Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003112.1 Hibiscus syriacus cultivar Beakdansim tig00006507_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: 642031
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:162454 original size:20 final size:19
Alignment explanation
Indices: 162420--162474 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
162410 TTGCGATTTT
*
162420 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
162439 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
162459 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
162475 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:162982 original size:18 final size:18
Alignment explanation
Indices: 162956--163000 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
162946 GTCGATCAGA
*
162956 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
162974 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
162992 TGATGGCTC
1 TGATGGCTC
163001 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:164648 original size:22 final size:22
Alignment explanation
Indices: 164621--164664 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
164611 GATGGAGATA
164621 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
164643 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
164665 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:164895 original size:41 final size:41
Alignment explanation
Indices: 164835--164929 Score: 145
Period size: 41 Copynumber: 2.3 Consensus size: 41
164825 TTTGAAAATT
* *
164835 GCATTGCGATTATGTATTATCGCGTTGCAAAAGTCAGTATC
1 GCATTGCGATTTTGTATTATCGCATTGCAAAAGTCAGTATC
* * *
164876 GCGTTGCGATTTTGTATTATCGCATTGCGATAGTCAGTATC
1 GCATTGCGATTTTGTATTATCGCATTGCAAAAGTCAGTATC
164917 GCATTGCGATTTT
1 GCATTGCGATTTT
164930 CCCAATTCGC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.38
Consensus pattern (41 bp):
GCATTGCGATTTTGTATTATCGCATTGCAAAAGTCAGTATC
Found at i:164898 original size:21 final size:21
Alignment explanation
Indices: 164838--164927 Score: 71
Period size: 20 Copynumber: 4.4 Consensus size: 21
164828 GAAAATTGCA
164838 TTGCGATTATGTATTATCGCG
1 TTGCGATTATGTATTATCGCG
* * *
164859 TTGC-A-AAAGTCAGTATCGCG
1 TTGCGATTATGT-ATTATCGCG
* *
164879 TTGCGATTTTGTATTATCGCA
1 TTGCGATTATGTATTATCGCG
* *
164900 TTGCGA-TA-GTCAGTATCGCA
1 TTGCGATTATGT-ATTATCGCG
164920 TTGCGATT
1 TTGCGATT
164928 TTCCCAATTC
Statistics
Matches: 54, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
19 5 0.09
20 28 0.52
21 19 0.35
22 2 0.04
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.38
Consensus pattern (21 bp):
TTGCGATTATGTATTATCGCG
Found at i:164945 original size:41 final size:41
Alignment explanation
Indices: 164852--164947 Score: 113
Period size: 41 Copynumber: 2.3 Consensus size: 41
164842 GATTATGTAT
* * * ** *
164852 TATCGCGTTGCAAAAGTCAGTATCGCGTTGCGATTTTGTAT
1 TATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAA
*
164893 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAA
1 TATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTT-CCAA
164935 T-TCGCGTTGCGAT
1 TATCGCGTTGCGAT
164948 TTACTTATTC
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
41 44 0.96
42 2 0.04
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (41 bp):
TATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAA
Found at i:169342 original size:46 final size:46
Alignment explanation
Indices: 169275--169629 Score: 570
Period size: 46 Copynumber: 7.8 Consensus size: 46
169265 CTATTTCCTA
*
169275 CATCTATAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
169321 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
* * *
169367 CATTTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACATTTGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
*
169413 CATCTATAAGTCCTTCAGTGCATGATGTTATC-AAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
*
169458 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACTTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
169504 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
* *
169550 CATCTGTATGTCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
** * * * *
169595 CATCCATAAGACCTACAGTGCAGGATGTTCTCAAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAA
169630 TGAGATTTTT
Statistics
Matches: 287, Mismatches: 20, Indels: 4
0.92 0.06 0.01
Matches are distributed among these distances:
45 80 0.28
46 207 0.72
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (46 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
Found at i:169522 original size:137 final size:137
Alignment explanation
Indices: 169275--169629 Score: 584
Period size: 137 Copynumber: 2.6 Consensus size: 137
169265 CTATTTCCTA
169275 CATCTATAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGT
1 CATCTATAAGTCCTTCAGTGCATGATGTTATC-AAAACCTTCGGGTCATCTGTAAGTCCTTCAGT
*
169340 GCATGATGTTATCAAAAACCTTCGGGTCATTTGTAAGTCCTTCAGTGCATGATGTTATCAAAAAC
65 GCATGATGTTATCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAAC
*
169405 ATTTGGGT
130 ATTCGGGT
169413 CATCTATAAGTCCTTCAGTGCATGATGTTATCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTG
1 CATCTATAAGTCCTTCAGTGCATGATGTTATCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTG
* *
169478 CATGATGTTATCAAAAACTTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACC
66 CATGATGTTATCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACA
169543 TTCGGGT
131 TTCGGGT
* * * ** * *
169550 CATCTGTATGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTG
1 CATCTATAAGTCCTTCAGTGCATGATGTTATCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTG
* *
169615 CAGGATGTTCTCAAA
66 CATGATGTTATCAAA
169630 TGAGATTTTT
Statistics
Matches: 204, Mismatches: 13, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
137 172 0.84
138 32 0.16
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (137 bp):
CATCTATAAGTCCTTCAGTGCATGATGTTATCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTG
CATGATGTTATCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACA
TTCGGGT
Found at i:169894 original size:3 final size:3
Alignment explanation
Indices: 169888--169960 Score: 94
Period size: 3 Copynumber: 24.0 Consensus size: 3
169878 TTTTGTTTTT
**
169888 TTA TTA TTA AAA TTA TTA TTA TTA TTA TTA TTA TATA TTA -TA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA T-TA
*
169934 TTA TTA TTT TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
169961 AATAAATATT
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
2 2 0.03
3 53 0.87
4 6 0.10
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:171716 original size:18 final size:18
Alignment explanation
Indices: 171684--171730 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
171674 TTAAATTATT
* *
171684 TTTATGAATAATTATTACA
1 TTTATTAATATTTATT-CA
*
171703 TTT-TTAATATTTATTTA
1 TTTATTAATATTTATTCA
171720 TTTATTAATAT
1 TTTATTAATAT
171731 CGAAGAAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 4 0.17
18 17 0.71
19 3 0.12
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (18 bp):
TTTATTAATATTTATTCA
Found at i:174391 original size:25 final size:24
Alignment explanation
Indices: 174325--174471 Score: 161
Period size: 24 Copynumber: 6.0 Consensus size: 24
174315 AATTTTAAAT
* * *
174325 GTTTCTTAGGTTGAAGTGATTTAAG
1 GTTTTTTAGGTTAAAGTGGTTT-AG
174350 GTATTTTTAGGTTAAAGTGGTTTACG
1 GT-TTTTTAGGTTAAAGTGGTTTA-G
*
174376 GTTTTTTAGGTGAAAGTGGTTTAG
1 GTTTTTTAGGTTAAAGTGGTTTAG
* * * *
174400 GGTTTTTAGGTTAAAATGATTTTG
1 GTTTTTTAGGTTAAAGTGGTTTAG
* *
174424 GGTTTTAAGGTTAAAGTGGTTTAG
1 GTTTTTTAGGTTAAAGTGGTTTAG
*
174448 GTTTTTAAGG-TAAAGTGGTTTAG
1 GTTTTTTAGGTTAAAGTGGTTTAG
174471 G
1 G
174472 GTTAGATTAA
Statistics
Matches: 106, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
23 14 0.13
24 49 0.46
25 23 0.22
26 20 0.19
ACGTcount: A:0.24, C:0.01, G:0.30, T:0.45
Consensus pattern (24 bp):
GTTTTTTAGGTTAAAGTGGTTTAG
Found at i:174602 original size:28 final size:27
Alignment explanation
Indices: 174568--174642 Score: 107
Period size: 27 Copynumber: 2.7 Consensus size: 27
174558 AAAATTCAAT
*
174568 TACATTGAAATATTAGAAACAA-AATACA
1 TACATTGAAATATTAGAAA-AATAAGA-A
*
174596 TACATTGAAATATTAGAAAAATAAGAT
1 TACATTGAAATATTAGAAAAATAAGAA
174623 TACATTGAAATATTAGAAAA
1 TACATTGAAATATTAGAAAA
174643 GCACATACAT
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
27 22 0.50
28 22 0.50
ACGTcount: A:0.56, C:0.07, G:0.09, T:0.28
Consensus pattern (27 bp):
TACATTGAAATATTAGAAAAATAAGAA
Found at i:174634 original size:27 final size:26
Alignment explanation
Indices: 174550--174696 Score: 113
Period size: 28 Copynumber: 5.5 Consensus size: 26
174540 ACATTAAAAA
* *
174550 AAAT-TTAGAAAATTCAATTACATTG
1 AAATATTAGAAAAATAAATTACATTG
*
174575 AAATATTAGAAACAA-AATACATACATTG
1 AAATATTAGAAA-AATAA-A-TTACATTG
174603 AAATATTAGAAAAATAAGATTACATTG
1 AAATATTAGAAAAATAA-ATTACATTG
** * *
174630 AAATATTAGAAAAGCACA-TACATTA
1 AAATATTAGAAAAATAAATTACATTG
* * *
174655 AAATAGTAGAAAAGTACA-TACAATATTG
1 AAATATTAGAAAAATAAATTAC---ATTG
174683 AAATATTAGAAAAA
1 AAATATTAGAAAAA
174697 CACAAACATA
Statistics
Matches: 100, Mismatches: 14, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
25 29 0.29
26 9 0.09
27 25 0.25
28 37 0.37
ACGTcount: A:0.56, C:0.07, G:0.10, T:0.27
Consensus pattern (26 bp):
AAATATTAGAAAAATAAATTACATTG
Found at i:174658 original size:25 final size:25
Alignment explanation
Indices: 174568--174710 Score: 115
Period size: 28 Copynumber: 5.4 Consensus size: 25
174558 AAAATTCAAT
**
174568 TACATTGAAATATTAGAAACAAAATACA
1 TACATTGAAATATTAG--A-AAAGCACA
** *
174596 TACATTGAAATATTAGAAAAATAAGA
1 TACATTGAAATATTAG-AAAAGCACA
174622 TTACATTGAAATATTAGAAAAGCACA
1 -TACATTGAAATATTAGAAAAGCACA
* * *
174648 TACATTAAAATAGTAGAAAAGTACA
1 TACATTGAAATATTAGAAAAGCACA
*
174673 TACAATATTGAAATATTAGAAAAACACA
1 TAC---ATTGAAATATTAGAAAAGCACA
* *
174701 AACATAGAAA
1 TACATTGAAA
174711 ATACAATTAA
Statistics
Matches: 96, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
25 31 0.32
26 11 0.11
27 18 0.19
28 36 0.38
