1 TATTTCATTAATAAATATGTTATAAATGATTAA
*
121402 TATTTTATTAAAATAAATATGTTATAAATGATTAA
1 TATTTCATT--AATAAATATGTTATAAATGATTAA
121437 T
1 T
121438 TTATTTTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 8 0.26
34 1 0.03
35 22 0.71
ACGTcount: A:0.46, C:0.01, G:0.06, T:0.46
Consensus pattern (33 bp):
TATTTCATTAATAAATATGTTATAAATGATTAA
Found at i:121427 original size:35 final size:37
Alignment explanation
Indices: 121381--121459 Score: 135
Period size: 35 Copynumber: 2.2 Consensus size: 37
121371 TATTTCATTA
121381 AAATATGTTATAAATGATTAA-TA-TTTTATTAAAAT
1 AAATATGTTATAAATGATTAATTATTTTTATTAAAAT
121416 AAATATGTTATAAATGATTAATTTATTTTTATTAAAAT
1 AAATATGTTATAAATGATTAA-TTATTTTTATTAAAAT
121454 AAATAT
1 AAATAT
121460 TCAGGTGGGA
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
35 21 0.51
37 2 0.05
38 18 0.44
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (37 bp):
AAATATGTTATAAATGATTAATTATTTTTATTAAAAT
Found at i:127658 original size:20 final size:20
Alignment explanation
Indices: 127633--127671 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
127623 GAGGGCTGGA
127633 AACCGGTTT-GACCGGTTTTC
1 AACCGGTTTCGACC-GTTTTC
127653 AACCGGTTTCGACCGTTTT
1 AACCGGTTTCGACCGTTTT
127672 GACCATTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.15, C:0.26, G:0.23, T:0.36
Consensus pattern (20 bp):
AACCGGTTTCGACCGTTTTC
Found at i:127667 original size:10 final size:9
Alignment explanation
Indices: 127634--127722 Score: 70
Period size: 9 Copynumber: 9.3 Consensus size: 9
127624 AGGGCTGGAA
127634 ACCGGTTTG
1 ACCGGTTTG
*
127643 ACCGGTTTTCA
1 ACCGG-TTT-G
127654 ACCGGTTTCG
1 ACCGGTTT-G
*
127664 ACCGTTTTG
1 ACCGGTTTG
**
127673 ACCATTTTCG
1 ACCGGTTT-G
*
127683 ACCGATTTG
1 ACCGGTTTG
*
127692 ACCGGTCTG
1 ACCGGTTTG
127701 AACCGGTTTG
1 -ACCGGTTTG
*
127711 ACCGGTCTG
1 ACCGGTTTG
127720 ACC
1 ACC
127723 CGACCCGACC
Statistics
Matches: 66, Mismatches: 10, Indels: 8
0.79 0.12 0.10
Matches are distributed among these distances:
9 32 0.48
10 29 0.44
11 5 0.08
ACGTcount: A:0.16, C:0.28, G:0.25, T:0.31
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:127705 original size:19 final size:19
Alignment explanation
Indices: 127683--127725 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
127673 ACCATTTTCG
127683 ACCGATTTGACCGGTCTGA
1 ACCGATTTGACCGGTCTGA
*
127702 ACCGGTTTGACCGGTCTGA
1 ACCGATTTGACCGGTCTGA
*
127721 CCCGA
1 ACCGA
127726 CCCGACCGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.19, C:0.30, G:0.28, T:0.23
Consensus pattern (19 bp):
ACCGATTTGACCGGTCTGA
Found at i:127740 original size:17 final size:17
Alignment explanation
Indices: 127718--127755 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
127708 TTGACCGGTC
127718 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
127735 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
127752 TGAC
1 TGAC
127756 TTCCTTTGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.18, C:0.45, G:0.24, T:0.13
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:134892 original size:10 final size:9
Alignment explanation
Indices: 134857--134936 Score: 52
Period size: 10 Copynumber: 8.3 Consensus size: 9
134847 AGGGCTGGAA
134857 ACCGGTTTG
1 ACCGGTTTG
*
134866 ACCGGTTTTCA
1 ACCGG-TTT-G
*
134877 ATCGGTTTCG
1 ACCGGTTT-G
134887 ACCGGTTTG
1 ACCGGTTTG
**
134896 ACCATTTTTG
1 ACC-GGTTTG
*
134906 ACCGGTTCG
1 ACCGGTTTG
*
134915 AATCGGTTTG
1 -ACCGGTTTG
*
134925 ACCGGTCTG
1 ACCGGTTTG
134934 ACC
1 ACC
134937 TGACCCGACC
Statistics
Matches: 54, Mismatches: 13, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
9 22 0.41
10 28 0.52
11 4 0.07
ACGTcount: A:0.15, C:0.25, G:0.26, T:0.34
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:134924 original size:19 final size:19
Alignment explanation
Indices: 134859--134930 Score: 60
Period size: 19 Copynumber: 3.7 Consensus size: 19
134849 GGCTGGAAAC
134859 CGGTTTGACCGGTTTTC-AAT
1 CGGTTTGACCGG--TTCGAAT
*
134879 CGGTTTCGACCGGTTTGACCAT
1 CGGTTT-GACCGGTTCGA--AT
*
134901 --TTTTGACCGGTTCGAAT
1 CGGTTTGACCGGTTCGAAT
134918 CGGTTTGACCGGT
1 CGGTTTGACCGGT
134931 CTGACCTGAC
Statistics
Matches: 42, Mismatches: 4, Indels: 13
0.71 0.07 0.22
Matches are distributed among these distances:
17 2 0.05
19 22 0.52
20 10 0.24
21 6 0.14
22 2 0.05
ACGTcount: A:0.14, C:0.22, G:0.28, T:0.36
Consensus pattern (19 bp):
CGGTTTGACCGGTTCGAAT
Found at i:141408 original size:21 final size:21
Alignment explanation
Indices: 141368--141422 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
141358 GATTCTTGAC
141368 AATCGCAATGCGATAGTACA-
1 AATCGCAATGCGATAGTACAG
* **
141388 AATTCGCATTGCGATTTTACAG
1 AA-TCGCAATGCGATAGTACAG
*
141410 AATCGCAACGCGA
1 AATCGCAATGCGA
141423 ATATGAAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 2 0.07
21 24 0.86
22 2 0.07
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.24
Consensus pattern (21 bp):
AATCGCAATGCGATAGTACAG
Found at i:141435 original size:20 final size:20
Alignment explanation
Indices: 141410--141602 Score: 237
Period size: 20 Copynumber: 9.6 Consensus size: 20
141400 GATTTTACAG
* ** *
141410 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
