Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008727.1 Hibiscus syriacus cultivar Beakdansim tig00111794_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: 1388410
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 8
Found at i:200054 original size:75 final size:74
Alignment explanation
Indices: 199902--200180 Score: 281
Period size: 75 Copynumber: 3.8 Consensus size: 74
199892 TTTTTAAAAA
* * * * *
199902 ATTTCAAAACTATACATTATAT-AGTTTTCAAAAAT-TGTTT-AAA--A-ATATTATATAAGTTT
1 ATTTTAAAACTATATATTATATAATTTTTAAAAAATGTTTTTAAAACTATATATTATATAA-TTT
*
199961 TTTAAAAATG
65 TTCAAAAATG
*
199971 TTTTTAAAACTATATATTATATAATTTTTAAAAAATGTTTTTAAAACTATATATTATATAATTTT
1 ATTTTAAAACTATATATTATATAATTTTTAAAAAATGTTTTTAAAACTATATATTATATAATTTT
200036 TCAAAAAATG
66 TC-AAAAATG
* * * * * *
200046 ATTATAAAAATATATATTATGTAATTTTTCAAAAATGATTTTAAAATTATATATTATATAA-TTT
1 ATTTTAAAACTATATATTATATAATTTTTAAAAAATGTTTTTAAAACTATATATTATATAATTTT
200110 TC-AAAATG
66 TCAAAAATG
* * *
200118 ATTTTAGAAATTATATATTATATACGTATTTTTAAAAACTG--TTTACAAACTATATAATATATA
1 ATTTTA-AAACTATATATTATATA---ATTTTTAAAAAATGTTTTTA-AAACTATATATTATATA
200181 TATATATATA
Statistics
Matches: 177, Mismatches: 21, Indels: 18
0.82 0.10 0.08
Matches are distributed among these distances:
69 19 0.11
70 11 0.06
71 4 0.02
72 14 0.08
73 15 0.08
74 15 0.08
75 87 0.49
76 12 0.07
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.46
Consensus pattern (74 bp):
ATTTTAAAACTATATATTATATAATTTTTAAAAAATGTTTTTAAAACTATATATTATATAATTTT
TCAAAAATG
Found at i:200221 original size:10 final size:10
Alignment explanation
Indices: 200206--200244 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
200196 ACAAAATAAA
200206 AATAAAAAAT
1 AATAAAAAAT
200216 AATAAAAAAAT
1 AAT-AAAAAAT
*
200227 AATAATAAAT
1 AATAAAAAAT
*
200237 GATAAAAA
1 AATAAAAA
200245 TGAGTGTCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 15 0.60
11 10 0.40
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.21
Consensus pattern (10 bp):
AATAAAAAAT
Found at i:200230 original size:21 final size:20
Alignment explanation
Indices: 200198--200244 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
200188 ATATATTCAC
200198 AAAATAAAAATAAAAAATAAT
1 AAAA-AAAAATAAAAAATAAT
* *
200219 AAAAAAATAATAATAAATGAT
1 AAAAAAA-AATAAAAAATAAT
200240 AAAAA
1 AAAAA
200245 TGAGTGTCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (20 bp):
AAAAAAAAATAAAAAATAAT
Found at i:200633 original size:19 final size:19
Alignment explanation
Indices: 200609--200645 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
200599 ATGACCAACA
*
200609 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
200628 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
200646 CATTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:200777 original size:41 final size:42
Alignment explanation
Indices: 200751--200842 Score: 125
Period size: 41 Copynumber: 2.2 Consensus size: 42
200741 CGAATATGTA
200751 AATCGCAACGCGATAACACGTGATCGCAACGCG-ATTCGGAC
1 AATCGCAACGCGATAACACGTGATCGCAACGCGAATTCGGAC
* * * *
200792 TATTGCAACGCGATAATACGTGATCGCAACGCG-ATTCTGAC
1 AATCGCAACGCGATAACACGTGATCGCAACGCGAATTCGGAC
*
200833 TATCGCAACG
1 AATCGCAACG
200843 AGATTCTGAC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.30, C:0.27, G:0.23, T:0.20
Consensus pattern (42 bp):
AATCGCAACGCGATAACACGTGATCGCAACGCGAATTCGGAC