ACGTcount: A:0.57, C:0.09, G:0.10, T:0.24
Consensus pattern (25 bp):
TACATTGAAATATTAGAAAAGCACA
Found at i:177684 original size:170 final size:168
Alignment explanation
Indices: 177426--177934 Score: 612
Period size: 170 Copynumber: 3.0 Consensus size: 168
177416 AATATGCTTA
* * * *
177426 ATGGGATGAGACACTATGACATGGTAGAGATTATCTGAAAAGGTGAAAGCGCTTCTTGTGGGATG
1 ATGGGATGAGACACTATGACATGGCAAAGATTATATGAAAAGGTGAAAGAGCTTCTTGTGGGATG
* *
177491 TTCCTTCCCTTTTCGTCAGAGATTCTCTGCATTTTTCAATTAATAATAGCCCTAATTGATGTTCA
66 TGCCTTCCCTTTTCGTCAGAGATTCTCTACATTTTTCAATTAATAATAGCCCTAATTGATGTTC-
* * *
177556 CCATTGGGGAACTATTTACGCCAACACCTATTATGTTTG
130 CCATCGGGGAACTATTTACACCAACACCTATTATATTTG
* * * * *
177595 ATGGGATGAGACAATATGACATGACAAAGATTATTTGACAAAGGTGAAAGTGCTTTTTGTGGGAT
1 ATGGGATGAGACACTATGACATGGCAAAGATTATATGA-AAAGGTGAAAGAGCTTCTTGTGGGAT
* * *
177660 GAGCCTTCCCTTTTCGTAAGAGATTCTCTACATTTTTCAATTAATAATATCCCTAATTGATGTTT
65 GTGCCTTCCCTTTTCGTCAGAGATTCTCTACATTTTTCAATTAATAATAGCCCTAATTGATG-TT
* *
177725 CCCATCGGGGAACTATTTATATCAACACCTATTATATTTG
129 CCCATCGGGGAACTATTTACACCAACACCTATTATATTTG
* * *
177765 AT-GGACGAGACACTATGGCATGGCATAGATTATATGAAAAAAGGTAGAAA-AGCTTCTTGTGGG
1 ATGGGATGAGACACTATGACATGGCAAAGATTATATG--AAAAGGT-GAAAGAGCTTCTTGTGGG
* * * * *
177828 ACGTGCCTTCCATTTTCGTCAGAGATTCGT-TATATTTTTCAGTTAATAATAGCCCTAATTGTTG
63 ATGTGCCTTCCCTTTTCGTCAGAGATTC-TCTACATTTTTCAATTAATAATAGCCCTAATTGATG
**** * *
177892 TTATTTGTCGGGGAACTATTCACATCC-ACACCTATTATGTTTG
127 TT-CCCATCGGGGAACTATTTACA-CCAACACCTATTATATTTG
177935 TGGTCATAAA
Statistics
Matches: 291, Mismatches: 41, Indels: 15
0.84 0.12 0.04
Matches are distributed among these distances:
169 63 0.22
170 218 0.75
171 10 0.03
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (168 bp):
ATGGGATGAGACACTATGACATGGCAAAGATTATATGAAAAGGTGAAAGAGCTTCTTGTGGGATG
TGCCTTCCCTTTTCGTCAGAGATTCTCTACATTTTTCAATTAATAATAGCCCTAATTGATGTTCC
CATCGGGGAACTATTTACACCAACACCTATTATATTTG
Found at i:178132 original size:33 final size:34
Alignment explanation
Indices: 178061--178142 Score: 139
Period size: 34 Copynumber: 2.4 Consensus size: 34
178051 TATACATAAG
178061 ATTTTGTTTGTGGTCCAAACTTTCAAAACTTCTC
1 ATTTTGTTTGTGGTCCAAACTTTCAAAACTTCTC
* *
178095 ATTTTGTTTGTGGTCCTAACTTTTAAAA-TTCTC
1 ATTTTGTTTGTGGTCCAAACTTTCAAAACTTCTC
178128 ATTTTGTTTGTGGTC
1 ATTTTGTTTGTGGTC
178143 ATCACTTCCC
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
33 20 0.43
34 26 0.57
ACGTcount: A:0.20, C:0.16, G:0.15, T:0.50
Consensus pattern (34 bp):
ATTTTGTTTGTGGTCCAAACTTTCAAAACTTCTC
Found at i:178163 original size:33 final size:33
Alignment explanation
Indices: 178061--178150 Score: 112
Period size: 33 Copynumber: 2.7 Consensus size: 33
178051 TATACATAAG
178061 ATTTTGTTTGTGGTCCA-AACTTTCAAAACTTCTC
1 ATTTTGTTTGTGGT-CATAAC-TTCAAAACTTCTC
* *
178095 ATTTTGTTTGTGGTCCTAACTTTTAAAA-TTCTC
1 ATTTTGTTTGTGGTCATAAC-TTCAAAACTTCTC
*
178128 ATTTTGTTTGTGGTCATCACTTC
1 ATTTTGTTTGTGGTCATAACTTC
178151 CCAACTTTTC
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
32 2 0.04
33 24 0.48
34 24 0.48
ACGTcount: A:0.20, C:0.18, G:0.13, T:0.49
Consensus pattern (33 bp):
ATTTTGTTTGTGGTCATAACTTCAAAACTTCTC
Found at i:179243 original size:18 final size:18
Alignment explanation
Indices: 179217--179260 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
179207 AATAATAAAT
179217 CATTAAACATTTAACAAA
1 CATTAAACATTTAACAAA
*
179235 CATTTAACATTTAACAAA
1 CATTAAACATTTAACAAA
179253 CA-TAAACA
1 CATTAAACA
179261 AATATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 5 0.21
18 19 0.79
ACGTcount: A:0.55, C:0.18, G:0.00, T:0.27
Consensus pattern (18 bp):
CATTAAACATTTAACAAA
Found at i:181097 original size:30 final size:30
Alignment explanation
Indices: 181063--181121 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
181053 TTAAAAGATG
181063 AGGAAGTTATGGAAGATTAAAGAGAATGGT
1 AGGAAGTTATGGAAGATTAAAGAGAATGGT
181093 AGGAAGTTATGGAAGATTAAAGAGAATGG
1 AGGAAGTTATGGAAGATTAAAGAGAATGG
181122 GTTTTTAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.44, C:0.00, G:0.34, T:0.22
Consensus pattern (30 bp):
AGGAAGTTATGGAAGATTAAAGAGAATGGT
Found at i:182185 original size:12 final size:12
Alignment explanation
Indices: 182170--182217 Score: 64
Period size: 12 Copynumber: 4.2 Consensus size: 12
182160 AGCACTGTAT
182170 ATGGTACTGTTC
1 ATGGTACTGTTC
*
182182 ATGGTATTGTTC
1 ATGGTACTGTTC
182194 --GGTACTGTTC
1 ATGGTACTGTTC
*
182204 ACGGTACTGTTC
1 ATGGTACTGTTC
182216 AT
1 AT
182218 ACCGTATAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
10 9 0.29
12 22 0.71
ACGTcount: A:0.17, C:0.17, G:0.25, T:0.42
Consensus pattern (12 bp):
ATGGTACTGTTC
Found at i:182197 original size:22 final size:22
Alignment explanation
Indices: 182172--182215 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
182162 CACTGTATAT
* *
182172 GGTACTGTTCATGGTATTGTTC
1 GGTACTGTTCACGGTACTGTTC
182194 GGTACTGTTCACGGTACTGTTC
1 GGTACTGTTCACGGTACTGTTC
182216 ATACCGTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.14, C:0.18, G:0.27, T:0.41
Consensus pattern (22 bp):
GGTACTGTTCACGGTACTGTTC
Found at i:184309 original size:2 final size:2
Alignment explanation
Indices: 184302--184369 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
184292 AATCATCAAT
184302 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
184344 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
184370 ATCTAAAACC
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:186061 original size:23 final size:22
Alignment explanation
Indices: 186012--186055 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
186002 AGTCTCTATT
* *
186012 AATTTAAATATTATTTAATCTA
1 AATTTAAATATTAATAAATCTA
186034 AATTTAAATATTTAATAAATCT
1 AATTTAAATA-TTAATAAATCT
186056 CTATTTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (22 bp):
AATTTAAATATTAATAAATCTA
Found at i:192710 original size:20 final size:20
Alignment explanation
Indices: 192687--192734 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
192677 GAACAAATTT
*
192687 TCTTGCCAAGGCGAGTTTTA
1 TCTTGCAAAGGCGAGTTTTA
192707 TCTTGCAAAGGCGAGTTTTA
1 TCTTGCAAAGGCGAGTTTTA
192727 TCTTGCAA
1 TCTTGCAA
192735 GTCTAACACA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (20 bp):
TCTTGCAAAGGCGAGTTTTA
Found at i:193721 original size:20 final size:20
Alignment explanation
Indices: 193696--193736 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
193686 ATCATCCTAG
193696 ACATAGAATAATTTCTTGCT
1 ACATAGAATAATTTCTTGCT
193716 ACATAGAATAATTTCTTGCT
1 ACATAGAATAATTTCTTGCT
193736 A
1 A
193737 TAGGAAAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.39
Consensus pattern (20 bp):
ACATAGAATAATTTCTTGCT
Found at i:196269 original size:18 final size:18
Alignment explanation
Indices: 196246--196280 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
196236 GTTTTTTGGG
196246 TTTATGAAATTTAAGAAT
1 TTTATGAAATTTAAGAAT
* *
196264 TTTATGATATTTTAGAA
1 TTTATGAAATTTAAGAA
196281 AATTTATGAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (18 bp):
TTTATGAAATTTAAGAAT
Found at i:196277 original size:28 final size:25
Alignment explanation
Indices: 196246--196307 Score: 70
Period size: 28 Copynumber: 2.3 Consensus size: 25
196236 GTTTTTTGGG
196246 TTTATGAAATTTAAGAATTTTATGATAT
1 TTTA-GAAATTTAAG-ATTTT-TGATAT
* *
196274 TTTAGAAAATTTATGATTTTTTATAT
1 TTTAG-AAATTTAAGATTTTTGATAT
196300 TTTAGAAA
1 TTTAGAAA
196308 AAATTAGGGC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
25 3 0.10
26 10 0.32
27 6 0.19
28 12 0.39
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.52
Consensus pattern (25 bp):
TTTAGAAATTTAAGATTTTTGATAT
Found at i:196286 original size:19 final size:18
Alignment explanation
Indices: 196246--196296 Score: 57
Period size: 19 Copynumber: 2.8 Consensus size: 18
196236 GTTTTTTGGG
* * *
196246 TTTATGAAATTTAAGAAT
1 TTTATGATATTTTAGAAA
196264 TTTATGATATTTTAGAAAA
1 TTTATGATATTTTAG-AAA
*
196283 TTTATGATTTTTTA
1 TTTATGATATTTTA
196297 TATTTTAGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
18 13 0.46
19 15 0.54
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (18 bp):
TTTATGATATTTTAGAAA
Found at i:196312 original size:28 final size:28
Alignment explanation
Indices: 196252--196308 Score: 82
Period size: 26 Copynumber: 2.1 Consensus size: 28
196242 TGGGTTTATG
196252 AAATTTAAGAATTTTATGATATTTTAGA
1 AAATTTAAGAATTTTATGATATTTTAGA
* *
196280 AAATTTATG-ATTTT-TTATATTTTAGA
1 AAATTTAAGAATTTTATGATATTTTAGA
196306 AAA
1 AAA
196309 AATTAGGGCC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 14 0.52
27 5 0.19
28 8 0.30
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (28 bp):
AAATTTAAGAATTTTATGATATTTTAGA
Found at i:196469 original size:31 final size:31
Alignment explanation
Indices: 196426--196554 Score: 118
Period size: 31 Copynumber: 4.2 Consensus size: 31
196416 GTAACAGACC
* *
196426 AGACACATAAAAGTGTAACAGAGAAAAAGTT
1 AGACACCTAAAAGTGTAACGGAGAAAAAGTT
* ** * *
196457 AAACACCTAAAAGTGTAGTGGATAAAACGTT
1 AGACACCTAAAAGTGTAACGGAGAAAAAGTT
**
196488 AGACACCTAAAAGTAAAACGGAGAAAACA-TT
1 AGACACCTAAAAGTGTAACGGAGAAAA-AGTT
** *
196519 AGACACCTAAAAGTAAAACGAAGAAAACA-TT
1 AGACACCTAAAAGTGTAACGGAGAAAA-AGTT
196550 AGACA
1 AGACA
196555 TATTTTTATC
Statistics
Matches: 82, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
31 82 1.00
ACGTcount: A:0.53, C:0.14, G:0.17, T:0.16
Consensus pattern (31 bp):
AGACACCTAAAAGTGTAACGGAGAAAAAGTT
Found at i:196967 original size:20 final size:20
Alignment explanation
Indices: 196942--196979 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
196932 GGCCGTTTCT
196942 AGCCGTTGG-GAGTGTTTTGG
1 AGCCGTTGGAGA-TGTTTTGG
196962 AGCCGTTGGAGATGTTTT
1 AGCCGTTGGAGATGTTTT
196980 TCTCTGCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.13, C:0.11, G:0.39, T:0.37
Consensus pattern (20 bp):
AGCCGTTGGAGATGTTTTGG
Found at i:198994 original size:2 final size:2
Alignment explanation
Indices: 198989--199013 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
198979 ATTAACACAC
198989 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