141430 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
141450 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
141470 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
141490 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
141510 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
141530 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* * *
141550 AATCACAACGAC-AATACGTAA
1 AATCGCAACG-CGTATCCGT-A
141571 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
141591 AATCGCAACGCG
1 AATCGCAACGCG
141603 AATTTTAAAG
Statistics
Matches: 149, Mismatches: 19, Indels: 10
0.84 0.11 0.06
Matches are distributed among these distances:
19 1 0.01
20 130 0.87
21 18 0.12
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:142021 original size:33 final size:33
Alignment explanation
Indices: 141982--142052 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
141972 TTCACTTAGA
141982 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
142015 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
142048 TTTCA
1 TTTCA
142053 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:142158 original size:21 final size:20
Alignment explanation
Indices: 142132--142206 Score: 96
Period size: 21 Copynumber: 3.6 Consensus size: 20
142122 TGCAGAAGAG
142132 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* **
142153 TCGCAACGTGAAAATGACTA
1 TCGCAACGAGAAAATGAAAA
142173 TCTGCAACGAGAAAAATGAAAA
1 TC-GCAACGAG-AAAATGAAAA
142195 TCGCAACGAGAA
1 TCGCAACGAGAA
142207 TTGCGATTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
20 11 0.24
21 25 0.54
22 10 0.22
ACGTcount: A:0.48, C:0.17, G:0.20, T:0.15
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:142231 original size:19 final size:19
Alignment explanation
Indices: 142207--142266 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 19
142197 GCAACGAGAA
142207 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
142226 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCGCG
142240 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
142259 TTGCGATT
1 TTGCGATT
142267 CTCTCGTTGC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 10 0.29
16 3 0.09
17 3 0.09
19 18 0.53
ACGTcount: A:0.10, C:0.22, G:0.22, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:142243 original size:14 final size:14
Alignment explanation
Indices: 142224--142278 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
142214 TTTCATTTCG
142224 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
142238 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
142257 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
142271 CGTTGCGA
1 CGTTGCGA
142279 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:142249 original size:33 final size:33
Alignment explanation
Indices: 142207--142278 Score: 144
Period size: 33 Copynumber: 2.2 Consensus size: 33
142197 GCAACGAGAA
142207 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
142240 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
142273 TTGCGA
1 TTGCGA
142279 CAGTCATTCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.44
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:142286 original size:33 final size:33
Alignment explanation
Indices: 142216--142300 Score: 125
Period size: 33 Copynumber: 2.5 Consensus size: 33
142206 ATTGCGATTT
***
142216 TCATTTCGCGTTGCGATTCTCTCGTTGCGATTT
1 TCATTTCGCGTTGCGATTCTCTCGTTGCGACAG
142249 TCATTTCGCGTTGCGATTCTCTCGTTGCGACAG
1 TCATTTCGCGTTGCGATTCTCTCGTTGCGACAG
*
142282 TCATTCTCTCGTTGCGATT
1 TCATT-TCGCGTTGCGATT
142301 TTCATTTCAA
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 35 0.74
34 12 0.26
ACGTcount: A:0.11, C:0.26, G:0.21, T:0.42
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTTGCGACAG
Found at i:142305 original size:20 final size:20
Alignment explanation
Indices: 142231--142306 Score: 67
Period size: 20 Copynumber: 4.2 Consensus size: 20
142221 TCGCGTTGCG
142231 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
142251 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
142264 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
142284 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
142304 ATT
1 ATT
142307 TCAACCAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 14
0.70 0.08 0.22
Matches are distributed among these distances:
13 3 0.07
14 9 0.20
19 9 0.20
20 23 0.52
ACGTcount: A:0.12, C:0.25, G:0.18, T:0.45
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:144152 original size:93 final size:93
Alignment explanation
Indices: 143993--144308 Score: 614
Period size: 93 Copynumber: 3.4 Consensus size: 93
143983 TAGATTGCTT
* *
143993 AGTAAATTTATTTGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
144058 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
144086 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
144151 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
144179 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
144244 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
144272 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