Found at i:200778 original size:21 final size:21
Alignment explanation
Indices: 200752--200826 Score: 84
Period size: 21 Copynumber: 3.6 Consensus size: 21
200742 GAATATGTAA
200752 ATCGCAACGCGATAACACGTG
1 ATCGCAACGCGATAACACGTG
*
200773 ATCGCAACGCGAT-TCGGAC-T-
1 ATCGCAACGCGATAAC--ACGTG
* *
200793 ATTGCAACGCGATAATACGTG
1 ATCGCAACGCGATAACACGTG
200814 ATCGCAACGCGAT
1 ATCGCAACGCGAT
200827 TCTGACTATC
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
19 2 0.05
20 14 0.32
21 26 0.59
22 2 0.05
ACGTcount: A:0.31, C:0.27, G:0.24, T:0.19
Consensus pattern (21 bp):
ATCGCAACGCGATAACACGTG
Found at i:200839 original size:20 final size:20
Alignment explanation
Indices: 200773--200852 Score: 90
Period size: 20 Copynumber: 4.0 Consensus size: 20
200763 ATAACACGTG
*
200773 ATCGCAACGCGATTCGGACT
1 ATCGCAACGCGATTCTGACT
* **
200793 ATTGCAACGCGATAAT-ACGT
1 ATCGCAACGCGATTCTGAC-T
200813 GATCGCAACGCGATTCTGACT
1 -ATCGCAACGCGATTCTGACT
*
200834 ATCGCAACGAGATTCTGAC
1 ATCGCAACGCGATTCTGAC
200853 AATTGCGTTG
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
19 2 0.04
20 31 0.63
21 14 0.29
22 2 0.04
ACGTcount: A:0.29, C:0.26, G:0.23, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:201057 original size:22 final size:22
Alignment explanation
Indices: 201028--201100 Score: 92
Period size: 22 Copynumber: 3.3 Consensus size: 22
201018 CTACGGCGAC
201028 ATCCGTCCCCATATCCGACGAA
1 ATCCGTCCCCATATCCGACGAA
* * * *
201050 ATCTGTCCCCATTTCTGGCGAA
1 ATCCGTCCCCATATCCGACGAA
* *
201072 ATCCATCCCCATCTCCGACGAA
1 ATCCGTCCCCATATCCGACGAA
201094 ATCCGTC
1 ATCCGTC
201101 TATCTCCATC
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.23, C:0.40, G:0.14, T:0.23
Consensus pattern (22 bp):
ATCCGTCCCCATATCCGACGAA
Found at i:201542 original size:20 final size:20
Alignment explanation
Indices: 201519--201562 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
201509 ATTCACGTTA
201519 CGATAATCATTTTCGTGTTG
1 CGATAATCATTTTCGTGTTG
**
201539 CGATTTTCATTTTCGTGTTG
1 CGATAATCATTTTCGTGTTG
201559 CGAT
1 CGAT
201563 TTTAAGTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.16, C:0.16, G:0.20, T:0.48
Consensus pattern (20 bp):
CGATAATCATTTTCGTGTTG
Found at i:201563 original size:20 final size:20
Alignment explanation
Indices: 201525--201565 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
201515 GTTACGATAA
201525 TCATTTTCGTGTTGCGATTT
1 TCATTTTCGTGTTGCGATTT
201545 TCATTTTCGTGTTGCGATTT
1 TCATTTTCGTGTTGCGATTT
201565 T
1 T
201566 AAGTTTCAGA
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:0.10, C:0.15, G:0.20, T:0.56
Consensus pattern (20 bp):
TCATTTTCGTGTTGCGATTT
Found at i:201572 original size:20 final size:20
Alignment explanation
Indices: 201529--201572 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
201519 CGATAATCAT
* *
201529 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
201549 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
201569 TTTC
1 TTTC
201573 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:203615 original size:20 final size:19
Alignment explanation
Indices: 203568--203689 Score: 85
Period size: 20 Copynumber: 6.4 Consensus size: 19
203558 AGAAGAATAG
* *
203568 TCGCAACACGAAAATGATTA
1 TCGCAACGCG-AAATGACTA
*
203588 TCGCAACGCGAATTTGACTA
1 TCGCAACGCGAA-ATGACTA
*
203608 TCGCAACG-G-GAT-A--A
1 TCGCAACGCGAAATGACTA
* *
203622 TCGCAATGCGAAAACGACTA
1 TCGCAACGCG-AAATGACTA
*