199014 AGCCATGCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:201104 original size:111 final size:110
Alignment explanation
Indices: 200851--201414 Score: 729
Period size: 110 Copynumber: 5.1 Consensus size: 110
200841 CTTAGGGAAG
** * * * * * *
200851 ATTGAATTGATGCAGACTTATTCCGCTATCACTCAAGGAATATCAAATCTTGAAAGAGAGGGGTC
1 ATTGAATTGGGGCAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGATATGGATC
* * * *
200916 TATT-TAGCTTATT-TAAAAGGGAATATCAAATATGGGGGAGTTGATCC
66 TGTTCCA-CTTCTTCT--AAGGGAATATCAGATAT-GGGGAGTTGATCC
* * * * * *
200963 ATTGAATCGGGGAAGACTTATTCCGATGTCACTCAGGGAATACCAAATCTTGAAAGAGATGGATC
1 ATTGAATTGGGGCAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGATATGGATC
* * * *
201028 TGTTCCACTTCTTTTAAGGGAATATCATATCTGGGGGAGTTTATCC
66 TGTTCCACTTCTTCTAAGGGAATATCAGATAT-GGGGAGTTGATCC
* * *
201074 ATTGAATTGGGGCAAACTTGTTCCGCTGTCACTCAGGGAATATCAAATATTGAAAGATATGGATT
1 ATTGAATTGGGGCAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGATATGGATC
* *
201139 TATTCCACTTCTTCTAAGGGAATATCAGATATGGGAAGTTGATCC
66 TGTTCCACTTCTTCTAAGGGAATATCAGATATGGGGAGTTGATCC
* * *
201184 ATTGAATTGGGACAGACTTGTTCCACTGTCACTCATGGAATATCAAATCTTGAAAGATATGGATC
1 ATTGAATTGGGGCAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGATATGGATC
* *
201249 TGTTCCACTTCTTCTAAGGTAATATCAGATCTGGGGAGTTGATCC
66 TGTTCCACTTCTTCTAAGGGAATATCAGATATGGGGAGTTGATCC
* * *
201294 ATTGAATCT-GGGCAGACTTGTTCCACTGTCACTCAGGGAATATCAATTCTTAAAAGATATGGAT
1 ATTGAAT-TGGGGCAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGATATGGAT
*
201358 CTGTTCCACTTCTTCTAAGGGAATATCATATATGGGGAGTTGATCC
65 CTGTTCCACTTCTTCTAAGGGAATATCAGATATGGGGAGTTGATCC
201404 ATTGAATTGGG
1 ATTGAATTGGG
201415 ATTGAACATG
Statistics
Matches: 400, Mismatches: 48, Indels: 10
0.87 0.10 0.02
Matches are distributed among these distances:
109 1 0.00
110 221 0.55
111 113 0.28
112 63 0.16
113 2 0.00
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (110 bp):
ATTGAATTGGGGCAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGATATGGATC
TGTTCCACTTCTTCTAAGGGAATATCAGATATGGGGAGTTGATCC
Found at i:202585 original size:13 final size:12
Alignment explanation
Indices: 202562--202595 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
202552 TGAACCTTCA
202562 TTTTATTTTTTC
1 TTTTATTTTTTC
202574 TTTTATTTTTT-
1 TTTTATTTTTTC
*
202585 TTTCATTTTTT
1 TTTTATTTTTT
202596 AGTCTTTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.09, C:0.06, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTATTTTTTC
Found at i:202595 original size:18 final size:18
Alignment explanation
Indices: 202574--202624 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
202564 TTATTTTTTC
*
202574 TTTTATTTTTTTTTCATT
1 TTTTATTTCTTTTTCATT
*
202592 TTTTA-GTCTTTTTCATT
1 TTTTATTTCTTTTTCATT
202609 TTCTT-TTTCTTTTTCA
1 TT-TTATTTCTTTTTCA
202625 GGCGAAATAC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
17 12 0.43
18 16 0.57
ACGTcount: A:0.10, C:0.12, G:0.02, T:0.76
Consensus pattern (18 bp):
TTTTATTTCTTTTTCATT
Found at i:209290 original size:24 final size:24
Alignment explanation
Indices: 209250--209295 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
209240 TTTGTTCCCA
*
209250 TTCTTTTTTAATCTCCTTATCCTG
1 TTCTTTTTTAATCTCCTCATCCTG
*
209274 TTCTTTTTT-GTCTTCCTCATCC
1 TTCTTTTTTAATC-TCCTCATCC
209296 AAATCAAGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 2 0.11
24 17 0.89
ACGTcount: A:0.09, C:0.28, G:0.04, T:0.59
Consensus pattern (24 bp):
TTCTTTTTTAATCTCCTCATCCTG
Found at i:223566 original size:40 final size:40
Alignment explanation
Indices: 223521--223623 Score: 197
Period size: 40 Copynumber: 2.6 Consensus size: 40
223511 AACGAGCCCT
223521 TTGTTCATGTTCGTTCATTTAATTAAACGAACGCAAAATC
1 TTGTTCATGTTCGTTCATTTAATTAAACGAACGCAAAATC
223561 TTGTTCATGTTCGTTCATTTAATTAAACGAACGCAAAATC
1 TTGTTCATGTTCGTTCATTTAATTAAACGAACGCAAAATC
*
223601 TTATTCATGTTCGTTCATTTAAT
1 TTGTTCATGTTCGTTCATTTAAT
223624 AAATAAACGA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 62 1.00
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.42
Consensus pattern (40 bp):
TTGTTCATGTTCGTTCATTTAATTAAACGAACGCAAAATC
Found at i:224066 original size:2 final size:2
Alignment explanation
Indices: 224061--224141 Score: 162
Period size: 2 Copynumber: 40.5 Consensus size: 2
224051 AGCGTGTGTT
224061 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
224103 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
224142 GTTTTAAATA
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 79 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:227810 original size:24 final size:24
Alignment explanation
Indices: 227783--227889 Score: 94
Period size: 24 Copynumber: 4.5 Consensus size: 24
227773 AAATAATTTA
*
227783 TCTGATTTCCGACTTGAATTCTGT
1 TCTGATTTCTGACTTGAATTCTGT
* *
227807 TCTGA-TACATGACCTGAATTCTGT
1 TCTGATTTC-TGACTTGAATTCTGT
*
227831 TCTGATTTCTGA-TATGGATTCTGT
1 TCTGATTTCTGACT-TGAATTCTGT
* * **
227855 TCTGATATATTTC-TGAATTCTGT
1 TCTGATTTCTGACTTGAATTCTGT
*
227878 TTTGATTTCTGA
1 TCTGATTTCTGA
227890 TATCTCCGTT
Statistics
Matches: 63, Mismatches: 16, Indels: 9
0.72 0.18 0.10
Matches are distributed among these distances:
23 18 0.29
24 43 0.68
25 2 0.03
ACGTcount: A:0.20, C:0.16, G:0.17, T:0.48
Consensus pattern (24 bp):
TCTGATTTCTGACTTGAATTCTGT
Found at i:227835 original size:12 final size:12
Alignment explanation
Indices: 227797--227888 Score: 55
Period size: 12 Copynumber: 7.8 Consensus size: 12
227787 ATTTCCGACT
227797 TGAATTCTGTTC
1 TGAATTCTGTTC
* **
227809 TG-ATACATGACC
1 TGAATTC-TGTTC
227821 TGAATTCTGTTC
1 TGAATTCTGTTC
* * *
227833 TGATTTCTGATA
1 TGAATTCTGTTC
*
227845 TGGATTCTGTTC
1 TGAATTCTGTTC
*
227857 TG-ATATAT-TTC
1 TGAAT-TCTGTTC
*
227868 TGAATTCTGTTT
1 TGAATTCTGTTC
*
227880 TGATTTCTG
1 TGAATTCTG
227889 ATATCTCCGT
Statistics
Matches: 58, Mismatches: 17, Indels: 10
0.68 0.20 0.12
Matches are distributed among these distances:
11 12 0.21
12 43 0.74
13 3 0.05
ACGTcount: A:0.20, C:0.14, G:0.17, T:0.49
Consensus pattern (12 bp):
TGAATTCTGTTC
Found at i:227842 original size:19 final size:19
Alignment explanation
Indices: 227820--227889 Score: 50
Period size: 19 Copynumber: 3.2 Consensus size: 19
227810 GATACATGAC
227820 CTGAATTCTGTTCTGATTT
1 CTGAATTCTGTTCTGATTT
227839 CTGATATGGATTCTGTTCTGATATATTT
1 CTG--A---ATTCTGTTCTG----ATTT
*
227867 CTGAATTCTGTTTTGATTT
1 CTGAATTCTGTTCTGATTT
227886 CTGA
1 CTGA
227890 TATCTCCGTT
Statistics
Matches: 41, Mismatches: 1, Indels: 18
0.68 0.02 0.30
Matches are distributed among these distances:
19 11 0.27
21 1 0.02
23 10 0.24
24 11 0.27
26 1 0.02
28 7 0.17
ACGTcount: A:0.19, C:0.13, G:0.17, T:0.51
Consensus pattern (19 bp):
CTGAATTCTGTTCTGATTT
Found at i:227887 original size:47 final size:48
Alignment explanation
Indices: 227783--227892 Score: 143
Period size: 48 Copynumber: 2.3 Consensus size: 48
227773 AAATAATTTA
* *
227783 TCTGATTTCCGACT-TGAATTCTGTTCTGATACATGACCTGAATTCTGT
1 TCTGATTTCTGA-TATGGATTCTGTTCTGATACATGACCTGAATTCTGT
* **
227831 TCTGATTTCTGATATGGATTCTGTTCTGATATAT-TTCTGAATTCTGT
1 TCTGATTTCTGATATGGATTCTGTTCTGATACATGACCTGAATTCTGT
*
227878 TTTGATTTCTGATAT
1 TCTGATTTCTGATAT
227893 CTCCGTTTAT
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
47 26 0.47
48 29 0.53
ACGTcount: A:0.20, C:0.15, G:0.16, T:0.48
Consensus pattern (48 bp):
TCTGATTTCTGATATGGATTCTGTTCTGATACATGACCTGAATTCTGT
Found at i:232586 original size:12 final size:12
Alignment explanation
Indices: 232549--232641 Score: 66
Period size: 12 Copynumber: 7.8 Consensus size: 12
232539 ATTTTCGACT
232549 TGAATTCTGTTC
1 TGAATTCTGTTC
* *
232561 TG-ATACATGATC
1 TGAATTC-TGTTC
232573 TGAATTCTGTTC
1 TGAATTCTGTTC
* *
232585 TGATTTCTGATC
1 TGAATTCTGTTC
*
232597 T-AGATTCTGTTT
1 TGA-ATTCTGTTC
*
232609 TG-ATGTCTGTTA
1 TGAAT-TCTGTTC
*
232621 TGAATTCTGTTT
1 TGAATTCTGTTC
*
232633 TGATTTCTG
1 TGAATTCTG
232642 ATATCTCTGT
Statistics
Matches: 63, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
11 6 0.10
12 52 0.83
13 5 0.08
ACGTcount: A:0.18, C:0.13, G:0.18, T:0.51
Consensus pattern (12 bp):
TGAATTCTGTTC
Found at i:232595 original size:24 final size:24
Alignment explanation
Indices: 232549--232643 Score: 104
Period size: 24 Copynumber: 4.0 Consensus size: 24
232539 ATTTTCGACT
*
232549 TGAATTCTGTTCTGA-TACATGATC
1 TGAATTCTGTTCTGATTTC-TGATC
232573 TGAATTCTGTTCTGATTTCTGATC
1 TGAATTCTGTTCTGATTTCTGATC
* * * *
232597 T-AGATTCTGTTTTGATGTCTGTTA
1 TGA-ATTCTGTTCTGATTTCTGATC
*
232621 TGAATTCTGTTTTGATTTCTGAT
1 TGAATTCTGTTCTGATTTCTGAT
232644 ATCTCTGTTT
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
23 1 0.02
24 57 0.93
25 3 0.05
ACGTcount: A:0.19, C:0.13, G:0.18, T:0.51
Consensus pattern (24 bp):
TGAATTCTGTTCTGATTTCTGATC
Found at i:232605 original size:48 final size:48
Alignment explanation
Indices: 232552--232643 Score: 123
Period size: 48 Copynumber: 1.9 Consensus size: 48
232542 TTCGACTTGA
*
232552 ATTCTGTTCTGAT-ACATGATCTGAATTCTGTTCTGATTTCTGATCTAG
1 ATTCTGTTCTGATGAC-TGATATGAATTCTGTTCTGATTTCTGATCTAG
* * * *
232600 ATTCTGTTTTGATGTCTGTTATGAATTCTGTTTTGATTTCTGAT
1 ATTCTGTTCTGATGACTGATATGAATTCTGTTCTGATTTCTGAT
232644 ATCTCTGTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
48 37 0.97
49 1 0.03
ACGTcount: A:0.18, C:0.13, G:0.17, T:0.51
Consensus pattern (48 bp):
ATTCTGTTCTGATGACTGATATGAATTCTGTTCTGATTTCTGATCTAG
Found at i:240114 original size:21 final size:21
Alignment explanation
Indices: 240082--240143 Score: 106
Period size: 21 Copynumber: 3.0 Consensus size: 21
240072 TAATGAACAG
*
240082 TGCTATAGTGCATCGATGCAT
1 TGCTACAGTGCATCGATGCAT
*
240103 TGCTACATTGCATCGATGCAT
1 TGCTACAGTGCATCGATGCAT
240124 TGCTACAGTGCATCGATGCA
1 TGCTACAGTGCATCGATGCA
240144 CATAAATTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.31
Consensus pattern (21 bp):
TGCTACAGTGCATCGATGCAT
Found at i:240860 original size:31 final size:31
Alignment explanation
Indices: 240825--240885 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
240815 CCGAAGGACT
* *
240825 AGTCCATATATTCC-AAAGAACCTAGGTAAAC
1 AGTCCATAT-GTCCTAAAGAACATAGGTAAAC