144309 AATACCCTGA
Statistics
Matches: 221, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 221 1.00
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:144462 original size:14 final size:14
Alignment explanation
Indices: 144441--144499 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
144431 ACGCGAAATG
144441 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
144455 AGAATCGCAACGCGAAACC
1 AAAATCGCAA--CG--A-C
144474 AAAATCGCAACGAC
1 AAAATCGCAACGAC
144488 AAAATCGCAACG
1 AAAATCGCAACG
144500 CGAAACCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.47, C:0.29, G:0.17, T:0.07
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:144466 original size:33 final size:33
Alignment explanation
Indices: 144422--144515 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
144412 CACGAAACTT
**
144422 AAAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAAATCGCAACGCGAAACCAAAATCGCAACGAC
*
144455 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 AAAATCGCAACGCGAAACCAAAATCGCAACGAC
144488 AAAATCGCAACGCGAAACCAAAATCGCA
1 AAAATCGCAACGCGAAACCAAAATCGCA
144516 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.48, C:0.28, G:0.17, T:0.07
Consensus pattern (33 bp):
AAAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:144511 original size:19 final size:19
Alignment explanation
Indices: 144406--144515 Score: 96
Period size: 19 Copynumber: 6.3 Consensus size: 19
144396 TAGTTTACTT
* *
144406 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
**
144426 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
144445 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
144459 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
144478 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAACCAAAA
144492 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
144511 TCGCA
1 TCGCA
144516 TTGCGATTTT
Statistics
Matches: 74, Mismatches: 6, Indels: 21
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.27
15 2 0.03
16 4 0.05
17 4 0.05
18 2 0.03
19 30 0.41
20 12 0.16
ACGTcount: A:0.46, C:0.28, G:0.16, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:144533 original size:19 final size:19
Alignment explanation
Indices: 144511--144683 Score: 150
Period size: 19 Copynumber: 9.6 Consensus size: 19
144501 GAAACCAAAA
*
144511 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
144530 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
144544 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
144563 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
*
144579 T--CGTTGTGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
144596 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
144615 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
144634 TCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
144653 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
144673 TCGTGTTGCGA
1 TCGCGTTGCGA
144684 AAGTAAACTA
Statistics
Matches: 124, Mismatches: 19, Indels: 21
0.76 0.12 0.13
Matches are distributed among these distances:
14 16 0.13
16 8 0.06
17 8 0.06
19 80 0.65
20 12 0.10
ACGTcount: A:0.10, C:0.20, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:144641 original size:38 final size:38
Alignment explanation
Indices: 144511--144683 Score: 159
Period size: 33 Copynumber: 4.8 Consensus size: 38
144501 GAAACCAAAA
*
144511 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTC---
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* *
144546 T--CGTTGCGATTTTCATTTCGCATTGCGA-T-TC-TG
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* * **
144579 T--CGTTGTGATTTTCATTTCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
** *
144615 TCGCGTTGCGATTTTGGTTTCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* *
144653 TCGCGTTGCGATTTTAAGTTTCGTGTTGCGA
1 TCGCGTTGCGATTTTCA-TTTCGCGTTGCGA
144684 AAGTAAACTA
Statistics
Matches: 113, Mismatches: 17, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
31 2 0.02
32 1 0.01
33 51 0.45
34 1 0.01
35 2 0.02
36 2 0.02
38 43 0.38
39 11 0.10
ACGTcount: A:0.10, C:0.20, G:0.24, T:0.46
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
Found at i:145512 original size:14 final size:14
Alignment explanation
Indices: 145493--145525 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
145483 GTTTAATTGG
145493 TTTGTAAAAGATGA
1 TTTGTAAAAGATGA
*
145507 TTTGTAAAAGTTGA
1 TTTGTAAAAGATGA
145521 TTTGT
1 TTTGT
145526 GTAATTGATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.45
Consensus pattern (14 bp):
TTTGTAAAAGATGA
Found at i:145640 original size:19 final size:19
Alignment explanation
Indices: 145616--145703 Score: 123
Period size: 19 Copynumber: 4.8 Consensus size: 19
145606 GCATTATGTT
145616 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAATGC
145635 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAATGC
*
145652 G--A-GAGAATCGCAATGC
1 GAAATGAAAATCGCAATGC
145668 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAATGC
145687 GGAAATGAAAATCGCAA
1 -GAAATGAAAATCGCAA
145704 CGAGAGAATC
Statistics
Matches: 61, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