240856 AGTCCATATGTCCTAAAGAACATAGGTAAA
1 AGTCCATATGTCCTAAAGAACATAGGTAAA
240886 ACCTCGACCC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 3 0.11
31 24 0.89
ACGTcount: A:0.43, C:0.20, G:0.15, T:0.23
Consensus pattern (31 bp):
AGTCCATATGTCCTAAAGAACATAGGTAAAC
Found at i:251041 original size:24 final size:24
Alignment explanation
Indices: 251009--251058 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
250999 TGTATCATAC
251009 TTATACTAAACACACAGAAAAGGT
1 TTATACTAAACACACAGAAAAGGT
251033 TTATACTAAACACACAGAAAAGGT
1 TTATACTAAACACACAGAAAAGGT
251057 TT
1 TT
251059 TCTCTTCCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.48, C:0.16, G:0.12, T:0.24
Consensus pattern (24 bp):
TTATACTAAACACACAGAAAAGGT
Found at i:253321 original size:55 final size:54
Alignment explanation
Indices: 253222--253329 Score: 162
Period size: 55 Copynumber: 2.0 Consensus size: 54
253212 ATGTATGTTG
* * *
253222 ATTCACATGAGTCAACACATAAAAAAGTAAACAAAGTAAGTGCATACATGGTCA
1 ATTCACATGAGTCAAAACACAAAAAAGAAAACAAAGTAAGTGCATACATGGTCA
* *
253276 ATTCACATGAGTCAAAAACACAAAAAGGAAAACAAGGTAAGTGCATACATGGTC
1 ATTCACATGAGTC-AAAACACAAAAAAGAAAACAAAGTAAGTGCATACATGGTC
253330 TCAGGGTCTG
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
54 13 0.27
55 35 0.73
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.19
Consensus pattern (54 bp):
ATTCACATGAGTCAAAACACAAAAAAGAAAACAAAGTAAGTGCATACATGGTCA
Found at i:260921 original size:18 final size:18
Alignment explanation
Indices: 260898--260936 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
260888 AAAGGCGATG
*
260898 GCGGCATCATATATGGCT
1 GCGGCATCATATATGCCT
260916 GCGGCATCATATATGCCT
1 GCGGCATCATATATGCCT
260934 GCG
1 GCG
260937 ATGGCTGCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.26, G:0.28, T:0.26
Consensus pattern (18 bp):
GCGGCATCATATATGCCT
Found at i:262632 original size:111 final size:111
Alignment explanation
Indices: 262445--262769 Score: 506
Period size: 111 Copynumber: 3.0 Consensus size: 111
262435 ATTACAAAAA
262445 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAA--T---TTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
262505 AATT-AAA--TTAAAATGTTACTGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACTGTATCAGCAAAGTGTCGAGATAT
*
262548 TTAATTCTTAATCTAATAATCATGCATTAAATAAATTAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
* * *
262613 AATTAAAACGTTAAAATGTTA-TCGTATCAGCAAAATATCGATATAT
66 AATTAAAACGTTAAAATGTTACT-GTATCAGCAAAGTGTCGAGATAT
*
262659 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
** *
262724 AATTAAAACGTTAAAATGTTACCATATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACTGTATCAGCAAAGTGTCGAGATAT
262770 ATGATTTCTA
Statistics
Matches: 200, Mismatches: 12, Indels: 12
0.89 0.05 0.05
Matches are distributed among these distances:
103 55 0.28
105 1 0.00
108 7 0.04
109 3 0.01
110 1 0.00
111 133 0.67
ACGTcount: A:0.46, C:0.10, G:0.07, T:0.37
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACTGTATCAGCAAAGTGTCGAGATAT
Found at i:263629 original size:31 final size:30
Alignment explanation
Indices: 263594--263761 Score: 103
Period size: 31 Copynumber: 5.5 Consensus size: 30
263584 TAGATATCTT
* * *
263594 TAAAATGTTAAATGTGATAGTTATTATTTGA
1 TAAAATATTTAATATGATA-TTATTATTTGA
*
263625 TAAAATATTTAATAT-ATATTTTTATTTTGA
1 TAAAATATTTAATATGATATTATTA-TTTGA
*
263655 TAAAAATATTTAATATGATATT-TACATTTGA
1 T-AAAATATTTAATATGATATTAT-TATTTGA
* * * * * *
263686 TAAAAATATTTGATGTAACACTT-GTATTT-T
1 T-AAAATATTTAATATGATA-TTATTATTTGA
* *
263716 TAAAATATCTAATATGATACTTA-TACTTTGT
1 TAAAATATTTAATATGATA-TTATTA-TTTGA
*
263747 TAAAATATCTAATAT
1 TAAAATATTTAATAT
263762 AGTACTTGAA
Statistics
Matches: 112, Mismatches: 17, Indels: 16
0.77 0.12 0.11
Matches are distributed among these distances:
29 23 0.21
30 13 0.12
31 68 0.61
32 8 0.07
ACGTcount: A:0.41, C:0.04, G:0.08, T:0.47
Consensus pattern (30 bp):
TAAAATATTTAATATGATATTATTATTTGA
Found at i:263737 original size:29 final size:31
Alignment explanation
Indices: 263705--263769 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
263695 TTGATGTAAC
263705 ACTTGTA-TTT-TTAAAATATCTAATAT-GAT
1 ACTTGTACTTTGTTAAAATATCTAATATAG-T
*
263734 ACTTATACTTTGTTAAAATATCTAATATAGT
1 ACTTGTACTTTGTTAAAATATCTAATATAGT
263765 ACTTG
1 ACTTG
263770 AACTATCATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 6 0.19
30 3 0.10
31 21 0.68
32 1 0.03
ACGTcount: A:0.37, C:0.09, G:0.08, T:0.46
Consensus pattern (31 bp):
ACTTGTACTTTGTTAAAATATCTAATATAGT
Found at i:263769 original size:60 final size:60
Alignment explanation
Indices: 263619--263769 Score: 146
Period size: 60 Copynumber: 2.5 Consensus size: 60
263609 GATAGTTATT
* * * *
263619 ATTTGATAAAATATTTAATATATATTTTTATTTTGATAAAAATATTTAATATGATATTTAC
1 ATTTGTTAAAATATTTAATATATACTTGTATTTT-ATAAAAATATCTAATATGATATTTAC
* * * *
263680 ATTTGATAAAAATATTTGATGTAACACTTGTATTTT-T-AAAATATCTAATATGATACTTATAC
1 ATTTG-TTAAAATATTTAATAT-ATACTTGTATTTTATAAAAATATCTAATATGATA-TT-TAC
*
263742 -TTTGTTAAAATATCTAATATAGTACTTG
1 ATTTGTTAAAATATTTAATATA-TACTTG
263770 AACTATCATT
Statistics
Matches: 72, Mismatches: 13, Indels: 11
0.75 0.14 0.11
Matches are distributed among these distances:
59 1 0.01
60 34 0.47
61 12 0.17
62 15 0.21
63 10 0.14
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.47
Consensus pattern (60 bp):
ATTTGTTAAAATATTTAATATATACTTGTATTTTATAAAAATATCTAATATGATATTTAC
Found at i:265376 original size:29 final size:29
Alignment explanation
Indices: 265333--265442 Score: 195
Period size: 29 Copynumber: 3.8 Consensus size: 29
265323 TTTTATATGT
265333 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
265361 TCATGTAGTTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
265390 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
265419 TCATGTAGCTCATGTCATGTTCTC
1 TCATGTAGCTCATGTCAT-TTCTC
265443 ATATCACATA
Statistics
Matches: 78, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
28 7 0.09
29 66 0.85
30 5 0.06
ACGTcount: A:0.17, C:0.21, G:0.16, T:0.45
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:265886 original size:64 final size:63
Alignment explanation
Indices: 265813--265969 Score: 167
Period size: 64 Copynumber: 2.5 Consensus size: 63
265803 TAATGAAGGT
* * **
265813 ATGCATCGATGCACTACTTGTGCATCGGTGCA-TAAAGTGCATTCGATG-TTTTATTATTAATGG
1 ATGCATCGATGCACTACTTGTGCATCGATGCACT-AAGTGCATTCGATGCTTATATT-TTAA-AA
265876 G
63 G
* * *
265877 ATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTCGATGCTTATATTTTAAAAG
1 ATGCATCGATGCACT-ACTTGTGCATCGATGCACTAAGTGCATTCGATGCTTATATTTTAAAAG
* *
265940 AGTGCATCAATGCACTACCTGTGCATCGAT
1 A-TGCATCGATGCACTACTTGTGCATCGAT
265970 ACACCTTCAA
Statistics
Matches: 77, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
63 3 0.04
64 66 0.86
65 8 0.10
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTGTGCATCGATGCACTAAGTGCATTCGATGCTTATATTTTAAAAG
Found at i:272274 original size:29 final size:29
Alignment explanation
Indices: 272231--272340 Score: 177
Period size: 29 Copynumber: 3.8 Consensus size: 29
272221 TTTTATATGT
272231 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
272259 TCATGTAGTTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
272288 TCATGTAGCTCATGTCATTTCTCTTGGGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
272317 TCACGTAGCTCATGTCATGTTCTC
1 TCATGTAGCTCATGTCAT-TTCTC
272341 ATATCACATA
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
28 7 0.09
29 64 0.84
30 5 0.07
ACGTcount: A:0.17, C:0.22, G:0.17, T:0.44
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:272867 original size:64 final size:64
Alignment explanation
Indices: 272715--272871 Score: 151
Period size: 64 Copynumber: 2.5 Consensus size: 64
272705 TAATGAAGGT
** * * *
272715 ATGCATCGATGCACTATTTGTGCATCGGTGCATAAAATACATTCGATGTTTTATTATTAATGGG
1 ATGCATCGATGCACTACCTGTGCATCGATGCATAAAATACATTCGATGTTTTATTATTAAAGAG
* * * * * *
272779 ATGCATTGATGCA-TGCCTTATGCATCGATGCACT-AATTGCATTTGATGTTTATATT-TTAAA-
1 ATGCATCGATGCACTACC-TGTGCATCGATGCA-TAAAATACATTCGATGTTT-TATTATTAAAG
272840 AG
63 AG
272842 AGTGCATCGATGCACTACCTGTGCATCGAT
1 A-TGCATCGATGCACTACCTGTGCATCGAT
272872 ACACCTTCAA
Statistics
Matches: 74, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
63 3 0.04
64 63 0.85
65 8 0.11
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (64 bp):
ATGCATCGATGCACTACCTGTGCATCGATGCATAAAATACATTCGATGTTTTATTATTAAAGAG
Found at i:274625 original size:16 final size:18
Alignment explanation
Indices: 274594--274632 Score: 64
Period size: 16 Copynumber: 2.3 Consensus size: 18
274584 TAATCATAAA
274594 AATATATTAAATAATTTT
1 AATATATTAAATAATTTT
274612 AATATATT-AA-AATTTT
1 AATATATTAAATAATTTT
274628 AATAT
1 AATAT
274633 TTTTTTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 11 0.52
17 2 0.10
18 8 0.38
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AATATATTAAATAATTTT
Found at i:280762 original size:29 final size:29
Alignment explanation
Indices: 280730--280787 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
280720 AACTCAAGTC
*
280730 ACCATTG-CTAATTATTCTTAACTCGAACA
1 ACCATTGTC-AATCATTCTTAACTCGAACA
*
280759 ACCATTGTCAATCATTCTTAACTGGAACA
1 ACCATTGTCAATCATTCTTAACTCGAACA
280788 TTTAAAACTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 25 0.96
30 1 0.04
ACGTcount: A:0.34, C:0.24, G:0.09, T:0.33
Consensus pattern (29 bp):
ACCATTGTCAATCATTCTTAACTCGAACA
Found at i:281950 original size:23 final size:23
Alignment explanation
Indices: 281924--281971 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
281914 ATAAAGTACA
*
281924 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
281947 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
281970 AT
1 AT
281972 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:282378 original size:21 final size:22
Alignment explanation
Indices: 282353--282404 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
282343 ACACTTTACA
*
282353 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
282376 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
282399 ATATAA
1 ATATAA
282405 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:282389 original size:23 final size:23
Alignment explanation
Indices: 282363--282425 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
282353 ATATAACCAC
282363 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
282386 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
282409 TACCTATTACATCATAT
1 TACCTATTACATTATAT
282426 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:282880 original size:39 final size:39
Alignment explanation
Indices: 282826--282951 Score: 234
Period size: 39 Copynumber: 3.2 Consensus size: 39
282816 TCAAGTTGTA
282826 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
282865 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
* *
282904 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
282943 GATTTTGAT
1 GATTTTGAT
282952 GAGCATCGGA
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 85 1.00
ACGTcount: A:0.17, C:0.13, G:0.21, T:0.48
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
Found at i:283233 original size:18 final size:18
Alignment explanation
Indices: 283210--283246 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
283200 CGAAATATAT
283210 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
283228 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
283246 A
1 A
283247 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:283528 original size:25 final size:25
Alignment explanation
Indices: 283494--283544 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
283484 TTAATCCAAA
*
283494 TAATGTACCCATAACAATGTTCAAT
1 TAATGTACCCACAACAATGTTCAAT
*
283519 TAATGTACCCACAACAATGTTTAAT
1 TAATGTACCCACAACAATGTTCAAT
283544 T
1 T
283545 GATTTGTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (25 bp):
TAATGTACCCACAACAATGTTCAAT
Found at i:283844 original size:23 final size:23
Alignment explanation
Indices: 283818--283880 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
283808 ATATAACCAC
283818 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
283841 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
283864 TACCTATTACATCATAT
1 TACCTATTACATTATAT
283881 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:284074 original size:29 final size:29
Alignment explanation
Indices: 284026--284090 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 29
284016 TCATTTGCAC
* * *
284026 AAAA-ATTATTTGATTGTTTTTATTTTAT
1 AAAATATTATTTGAATGTTTTAATTTAAT
284054 AAAATATTATTTAGAAT-TTTTAATTTAAT
1 AAAATATTATTT-GAATGTTTTAATTTAAT
284083 AATAATAT
1 AA-AATAT
284091 ACCGTAACGT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
28 4 0.13
29 19 0.61
30 8 0.26
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.54
Consensus pattern (29 bp):
AAAATATTATTTGAATGTTTTAATTTAAT
Found at i:284219 original size:22 final size:22
Alignment explanation
Indices: 284189--284230 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
284179 TTCCACAGTG
284189 AAAAAGTATCGACAC-TTTTAT
1 AAAAAGTATCGACACATTTTAT
284210 AAAAAGGTATCGACACATTTT
1 AAAAA-GTATCGACACATTTT
284231 TATACCGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 5 0.26
22 10 0.53
23 4 0.21
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.31
Consensus pattern (22 bp):
AAAAAGTATCGACACATTTTAT
Found at i:284645 original size:183 final size:183
Alignment explanation
Indices: 284226--284918 Score: 1223
Period size: 183 Copynumber: 3.8 Consensus size: 183
284216 GTATCGACAC
284226 ATTTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAA
1 ATTTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAA
284291 TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGAACAT-AAGTACCGACAC
66 TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGAACATAAAGTACCGACAC
284355 AATATTAGAAAGTGTCGATAAAGGTTGTAGACCTATTCGCTCATAAAACCGGT
131 AATATTAGAAAGTGTCGATAAAGGTTGTAGACCTATTCGCTCATAAAACCGGT
284408 ATTTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAA
1 ATTTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAA
284473 TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGAACATAAAGTACCGACAC
66 TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGAACATAAAGTACCGACAC
284538 AATATTAGAAAGTGTCGATAAAGGTTGTAGACCTATTCGCTCATAAAACCGGT
131 AATATTAGAAAGTGTCGATAAAGGTTGTAGACCTATTCGCTCATAAAACCGGT
*
284591 ATTTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGTAAA
1 ATTTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAA
*
284656 TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACAC
66 TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGAACATAAAGTACCGACAC
*
284721 AATATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGT
131 AATATTAGAAAGTGTCGATAAAGGTTGTAGACCTATTCGCTCATAAAACCGGT
* *
284774 ATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTTTTTT
1 ATTTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATG---TGT
* * * * * *
284839 CAA--TCGACACTTTTTTAAATGGTATCGACATA-TTTTCTTTCATTCTGGACATAAAGTACAGA
63 AAATGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGAACATAAAGTACCGA
*
284901 CACAATATTAAAAAGTGT
128 CACAATATTAGAAAGTGT
284919 GAAAACTTTG
Statistics
Matches: 495, Mismatches: 12, Indels: 7
0.96 0.02 0.01
Matches are distributed among these distances:
182 117 0.24
183 346 0.70
184 28 0.06
186 4 0.01
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.36
Consensus pattern (183 bp):
ATTTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAA
TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGAACATAAAGTACCGACAC
AATATTAGAAAGTGTCGATAAAGGTTGTAGACCTATTCGCTCATAAAACCGGT
Found at i:286117 original size:3 final size:3
Alignment explanation
Indices: 286109--286183 Score: 78
Period size: 3 Copynumber: 25.0 Consensus size: 3
286099 ACTTGTTTGG
* * * **
286109 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * *
286157 AGC TTC ATC GTC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC
286184 GTCAGCTTCA
Statistics
Matches: 57, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.25, C:0.35, G:0.05, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:288369 original size:392 final size:396
Alignment explanation
Indices: 287645--289004 Score: 2628
Period size: 392 Copynumber: 3.4 Consensus size: 396
287635 TATTTAAATT
287645 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
287710 TAATTGTACCGGTTAGATTGAAAAATTACATA-TACATTATACTTTTGGGTTCGATGATTTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
287774 ATCGACAC-TTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGG-A
131 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGAA
287837 AAAAGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCG
196 AAAAGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCG
287902 GTATAATTGTACCGGTTAGATTGAAAAATTACATATT-CATTATACTTTTGGGTTCGATGATTTT
261 GTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTT
287966 GGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGG
326 GGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGG
288031 GAAAAA
391 GAAAAA
288037 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
288102 TAATTGTACCGGTTAGATTG-AAAATTACATATTACATTATAC-TTTGGGTTCGATGATTTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
288165 ATCGACACTTTTTATATATGGATCGACAC-TTATGGGTGCACCTTGTTTCCATTCATTCTGGGAA
131 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGAA
*
288229 AAAAGTATCGACACAAACTATATTAGTGTCGATACATTATTTAGACATATTCTCTCAT-AAACCG
196 AAAAGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCG
288293 GTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTT
261 GTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTT
288358 GGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGG
326 GGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGG
288423 GAAAAA
391 GAAAAA
288429 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
288494 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
288559 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGAA
131 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGAA
288624 AAAAGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAAACC
196 AAAAGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCAT-AAAACC
288689 GGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTT
260 GGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTT
288754 TGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTG
325 TGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTG
288819 GGAAAAA
390 GGAAAAA
288826 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
288891 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
*
288956 ATTGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTT
131 ATCGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTT
289005 GGCCATATTG
Statistics
Matches: 955, Mismatches: 3, Indels: 14
0.98 0.00 0.01
Matches are distributed among these distances:
391 116 0.12
392 356 0.37
393 22 0.02
394 50 0.05
395 92 0.10
397 279 0.29
398 40 0.04
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.37
Consensus pattern (396 bp):
AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGAA
AAAAGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCG
GTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTT
GGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGG
GAAAAA
Found at i:288579 original size:198 final size:198
Alignment explanation
Indices: 287645--289004 Score: 2628
Period size: 198 Copynumber: 6.9 Consensus size: 198
287635 TATTTAAATT
287645 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
287710 TAATTGTACCGGTTAGATTGAAAAATTACATA-TACATTATACTTTTGGGTTCGATGATTTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
287774 ATCGACAC-TTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGG-A
131 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGAA
287837 AAA
196 AAA
287840 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
287905 TAATTGTACCGGTTAGATTGAAAAATTACATATT-CATTATACTTTTGGGTTCGATGATTTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