14 10 0.16
15 1 0.02
16 2 0.03
17 2 0.03
18 1 0.02
19 29 0.48
20 16 0.26
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAATGC
Found at i:145735 original size:53 final size:53
Alignment explanation
Indices: 145616--145722 Score: 207
Period size: 53 Copynumber: 2.0 Consensus size: 53
145606 GCATTATGTT
145616 GAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC
145668 GAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC
145721 GA
1 GA
145723 TTTTCATTTC
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 19 0.35
53 35 0.65
ACGTcount: A:0.46, C:0.17, G:0.24, T:0.13
Consensus pattern (53 bp):
GAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC
Found at i:145740 original size:19 final size:19
Alignment explanation
Indices: 145712--145953 Score: 265
Period size: 19 Copynumber: 13.7 Consensus size: 19
145702 AACGAGAGAA
*
145712 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
145731 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
145750 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
145767 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
145784 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
145800 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
145817 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
145836 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
145853 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
145870 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
145889 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
145908 TCCGCATTGCGATTTTC--T
1 T-CGCATTGCGATTTTCATT
*
145926 T-G---TGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
145941 TCGCATTGCGATT
1 TCGCATTGCGATT
145954 CTCTCGTTGC
Statistics
Matches: 190, Mismatches: 9, Indels: 48
0.77 0.04 0.19
Matches are distributed among these distances:
13 9 0.05
14 18 0.09
15 2 0.01
16 19 0.10
17 19 0.10
18 8 0.04
19 80 0.42
20 35 0.18
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:145775 original size:14 final size:14
Alignment explanation
Indices: 145756--145810 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
145746 CATTTCCGCA
145756 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
145770 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
145787 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
145803 TTGCGATT
1 TTGCGATT
145811 TTCATTTCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 14 0.41
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:145781 original size:53 final size:52
Alignment explanation
Indices: 145712--145961 Score: 262
Period size: 53 Copynumber: 4.8 Consensus size: 52
145702 AACGAGAGAA
* *
145712 TCGCAATGCGATTTTCATTTCGCATTGCGATT-T-TCATTTCCGCA-TTGCGATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC-GTTCCG-ATTTGC-ATT
* * * *
145764 CTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 -TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTCCGATTTGCATT
* *
145817 TCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGTTCCGATTTGCATT
*
145870 TCGCATTGCGATTTTCATTTCGCATTGCGATT-T-TCATTTCCGCA-TTGCGATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC-GTTCCG-ATTTGC-ATT
* * *
145922 T-TCTTGTGGGATTTTCATTTCGCATTGCGATTCTCTCGTT
1 TCGCAT-TGCGATTTTCATTTCGCATTGCGATTCTCTCGTT
145962 GCAATTGTAA
Statistics
Matches: 172, Mismatches: 15, Indels: 20
0.83 0.07 0.10
Matches are distributed among these distances:
50 2 0.01
51 10 0.06
52 60 0.35
53 88 0.51
54 10 0.06
55 2 0.01
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.46
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTCCGATTTGCATT
Found at i:145794 original size:33 final size:33
Alignment explanation
Indices: 145736--145829 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
145726 TCATTTCGCA
145736 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTT-CGCATTGCGATTCTCTCG
145770 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
145803 TTGCGATTTTCATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
145830 TTCATTTCCG
Statistics
Matches: 60, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 45 0.75
34 15 0.25
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:145820 original size:86 final size:89
Alignment explanation
Indices: 145718--145924 Score: 357
Period size: 86 Copynumber: 2.3 Consensus size: 89
145708 AGAATCGCAA
145718 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
145783 TTCGCATTGCGA-TTC-TCTCG-T
66 TTCGCATTGCGATTTCATCTCGAT
145804 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
*
145869 TTCGCATTGCGATTTTCATTTCGCAT
66 TTCGCATTGCGA-TTTCATCTCG-AT
145895 TGCGATTTTCATTTCCGCATTGCGATTTTC
1 TGCGATTTTCATTT-CGCATTGCGATTTTC
145925 TTGTGGGATT
Statistics
Matches: 114, Mismatches: 1, Indels: 6
0.94 0.01 0.05
Matches are distributed among these distances:
86 77 0.68
88 3 0.03
89 4 0.04
91 15 0.13
92 15 0.13
ACGTcount: A:0.14, C:0.24, G:0.17, T:0.46
Consensus pattern (89 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
TTCGCATTGCGATTTCATCTCGAT
Found at i:148268 original size:12 final size:12
Alignment explanation