287969 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGAA
131 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGAA
288034 AAA
196 AAA
288037 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
288102 TAATTGTACCGGTTAGATTG-AAAATTACATATTACATTATAC-TTTGGGTTCGATGATTTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
288165 ATCGACACTTTTTATATATGGATCGACAC-TTATGGGTGCACCTTGTTTCCATTCATTCTGGGAA
131 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGAA
288229 AAA
196 AAA
*
288232 AGTATCGACACAAACTATATTAGTGTCGATACATTATTTAGACATATTCTCTCAT-AAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
288296 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
288361 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGAA
131 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGAA
288426 AAA
196 AAA
288429 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
288494 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
288559 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGAA
131 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGAA
288624 AAA
196 AAA
288627 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAAACCGGT
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCAT-AAAACCGGT
288692 ATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
65 ATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
288757 GATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGA
130 GATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGA
288822 AAAA
195 AAAA
288826 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
288891 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
*
288956 ATTGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTT
131 ATCGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTT
289005 GGCCATATTG
Statistics
Matches: 1152, Mismatches: 3, Indels: 16
0.98 0.00 0.01
Matches are distributed among these distances:
194 29 0.03
195 249 0.22
196 168 0.15
197 189 0.16
198 279 0.24
199 238 0.21
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.37
Consensus pattern (198 bp):
AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTCCATTCATTCTGGGAA
AAA
Found at i:289166 original size:19 final size:19
Alignment explanation
Indices: 289120--289168 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
289110 TTATATTCAC
*
289120 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
289139 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
289158 ATACAAAATTA
1 ATACAAAATTA
289169 ACTTGACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:290991 original size:33 final size:30
Alignment explanation
Indices: 290954--291016 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 30
290944 CATCTTAATA
290954 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCC--AACA-CCCAACTTCTTTCACCACT
* *
290987 TCACCCCAACACTCTACTTCTTTCACCACT
1 TCACCCCAACACCCAACTTCTTTCACCACT
291017 CCATCTATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 17 0.61
31 4 0.14
33 7 0.25
ACGTcount: A:0.24, C:0.48, G:0.00, T:0.29
Consensus pattern (30 bp):
TCACCCCAACACCCAACTTCTTTCACCACT
Found at i:291090 original size:21 final size:21
Alignment explanation
Indices: 291050--291114 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
291040 CCCCTTATTC
* *
291050 CTCTCGAGTGTATCTTCGACT
1 CTCTCGAGTTTCTCTTCGACT
*
291071 CTCTCGAGTTTCTCTACGACT
1 CTCTCGAGTTTCTCTTCGACT
* *
291092 -TGATCAAGTTTCTCTTCGACT
1 CT-CTCGAGTTTCTCTTCGACT
291113 CT
1 CT
291115 TGATTGTCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.15, C:0.29, G:0.15, T:0.40
Consensus pattern (21 bp):
CTCTCGAGTTTCTCTTCGACT
Found at i:293389 original size:19 final size:18
Alignment explanation
Indices: 293335--293380 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 18
293325 ATCCGGTATC
293335 ATTTTACCGTTTTATCAT
1 ATTTTACCGTTTTATCAT
*
293353 TTTGTTACCGGTTTTATCAT
1 ATT-TTACC-GTTTTATCAT
293373 ATTTTACC
1 ATTTTACC
293381 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 2 0.08
19 10 0.42
20 12 0.50
ACGTcount: A:0.20, C:0.17, G:0.09, T:0.54
Consensus pattern (18 bp):
ATTTTACCGTTTTATCAT
Found at i:293526 original size:20 final size:20
Alignment explanation
Indices: 293500--293545 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
293490 CACTTTTAAA
293500 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
293519 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
293540 TTTACC
1 TTTACC
293546 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:294028 original size:229 final size:227
Alignment explanation
Indices: 293611--294059 Score: 776
Period size: 229 Copynumber: 2.0 Consensus size: 227
293601 TTAAAACTGC
293611 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
1 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
*
293676 TTAATTTAATAATTTAATTTACACAAAATTATATTTGATTGTTTTGATATTTTATAAAATTTATT
66 TTAATTTAATAATTTAATTTACACAAAAATATATTTGATTGTTTTGATATTTTATAAAATTTATT
* *
293741 TAGAATTTAAATTTAACAATATTAACCAAATATAATAATAAATATGTTTTCAACAGTGAAATAAG
131 TAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCAACAGTGAAATAAG
*
293806 TATGGACACTTTTATAAAAATGATATATACTT
196 TATGGACACTTTTATAAAAAGGATATATACTT
*
293838 TTTTGAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTTCCACCTACAA
1 TTTT-AAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATG-TTTTCCACCTACAA
*
293903 TATTAATTTAATAATTTCATTTACACAAAAA-ATTATTTGATTGTTTTGATATTTTATAAAATAT
64 TATTAATTTAATAATTTAATTTACACAAAAATA-TATTTGATTGTTTTGATATTTTATAAAAT-T
* *
293967 TATTTAGATTTTAAATTTAACAATATTAACTAAAGATAATAATAAATATATTTTC-ACAGTGAAA
127 TATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCAACAGTGAAA
294031 TAAGTATGGACACTTTTATAAAAAGGATA
192 TAAGTATGGACACTTTTATAAAAAGGATA
294060 GATAATTTAC
Statistics
Matches: 210, Mismatches: 8, Indels: 6
0.94 0.04 0.03
Matches are distributed among these distances:
227 4 0.02
228 45 0.21
229 109 0.52
230 52 0.25
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.45
Consensus pattern (227 bp):
TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
TTAATTTAATAATTTAATTTACACAAAAATATATTTGATTGTTTTGATATTTTATAAAATTTATT
TAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCAACAGTGAAATAAG
TATGGACACTTTTATAAAAAGGATATATACTT
Found at i:294405 original size:13 final size:13
Alignment explanation
Indices: 294389--294419 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
294379 ACAAAAATAT
294389 TTTTTAAAATCAC
1 TTTTTAAAATCAC
*
294402 TTTTCAAAATCAC
1 TTTTTAAAATCAC
294415 TTTTT
1 TTTTT
294420 CACGTTACTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (13 bp):
TTTTTAAAATCAC
Found at i:303457 original size:60 final size:60
Alignment explanation
Indices: 303359--303480 Score: 199
Period size: 60 Copynumber: 2.0 Consensus size: 60
303349 TTTAATAGTC
* *
303359 AAGGAACTCTCTATAGTCAGATGATCATTTTGTAACTTTTAATAGTTGAGGGACTCAACA
1 AAGGAACTCTCTATAGTCAGATGACCATTTTGTAACTTTTAACAGTTGAGGGACTCAACA
* * *
303419 AAGGAACTCTCTATAGTCGGATGACCATTTTGTTACTTTTAACAGTTGGGGGACTCAACA
1 AAGGAACTCTCTATAGTCAGATGACCATTTTGTAACTTTTAACAGTTGAGGGACTCAACA
303479 AA
1 AA
303481 ATAATATCCT
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (60 bp):
AAGGAACTCTCTATAGTCAGATGACCATTTTGTAACTTTTAACAGTTGAGGGACTCAACA
Found at i:303493 original size:60 final size:60
Alignment explanation
Indices: 303366--303517 Score: 175
Period size: 60 Copynumber: 2.5 Consensus size: 60
303356 GTCAAGGAAC
* * * * * *
303366 TCTCTATAGTCAGATGATCATTTTGTAACTTTTAATAGTTGAGGGACTCAACAAAGGAAC
1 TCTCTATAGTCGGATGACCATTTTGTTACTTTTAACAGTTGAGGGACTCAACAAAAGAAA
* *
303426 TCTCTATAGTCGGATGACCATTTTGTTACTTTTAACAGTTGGGGGACTCAACAAAATAATA
1 TCTCTATAGTCGGATGACCATTTTGTTACTTTTAACAGTTGAGGGACTCAACAAAAGAA-A
*
303487 TC-CTATAGTCAGG-GGACCA-TTTGTGTACTTT
1 TCTCTATAGTC-GGATGACCATTTTGT-TACTTT
303518 ACTTGATTTT
Statistics
Matches: 80, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
59 5 0.06
60 71 0.89
61 4 0.05
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (60 bp):
TCTCTATAGTCGGATGACCATTTTGTTACTTTTAACAGTTGAGGGACTCAACAAAAGAAA
Found at i:304360 original size:21 final size:21
Alignment explanation
Indices: 304336--304408 Score: 55
Period size: 21 Copynumber: 3.6 Consensus size: 21
304326 TATCATTTTG
* * *
304336 TATATATTTTTCTTTATATTA
1 TATATATTTCTATTTACATTA
*
304357 TATAGATTTCTATTTACATTA
1 TATATATTTCTATTTACATTA
* *
304378 -ATATA--TC-ATATATATATA
1 TATATATTTCTATTTACAT-TA
304396 TATATATTTCTAT
1 TATATATTTCTAT
304409 ATTATTAATT
Statistics
Matches: 40, Mismatches: 7, Indels: 9
0.71 0.12 0.16
Matches are distributed among these distances:
17 6 0.15
18 4 0.10
19 5 0.12
20 4 0.10
21 19 0.47
22 2 0.05
ACGTcount: A:0.36, C:0.07, G:0.01, T:0.56
Consensus pattern (21 bp):
TATATATTTCTATTTACATTA
Found at i:304462 original size:4 final size:4
Alignment explanation
Indices: 304434--304494 Score: 86
Period size: 4 Copynumber: 15.2 Consensus size: 4
304424 ACGATTTTCC
* * * *
304434 TATA TATA CATA CATA CATA CATA TATA TATA TATA TATA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
304482 TATA TATA TATA T
1 TATA TATA TATA T
304495 TTATTAAAAT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 55 1.00
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (4 bp):
TATA
Found at i:307799 original size:15 final size:17
Alignment explanation
Indices: 307779--307810 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
307769 GGTCCCCGCA
307779 GCATTCC-C-ATGATAT
1 GCATTCCTCAATGATAT
307794 GCATTCCTCAATGATAT
1 GCATTCCTCAATGATAT
307811 TATGTCATGG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 1 0.07
17 7 0.47
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.34
Consensus pattern (17 bp):
GCATTCCTCAATGATAT
Found at i:316986 original size:20 final size:21
Alignment explanation
Indices: 316961--317012 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
316951 TTTTCCCAAT
*
316961 TCGCAATGCGAATAAG-TAAA
1 TCGCAATGCGAATAAGAAAAA
* **
316981 TCGCAACGCGAATTGGAAAAA
1 TCGCAATGCGAATAAGAAAAA
317002 TCGCAATGCGA
1 TCGCAATGCGA
317013 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATAAGAAAAA
Found at i:317026 original size:20 final size:20
Alignment explanation
Indices: 317001--317114 Score: 106
Period size: 20 Copynumber: 5.7 Consensus size: 20
316991 AATTGGAAAA
317001 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
317021 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
317041 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
*
317062 ATCGCAACT-AGATACTGACT
1 ATCGCAA-TGCGATACTGACT
* * *
317082 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* *
317102 TTCGCAACGCGAT
1 ATCGCAATGCGAT
317115 TTACATAGCG
Statistics
Matches: 79, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
19 2 0.03
20 62 0.78
21 12 0.15
22 3 0.04
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:317045 original size:61 final size:61
Alignment explanation
Indices: 316998--317114 Score: 155
Period size: 61 Copynumber: 1.9 Consensus size: 61
316988 GCGAATTGGA
* * * *
316998 AAAATCGCAA-TGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACT-AGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
317059 AAAATCGCAACTAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACTAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGAT
317115 TTACATAGCG
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
61 47 0.98
62 1 0.02
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (61 bp):
AAAATCGCAACTAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:317719 original size:19 final size:19
Alignment explanation
Indices: 317672--317713 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
317662 ACGAGAGAAT
*
317672 CGCAACGCGAAATAAAAAA
1 CGCAACGCGAAACAAAAAA
*
317691 CGCAACGCGAAACAAAAAT
1 CGCAACGCGAAACAAAAAA
317710 CGCA
1 CGCA
317714 TTGCGATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.52, C:0.26, G:0.17, T:0.05
Consensus pattern (19 bp):
CGCAACGCGAAACAAAAAA
Found at i:317731 original size:19 final size:19
Alignment explanation
Indices: 317709--317873 Score: 134
Period size: 19 Copynumber: 9.1 Consensus size: 19
317699 GAAACAAAAA
*
317709 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
317728 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
317747 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
317766 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
317780 TCTCGTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
317799 TCACGTTGCGA--TT-A--
1 TCGCGTTGCGATTTTCATT
* **
317813 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
317832 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
317852 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
317872 TC
1 TC
317874 AACCAAAAGA
Statistics
Matches: 118, Mismatches: 16, Indels: 24
0.75 0.10 0.15
Matches are distributed among these distances:
14 19 0.16
16 4 0.03
17 4 0.03
19 59 0.50
20 31 0.26
21 1 0.01
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:317789 original size:38 final size:38
Alignment explanation
Indices: 317709--317873 Score: 125
Period size: 33 Copynumber: 4.6 Consensus size: 38
317699 GAAACAAAAA
* * *
317709 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATG
*
317747 TCGCGTTGCGATTTTTATTTCGCGTTGCGATTCTC---
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATG
* ** *
317782 T--CGTCGCGATAGTCATTTCACGTTGCGA-T-T-A--
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATG
* ** *
317813 TCTCGTTGCGATAGTCATTTCCGCGTTGCGATTCTCATTA
1 TCGCGTTGCGATTTTCATTT-CGCGTTGCGATTCTCA-TG
*
317853 TCTCGTTGCGATTTTCATTTC
1 TCGCGTTGCGATTTTCATTTC
317874 AACCAAAAGA
Statistics
Matches: 105, Mismatches: 12, Indels: 19
0.77 0.09 0.14
Matches are distributed among these distances:
31 2 0.02
32 1 0.01
33 38 0.36
34 9 0.09
35 2 0.02
36 1 0.01
37 1 0.01
38 32 0.30
39 1 0.01
40 18 0.17
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.44
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATG
Found at i:317800 original size:33 final size:33
Alignment explanation
Indices: 317763--317848 Score: 136
Period size: 33 Copynumber: 2.6 Consensus size: 33
317753 TGCGATTTTT
317763 ATTTCGCGTTGCGATTCTCTCGTCGCGATAGTC
1 ATTTCGCGTTGCGATTCTCTCGTCGCGATAGTC
* * *
317796 ATTTCACGTTGCGATTATCTCGTTGCGATAGTC
1 ATTTCGCGTTGCGATTCTCTCGTCGCGATAGTC
317829 ATTTCCGCGTTGCGATTCTC
1 ATTT-CGCGTTGCGATTCTC
317849 ATTATCTCGT
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 34 0.72
34 13 0.28
ACGTcount: A:0.14, C:0.26, G:0.22, T:0.38
Consensus pattern (33 bp):
ATTTCGCGTTGCGATTCTCTCGTCGCGATAGTC
Found at i:317850 original size:20 final size:20
Alignment explanation
Indices: 317816--317873 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
317806 GCGATTATCT
**
317816 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
317836 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
317856 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
317874 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:319950 original size:21 final size:21
Alignment explanation
Indices: 319926--319992 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
319916 TCATTCCTCG
319926 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * * * *
319947 AGAGGCCACTGCCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
319968 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
319989 AGAG
1 AGAG
319993 CCCGATTCAC
Statistics
Matches: 34, Mismatches: 11, Indels: 3
0.71 0.23 0.06
Matches are distributed among these distances:
20 1 0.03
21 32 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.37, G:0.21, T:0.18
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:319950 original size:42 final size:42
Alignment explanation
Indices: 319874--319953 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
319864 GACTCGCCTG
* * *
319874 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCTTA
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCTTA
* * *
319916 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
319954 ACTGCCATCG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.21, C:0.38, G:0.17, T:0.24
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCTTA
Found at i:321368 original size:14 final size:14
Alignment explanation
Indices: 321349--321384 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
321339 ATTGTTTAAT
321349 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
321363 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
321377 TGATTTGT
1 TGATTTGT
321385 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:321541 original size:33 final size:33
Alignment explanation
Indices: 321491--321580 Score: 135
Period size: 33 Copynumber: 2.7 Consensus size: 33
321481 AAAAAGTACT
*
321491 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
*
321524 ATCGTAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* * *
321557 ATCGCAATGCGAAATTAAATTCGC
1 ATCGCAACGCGAAATGAAAATCGC
321581 GTTGCGATTT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 51 1.00
ACGTcount: A:0.43, C:0.19, G:0.22, T:0.16
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:321551 original size:19 final size:19
Alignment explanation
Indices: 321491--321551 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 19
321481 AAAAAGTACT
*
321491 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
321510 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
*
321524 ATCGTAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
321543 ATCGCAACG
1 ATCGCAACG
321552 AGAGAATCGC
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
14 9 0.27
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 18 0.55
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:321598 original size:19 final size:19
Alignment explanation
Indices: 321576--321706 Score: 85
Period size: 19 Copynumber: 7.7 Consensus size: 19
321566 CGAAATTAAA
*
321576 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
321595 TTCGCATTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
321611 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
321628 TTCGCATTGCGA-----AA
1 TTCGCATTGCGATTTTCAT
* *
321642 TTAGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
321661 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
* *
321677 CTCG--TTGCGATTTTGAT
1 TTCGCATTGCGATTTTCAT
321694 TTCGCATTGCGAT
1 TTCGCATTGCGAT
321707 AGTAATTTCC
Statistics
Matches: 83, Mismatches: 14, Indels: 30
0.65 0.11 0.24
Matches are distributed among these distances:
14 23 0.28
16 12 0.14
17 13 0.16
19 35 0.42
ACGTcount: A:0.15, C:0.22, G:0.21, T:0.43
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:321622 original size:33 final size:32
Alignment explanation
Indices: 321580--321706 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
321570 ATTAAATTCG
321580 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
321613 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
321646 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
*
321679 CGTTGCGATTTTGATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
321707 AGTAATTTCC
Statistics
Matches: 85, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
31 3 0.04
33 79 0.93
35 3 0.04
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:321669 original size:66 final size:66
Alignment explanation
Indices: 321573--321705 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
321563 ATGCGAAATT
*
321573 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
321638 G
66 G
* *
321639 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTGATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
321704 G
66 G
321705 A
1 A
321706 TAGTAATTTC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.41
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:324012 original size:12 final size:12
Alignment explanation
Indices: 323995--324019 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
323985 TCTTCGGGGA
323995 CTTTTTCTTCTT
1 CTTTTTCTTCTT
324007 CTTTTTCTTCTT
1 CTTTTTCTTCTT
324019 C
1 C
324020 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:324228 original size:24 final size:24