Indices: 148251--148275 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
148241 TCTTCGGGGA
148251 CTTTTTCTTCTT
1 CTTTTTCTTCTT
148263 CTTTTTCTTCTT
1 CTTTTTCTTCTT
148275 C
1 C
148276 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:148484 original size:24 final size:24
Alignment explanation
Indices: 148450--148496 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
148440 CTGAAACATC
148450 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
148474 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
148497 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:149216 original size:20 final size:20
Alignment explanation
Indices: 149188--149397 Score: 210
Period size: 20 Copynumber: 10.5 Consensus size: 20
149178 AAATTTCAGT
* * * *
149188 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
149208 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
149228 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
149248 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
149268 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
149288 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
*
149308 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* * *
149328 ATTGCTATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
* *
149348 GTTGCGGTTTACGAATACGC
1 GTTGCGATTTACGGATACGC
* *
149368 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
149388 GTTGCGATTT
1 GTTGCGATTT
149398 TCATATTTGC
Statistics
Matches: 163, Mismatches: 22, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
19 3 0.02
20 158 0.97
21 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:150397 original size:13 final size:13
Alignment explanation
Indices: 150379--150403 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
150369 GTTAGACAGG
150379 TGTAATTTTCTTA
1 TGTAATTTTCTTA
150392 TGTAATTTTCTT
1 TGTAATTTTCTT
150404 GTGAGATCTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.08, G:0.08, T:0.64
Consensus pattern (13 bp):
TGTAATTTTCTTA
Found at i:154299 original size:23 final size:23
Alignment explanation
Indices: 154265--154323 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
154255 CATTTTCAAA
* *
154265 TATAATATTATATTT-TTTAGTAT
1 TATAATAATATATTTAATTA-TAT
154288 TATAATAATATATTTAATTATAT
1 TATAATAATATATTTAATTATAT
154311 TATAATAATATAT
1 TATAATAATATAT
154324 GATATGTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
23 30 0.91
24 3 0.09
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (23 bp):
TATAATAATATATTTAATTATAT
Found at i:154300 original size:28 final size:26
Alignment explanation
Indices: 154269--154351 Score: 73
Period size: 28 Copynumber: 3.2 Consensus size: 26
154259 TTCAAATATA
*
154269 ATATTATATTTTTTAGTATTATAATAAT
1 ATATTATA-TTATTA-TATTATAATAAT
154297 ATATT-TA--ATTATATTATAATAAT
1 ATATTATATTATTATATTATAATAAT
* * *
154320 ATATGATATGTATTCTTATTTTAATAAT
1 ATATTATAT-TATT-ATATTATAATAAT
154348 ATAT
1 ATAT
154352 AATAAAAATA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
23 16 0.35
24 5 0.11
27 5 0.11
28 20 0.43
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (26 bp):
ATATTATATTATTATATTATAATAAT
Found at i:163966 original size:13 final size:14
Alignment explanation
Indices: 163938--163971 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
163928 ATAATAAAAT
*
163938 AATCATTTATTTTC
1 AATCATTTACTTTC
163952 AATCATTT-CTTTC
1 AATCATTTACTTTC
163965 AATCATT
1 AATCATT
163972 CACCCCTCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.29, C:0.18, G:0.00, T:0.53
Consensus pattern (14 bp):
AATCATTTACTTTC
Found at i:166456 original size:61 final size:60
Alignment explanation
Indices: 166328--166502 Score: 185
Period size: 61 Copynumber: 2.9 Consensus size: 60
166318 ACCTTAATTT
** * * **
166328 TAAATT-GATCCCTAAACTTTTAAATATCCTAATTTCATCCTTAAATTATGGTAAACATTA
1 TAAATTAG-TCCCTAAACTTTTAAATATTTTAATTTCATCCTTAAACTATGATTTACATTA
* * * *
166388 TAGATTAGTCCTTAGAACTTTTAAATATTTTAATTTCATCCTTAAACTATGATTTTCATTC
1 TAAATTAGTCCCTA-AACTTTTAAATATTTTAATTTCATCCTTAAACTATGATTTACATTA
* * *
166449 TAAATTAGTCCCTAAACTTTTTGAATATTTCAATTTCAT-CTCAAACTAT-ATTTA
1 TAAATTAGTCCCTAAAC-TTTTAAATATTTTAATTTCATCCTTAAACTATGATTTA
166503 TATACTAATC
Statistics
Matches: 96, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
59 4 0.04
60 22 0.23
61 70 0.73
ACGTcount: A:0.35, C:0.16, G:0.05, T:0.44
Consensus pattern (60 bp):
TAAATTAGTCCCTAAACTTTTAAATATTTTAATTTCATCCTTAAACTATGATTTACATTA
Found at i:166740 original size:59 final size:60
Alignment explanation
Indices: 166611--166748 Score: 163
Period size: 59 Copynumber: 2.3 Consensus size: 60
166601 TTTGGATGAA
* * * *
166611 TTTGAGGATGAAATTGGAATATTCAAAAGTTTTGGGACTAATATAGAAAGAGGGTAATAG
1 TTTGAGGATGAAATTAGAATATTCAAAAGTTATGAGACTAATATAGAAAGAGAGTAATAG
* * * * *
166671 TTT-AGGGATGAAATTAGATTGTTCAAAAGTTAT-AGACTAATTTAGAATGAGAGTTATAG
1 TTTGA-GGATGAAATTAGAATATTCAAAAGTTATGAGACTAATATAGAAAGAGAGTAATAG
*
166730 TTTGATGATGAAATTAGAA
1 TTTGAGGATGAAATTAGAA
166749 AAAGTTTAAG
Statistics
Matches: 65, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
59 37 0.57
60 28 0.43
ACGTcount: A:0.40, C:0.03, G:0.24, T:0.33
Consensus pattern (60 bp):