Alignment explanation
Indices: 324194--324247 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
324184 CTGAAACATC
* * *
324194 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGAGTATTAACCAAG
*
324218 ATCAAAGTCCGAGTATTAACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
324242 ATCAAA
1 ATCAAA
324248 TTTCGAATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.43, C:0.20, G:0.13, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTAACCAAG
Found at i:325328 original size:20 final size:20
Alignment explanation
Indices: 325303--325360 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
325293 ATTCATTTGA
325303 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
325323 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
325343 CTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
325361 CGCAATGCGA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:325403 original size:14 final size:15
Alignment explanation
Indices: 325383--325455 Score: 60
Period size: 14 Copynumber: 4.5 Consensus size: 15
325373 TGAAAATCGC
325383 ATTGCGATTTTCTCG
1 ATTGCGATTTTCTCG
325398 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC---TCG
*
325415 CATTGCGATTTTATTTCG
1 -ATTGCGA-TTT-TCTCG
325433 CATTGCGATTTTCTCG
1 -ATTGCGATTTTCTCG
325449 -TTGCGAT
1 ATTGCGAT
325456 AGCCATTTCA
Statistics
Matches: 49, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
14 18 0.37
16 4 0.08
17 6 0.12
18 11 0.22
19 6 0.12
20 3 0.06
21 1 0.02
ACGTcount: A:0.14, C:0.19, G:0.19, T:0.48
Consensus pattern (15 bp):
ATTGCGATTTTCTCG
Found at i:325432 original size:18 final size:18
Alignment explanation
Indices: 325379--325444 Score: 86
Period size: 18 Copynumber: 3.8 Consensus size: 18
325369 GAAATGAAAA
*
325379 TCGCATTGCGA-TTT-TC
1 TCGCATTGCGATTTTATT
325395 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTT-ATT
325412 TCGCATTGCGATTTTATT
1 TCGCATTGCGATTTTATT
325430 TCGCATTGCGATTTT
1 TCGCATTGCGATTTT
325445 CTCGTTGCGA
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
14 6 0.14
15 3 0.07
16 3 0.07
17 4 0.09
18 18 0.41
19 10 0.23
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.48
Consensus pattern (18 bp):
TCGCATTGCGATTTTATT
Found at i:325581 original size:14 final size:14
Alignment explanation
Indices: 325562--325598 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
325552 CATCAATTAA
325562 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
325576 ACAAATCATCTTTT
1 ACAAATCAACATTT
325590 ACAAATCAA
1 ACAAATCAA
325599 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:327486 original size:20 final size:19
Alignment explanation
Indices: 327463--327530 Score: 82
Period size: 20 Copynumber: 3.5 Consensus size: 19
327453 GAAACTTAAA
327463 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCG-AAATGACT
*
327483 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
327503 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
327522 ATCGCAACG
1 ATCGCAACG
327531 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
19 14 0.34
20 26 0.63
21 1 0.02
ACGTcount: A:0.38, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:327538 original size:14 final size:14
Alignment explanation
Indices: 327519--327608 Score: 90
Period size: 14 Copynumber: 5.9 Consensus size: 14
327509 ATGCGAAATG
327519 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
327533 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
327549 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
*
327565 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
327581 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
327597 AAAATCGCAACG
1 AAAATCGCAACG
327609 CGAAACATAA
Statistics
Matches: 64, Mismatches: 4, Indels: 16
0.76 0.05 0.19
Matches are distributed among these distances:
14 30 0.47
16 16 0.25
18 18 0.28
ACGTcount: A:0.48, C:0.26, G:0.18, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:327561 original size:32 final size:32
Alignment explanation
Indices: 327503--327613 Score: 204
Period size: 32 Copynumber: 3.4 Consensus size: 32
327493 GGAAATGGCT
*
327503 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
327536 ATCGCAACGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
327568 ATCGCAACGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
327600 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
327614 CATAAATCGC
Statistics
Matches: 77, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
32 62 0.81
33 15 0.19
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (32 bp):
ATCGCAACGCGAAATGAAATCGCAACGACAAA
Found at i:327661 original size:14 final size:14
Alignment explanation
Indices: 327642--327699 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
327632 TTTCATTTCG
327642 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
327656 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
*
327672 CACATTGCGATTTTGT
1 --CGTTGCGATTTTGT
327688 CGTTGCGATTTT
1 CGTTGCGATTTT
327700 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.61
16 4 0.11
18 10 0.28
ACGTcount: A:0.12, C:0.17, G:0.22, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:327711 original size:33 final size:33
Alignment explanation
Indices: 327625--327715 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
327615 ATAAATCGCA
*
327625 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
327658 TTGCGA-TTTCATTTCACATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
327690 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
327716 AGCCATTTCC
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 30 0.56
33 24 0.44
ACGTcount: A:0.13, C:0.19, G:0.21, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:327722 original size:19 final size:20
Alignment explanation
Indices: 327700--327743 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
327690 TTGCGATTTT
327700 CATTT-CGCATTGCGATAGC
1 CATTTCCGCATTGCGATAGC
** *
327719 CATTTCCGTGTTGCGATAGT
1 CATTTCCGCATTGCGATAGC
327739 CATTT
1 CATTT
327744 TCGTGTTGCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.18, C:0.23, G:0.20, T:0.39
Consensus pattern (20 bp):
CATTTCCGCATTGCGATAGC
Found at i:327734 original size:20 final size:20
Alignment explanation
Indices: 327709--327754 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
327699 TCATTTCGCA
327709 TTGCGATAGCCATTTCCGTG
1 TTGCGATAGCCATTTCCGTG
* *
327729 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGCCATTTCCGTG
327749 TTGCGA
1 TTGCGA
327755 AAGTAAACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.15, C:0.20, G:0.26, T:0.39
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGTG
Found at i:328262 original size:18 final size:18
Alignment explanation
Indices: 328236--328280 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
328226 GTCGATCAGA
*
328236 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
328254 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
328272 TGATGGCTC
1 TGATGGCTC
328281 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:329933 original size:22 final size:22
Alignment explanation
Indices: 329906--329949 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
329896 GATGGAGATA
329906 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
329928 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
329950 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:330167 original size:20 final size:20
Alignment explanation
Indices: 330137--330250 Score: 113
Period size: 20 Copynumber: 5.7 Consensus size: 20
330127 GATTATGTAT
*
330137 TATCACGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
330157 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
330177 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* ** *
330197 TATCTCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
* *
330218 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
330238 TATCGCATTGCGA
1 TATCGCGTTGCGA
330251 TTTTCCCAAT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
19 3 0.04
20 62 0.78
21 12 0.15
22 2 0.03
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.31
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:330254 original size:41 final size:41
Alignment explanation
Indices: 330117--330252 Score: 150
Period size: 41 Copynumber: 3.3 Consensus size: 41
330107 CGCTTTGAAA
* *
330117 ATCGCATTGCGATTATGTATTATCACGTTGCGAAAGTCAGA
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
* * * *
330158 ATCGCGTTGCGA--AAGTCAGTATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATTATGT-ATTATCGCGTTGCGAAAGTCAGT
* * * * *
330198 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
330239 ATCGCATTGCGATT
1 ATCGCATTGCGATT
330253 TTCCCAATTC
Statistics
Matches: 77, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
39 3 0.04
40 30 0.39
41 42 0.55
42 2 0.03
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (41 bp):
ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
Found at i:330269 original size:21 final size:21
Alignment explanation
Indices: 330240--330332 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
330230 ATAGTCAGTA
330240 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
330261 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
330281 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
330302 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
330322 TCGCATTGCGA
1 TCGCATTGCGA
330333 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:330270 original size:41 final size:41
Alignment explanation
Indices: 330179--330313 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
330169 AAAGTCAGTA
* * * ** *
330179 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-GTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
330219 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
330261 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
330302 TCGCGTTGCGAT
1 TCGCGTTGCGAT
330314 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:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Done.