TTTGAGGATGAAATTAGAATATTCAAAAGTTATGAGACTAATATAGAAAGAGAGTAATAG
Found at i:175650 original size:16 final size:17
Alignment explanation
Indices: 175624--175656 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
175614 TTTTTTTATG
*
175624 TTTTTACCCTTTGGGTA
1 TTTTTACCCTTTAGGTA
175641 TTTTTA-CCTTTAGGTA
1 TTTTTACCCTTTAGGTA
175657 ATTGGATTCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.55
Consensus pattern (17 bp):
TTTTTACCCTTTAGGTA
Found at i:184608 original size:2 final size:2
Alignment explanation
Indices: 184601--184648 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
184591 GACGCTGTGA
184601 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
184643 AT AT AT
1 AT AT AT
184649 TGTAGTGATT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:185844 original size:2 final size:2
Alignment explanation
Indices: 185837--185863 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
185827 GCATAAACCC
185837 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
185864 GAAAATGTAG
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:186231 original size:30 final size:29
Alignment explanation
Indices: 186173--186232 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 29
186163 TCATTTTATA
* *
186173 ACTTATAATAGTGGAAAACTTAATAAAAC
1 ACTTATAATAGTGGAAAACTCAACAAAAC
*
186202 ACTTATAATAGTTGGGAAACTCAACAAAAC
1 ACTTATAATAG-TGGAAAACTCAACAAAAC
186232 A
1 A
186233 ACGTCCTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 11 0.41
30 16 0.59
ACGTcount: A:0.50, C:0.13, G:0.12, T:0.25
Consensus pattern (29 bp):
ACTTATAATAGTGGAAAACTCAACAAAAC
Found at i:189495 original size:16 final size:15
Alignment explanation
Indices: 189476--189519 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
189466 AACTAATATT
*
189476 AAAAATAAAGATAAAA
1 AAAAATAAA-ACAAAA
*
189492 AAAAATAAAACAAAT
1 AAAAATAAAACAAAA
189507 AAAAAT-AAACAAA
1 AAAAATAAAACAAA
189520 CAAACACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
14 7 0.27
15 10 0.38
16 9 0.35
ACGTcount: A:0.82, C:0.05, G:0.02, T:0.11
Consensus pattern (15 bp):
AAAAATAAAACAAAA
Found at i:192764 original size:24 final size:24
Alignment explanation
Indices: 192720--192769 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
192710 ATAAAGAACC
*
192720 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
192744 AAAATAAAGTTTAAACA-ACCATTA
1 AAAATAAA-CTTAAACATACCATTA
192768 AA
1 AA
192770 TCAACTACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:193658 original size:18 final size:19
Alignment explanation
Indices: 193623--193659 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
193613 TACGGAATGT
193623 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
193643 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
193660 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:203057 original size:228 final size:227
Alignment explanation
Indices: 202600--203092 Score: 884
Period size: 228 Copynumber: 2.2 Consensus size: 227
202590 GTTATATTGT
* * *
202600 AAAGTATCTATCTTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTA
1 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTA
*
202665 TCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAATATCAAAACAATCAAAT
66 TATTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAATATCAAAACAATCAAAT
202730 AATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAATGAAACACTATTAAAAA
131 AATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAATGAAACACTATTAAAAA
202795 AAATTGAAACATAAATTACATAACTTTAAAAA
196 AAATTGAAACATAAATTACATAACTTTAAAAA
202827 AAA-TATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTAGAAAACATATTTATTATT
1 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGT-GAAAACATATTTATTATT
202891 ATATTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAA
65 ATATTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTAT-AAATATCAAAACAATCAA
202956 ATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-
129 ATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGG-AAA-ATGAAACACTATTA
203020 AAAAAAATTGAAACATAAATTACATAACTTT-AAAA
192 AAAAAAATTGAAACATAAATTACATAACTTTAAAAA
*
203055 AAAGTATATATCATTTTTATAAAAGTGTTCATACTTAT
1 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTAT
203093 AAAAGTAGGT
Statistics
Matches: 256, Mismatches: 5, Indels: 8
0.95 0.02 0.03
Matches are distributed among these distances:
226 40 0.16
227 65 0.25
228 71 0.28
229 67 0.26
230 13 0.05
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.40
Consensus pattern (227 bp):
AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTA
TATTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAATATCAAAACAATCAAAT
AATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAATGAAACACTATTAAAAA
AAATTGAAACATAAATTACATAACTTTAAAAA
Found at i:203414 original size:19 final size:20
Alignment explanation
Indices: 203371--203416 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
203361 CGATATACCA
203371 GGTAAAAATATGATAAAACC
1 GGTAAAAATATGATAAAACC
203391 GGTAACAAA-ATGATAAAA-C
1 GGTAA-AAATATGATAAAACC
203410 GGTAAAA
1 GGTAAAA
203417 CGTTACCGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 2 0.08
19 6 0.24
20 14 0.56
21 3 0.12
ACGTcount: A:0.57, C:0.09, G:0.17, T:0.17
Consensus pattern (20 bp):
GGTAAAAATATGATAAAACC
Found at i:203619 original size:174 final size:179
Alignment explanation
Indices: 203159--203623 Score: 627
Period size: 174 Copynumber: 2.6 Consensus size: 179
203149 GATCCAAATT
* * *
203159 AAAAATGTGTCGATCCAAAATGATATAACAGGTAAAACTATGACTAAACCGGTAT-AGAAATGAT
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAA-TATGA-TAAAACGGTATCA-AAATGAT
* * * * *
203223 AAAACCGGTAAAGCGCTACCGGATACATTTAAAGTGTCGTTACTTTAATATAAGGATCGACACTT
63 AAAACC-GTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTT
*
203288 CGTGAATTTAAAAGAGAAGCAGTTTTAAATCCTATAAAGTGTCGATACTTTTA
127 CGTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTTA
** * *
203341 AAAAATGTATCGATCCAGTACGATATACCAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGT-AAAATATGATAAAA-CGGTATCAAAATGATA
* * * *
203406 AAACGGTAAAACGTTACCGGATATATTGAACGTGTCGATACTTT-ATATAAGGATCGACACTTTG
64 AAACCGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTCG
**
203470 TGAATTTAAAAGAGAAGCA-TTTTAGCGCCTAT-AA-TGTCGATAC-TTTA
129 TGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTTA
* *
203517 AAAAATATATCGATCCACAACGATATAACAGGTAAAATATGATAAAACGGTATCAAAATGATAAA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAATATGATAAAACGGTATCAAAATGATAAA
* *
203582 ACCGTAAAATGATACCGGATATATTGAAAATGTCGATACTTT
66 ACCGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTT
203624 CGTAAGTACG
Statistics
Matches: 252, Mismatches: 28, Indels: 14
0.86 0.10 0.05
Matches are distributed among these distances:
174 54 0.21
175 14 0.06
176 33 0.13
177 9 0.04
178 2 0.01
179 10 0.04
180 38 0.15
181 37 0.15
182 50 0.20
183 5 0.02
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (179 bp):
AAAAATGTATCGATCCAAAACGATATAACAGGTAAAATATGATAAAACGGTATCAAAATGATAAA
ACCGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTCGTG
AATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTTA
Found at i:205829 original size:21 final size:21
Alignment explanation
Indices: 205803--205866 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
205793 AAGACAATCA
*
205803 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAG
205824 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
205845 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
205866 A
1 A
205867 TGCATAAGGG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.42, C:0.11, G:0.30, T:0.17
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:205943 original size:33 final size:33
Alignment explanation
Indices: 205901--205966 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
205891 AAATAGATGG
*
205901 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
205934 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
205967 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:207779 original size:19 final size:19
Alignment explanation
Indices: 207755--207803 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
207745 AATGTAGGGT
207755 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
207774 TAATTTTGTATATGATTTA
1 TAATTTTGTATAAGATTTA
207793 TAATTTTGTAT
1 TAATTTTGTAT
207804 GTGAATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:207814 original size:18 final size:19
Alignment explanation
Indices: 207755--207815 Score: 79
Period size: 19 Copynumber: 3.3 Consensus size: 19
207745 AATGTAGGGT
* *
207755 TAATTTTGTATAAGATTTA
1 TAATTTTGTATATGATATA
*
207774 TAATTTTGTATATGATTTA
1 TAATTTTGTATATGATATA
*
207793 TAATTTTGTATGTGA-ATA
1 TAATTTTGTATATGATATA
207811 TAATT
1 TAATT
207816 ATGAATGAGA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
18 7 0.18
19 32 0.82
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.54
Consensus pattern (19 bp):
TAATTTTGTATATGATATA
Found at i:208447 original size:200 final size:200
Alignment explanation
Indices: 207896--209666 Score: 3293
Period size: 200 Copynumber: 8.9 Consensus size: 200
207886 ATACACATTA
*
207896 AGGGTGCAACCATAAAGTGTCGAACCATATATAAAAAAGTGTCGATCCCAAAAACATCGAAAACC
1 AGGGTGCAACCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAAACATCGAAAACC
207961 AAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGA
65 AAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGA
*
208026 ATATGTCTAAATAATGTGTCTACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATG
130 ATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATG
208091 GAAAAC
195 GAAAAC
208097 AGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAAACATCGAAAACC
1 AGGGTGCAACCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAAACATCGAAAACC
208162 AAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGA
65 AAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGA
*
208227 ATATGTCTAAATAATGTGTCGACATTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATG
130 ATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATG
208292 GAAAAC
195 GAAAAC
208298 AGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCA
1 AGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCA
208363 AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAA
66 AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAA
* *
208428 TATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATAGTTTTGGTCCAAAATGAATGG
131 TATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGG
208493 AAAAC
196 AAAAC
* * *
208498 AGGGTGCAACCATAAAGTGTCGATCTATATATACAAAGTGTCGATCCCAAAAACATCAAAAACCA
1 AGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCA
*
208563 AAAGTATAATGTAATATGTATTTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAA
66 AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAA
* *
208628 TATGTCTAAATAATGTGTCGACATTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGA
131 TATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGG
208693 AAAAC
196 AAAAC
*
208698 AGGGTGCAACCATAAAGTGTCGATCAATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCA
1 AGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCA
208763 AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAA
66 AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAA
* *
208828 TATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATAGTTTTGGTCCAAAATGAATGG
131 TATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGG
208893 AAAAC
196 AAAAC
* *
208898 AGGGTGCAACCATAAAGTGTCGATCCATATATACAAAGTGTCGATCCCAAAAACATCAAAAACCA
1 AGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCA
*
208963 AAAGTATAATGTAATATGTATTTTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGA
66 AAAGTATAATGTAATATGTA-ATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGA
209028 ATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATG
130 ATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATG
209093 GAAAAC
195 GAAAAC
209099 AGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCA
1 AGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCA
209164 AAAGTATAATGTAATATGTAATTTTTCAATCTAACC-GTACAAGTATACC-GTTTTATGAGAGAA
66 AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAA
209227 TATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGG
131 TATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGG
209292 AAAAC
196 AAAAC
209297 AGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCA
1 AGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCA
*
209362 AAAGTATAATGTAATATGTAATTTTTCAATCTAACCAGTACAAGTATACCGG-TTTATGAGAGAA
66 AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAA
*
209426 TATGTCTAAAT-ATGTGTCGACACTTTTTTAGTTTGTGTCGATAGTTTTGGTCCAGAATGAATGG
131 TATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGG
209490 AAAAC
196 AAAAC
*
209495 AGGGTGCAACCATAAAGTGTCGATCTATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCA
1 AGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCA
209560 AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTAT--GAGAA
66 AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAA
209623 TATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATA
131 TATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATA
209667 CTAATTTAAA
Statistics
Matches: 1531, Mismatches: 34, Indels: 13
0.97 0.02 0.01
Matches are distributed among these distances:
197 16 0.01
198 389 0.25
199 54 0.04
200 647 0.42
201 425 0.28
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (200 bp):
AGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCA
AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAA
TATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGG
AAAAC
Found at i:211130 original size:6 final size:6
Alignment explanation
Indices: 211119--211182 Score: 65
Period size: 6 Copynumber: 10.7 Consensus size: 6
211109 CAAGCGGTCA
* * * * *
211119 ATGAAG ATGAAG CTGACG ATGAAG ATGACG ATGATG ATGACG ATGAAG
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG
* *
211167 CTGACG ATGAAG ATGA
1 ATGAAG ATGAAG ATGA
211183 TGACGATGAC
Statistics
Matches: 46, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.39, C:0.09, G:0.33, T:0.19
Consensus pattern (6 bp):
ATGAAG
Found at i:211141 original size:12 final size:12
Alignment explanation
Indices: 211119--211203 Score: 95
Period size: 12 Copynumber: 7.3 Consensus size: 12
211109 CAAGCGGTCA
*
211119 ATGAAGATGAAG
1 ATGACGATGAAG
*
211131 CTGACGATGAAG
1 ATGACGATGAAG
*
211143 ATGACGATGATG
1 ATGACGATGAAG
211155 ATGACGATGAAG
1 ATGACGATGAAG
*
211167 CTGACGATGAAG
1 ATGACGATGAAG
*
211179 AT---GATGACG
1 ATGACGATGAAG
*
211188 ATGACGATGATG
1 ATGACGATGAAG
211200 ATGA
1 ATGA
211204 TGATCCAAAC
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
9 8 0.13
12 53 0.87
ACGTcount: A:0.38, C:0.09, G:0.33, T:0.20
Consensus pattern (12 bp):
ATGACGATGAAG
Found at i:211156 original size:3 final size:3
Alignment explanation
Indices: 211136--211207 Score: 63
Period size: 3 Copynumber: 24.0 Consensus size: 3
211126 TGAAGCTGAC
* * * * * * *
211136 GAT GAA GAT GAC GAT GAT GAT GAC GAT GAA GCT GAC GAT GAA GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
211184 GAC GAT GAC GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT
211208 CCAAACAAGT
Statistics
Matches: 51, Mismatches: 18, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.36, C:0.08, G:0.33, T:0.22
Consensus pattern (3 bp):
GAT
Done.