203642 TCGCAACGCGGAAATGATTA
1 TCGCAACGC-GAAATGACTA
203662 TCGCAACGC-AAATTTGACTA
1 TCGCAACGCGAAA--TGACTA
203682 TCGCAACG
1 TCGCAACG
203690 GGATAATGGA
Statistics
Matches: 80, Mismatches: 12, Indels: 20
0.71 0.11 0.18
Matches are distributed among these distances:
14 8 0.10
15 1 0.01
16 1 0.01
17 2 0.03
18 4 0.05
19 3 0.04
20 60 0.75
21 1 0.01
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (19 bp):
TCGCAACGCGAAATGACTA
Found at i:203633 original size:34 final size:34
Alignment explanation
Indices: 203587--203723 Score: 123
Period size: 34 Copynumber: 3.9 Consensus size: 34
203577 GAAAATGATT
**
203587 ATCGCAACGCGAATTTGACTATCGCAACGGGATA
1 ATCGCAACGCGAAAATGACTATCGCAACGGGATA
* *
203621 ATCGCAATGCGAAAACGACTATCGCAACGCGGAAATGA
1 ATCGCAACGCGAAAATGACTATCGCAACG-GG--AT-A
*
203659 TTATCGCAACGC-AAATTTGACTATCGCAACGGGATA
1 --ATCGCAACGCGAAA-ATGACTATCGCAACGGGATA
* * * *
203695 ATGGAAATGCGAAAATGACTATCACAACG
1 ATCGCAACGCGAAAATGACTATCGCAACG
203724 CGAATTTAGT
Statistics
Matches: 83, Mismatches: 12, Indels: 16
0.75 0.11 0.14
Matches are distributed among these distances:
34 45 0.54
35 5 0.06
36 1 0.01
37 4 0.05
38 1 0.01
39 5 0.06
40 22 0.27
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.19
Consensus pattern (34 bp):
ATCGCAACGCGAAAATGACTATCGCAACGGGATA
Found at i:203689 original size:74 final size:74
Alignment explanation
Indices: 203568--203727 Score: 257
Period size: 74 Copynumber: 2.2 Consensus size: 74
203558 AGAAGAATAG
* * *
203568 TCGCAACACGAAAATGATTATCGCAACGCGAATTTGACTATCGCAACGGGATAATCGCAATGCGA
1 TCGCAACGCGAAAATGATTATCGCAACGCAAATTTGACTATCGCAACGGGATAATCGAAATGCGA
203633 AAACGACTA
66 AAACGACTA
* *
203642 TCGCAACGCGGAAATGATTATCGCAACGCAAATTTGACTATCGCAACGGGATAATGGAAATGCGA
1 TCGCAACGCGAAAATGATTATCGCAACGCAAATTTGACTATCGCAACGGGATAATCGAAATGCGA
*
203707 AAATGACTA
66 AAACGACTA
*
203716 TCACAACGCGAA
1 TCGCAACGCGAA
203728 TTTAGTTTTG
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
74 78 1.00
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.19
Consensus pattern (74 bp):
TCGCAACGCGAAAATGATTATCGCAACGCAAATTTGACTATCGCAACGGGATAATCGAAATGCGA
AAACGACTA
Found at i:203754 original size:19 final size:19
Alignment explanation
Indices: 203732--203768 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
203722 CGCGAATTTA
*
203732 GTTTTGCGTTGCGATTTTG
1 GTTTCGCGTTGCGATTTTG
*
203751 GTTTCGCGTTGGGATTTT
1 GTTTCGCGTTGCGATTTT
203769 CTCGTTGCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.05, C:0.11, G:0.32, T:0.51
Consensus pattern (19 bp):
GTTTCGCGTTGCGATTTTG
Found at i:203796 original size:20 final size:20
Alignment explanation
Indices: 203771--203839 Score: 84
Period size: 20 Copynumber: 3.5 Consensus size: 20
203761 GGGATTTTCT
*
203771 CGTTGCGATAGTCAAATTTG
1 CGTTGCGATAGTCAAATTCG
*
203791 CGTTGCGATAGTTAAATTCG
1 CGTTGCGATAGTCAAATTCG
* **
203811 CGTTGCGATAATCATTTTCG
1 CGTTGCGATAGTCAAATTCG
*
203831 TGTTGCGAT
1 CGTTGCGAT
203840 TTTAAGTTTC
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.22, C:0.16, G:0.25, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:203849 original size:20 final size:20
Alignment explanation
Indices: 203826--203870 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
203816 CGATAATCAT
*
203826 TTTCGTGTTGCGATTTTAAG
1 TTTCATGTTGCGATTTTAAG
203846 TTTCATGTTGCGATTTTAAG
1 TTTCATGTTGCGATTTTAAG
203866 TTTCA
1 TTTCA
203871 GAAACTATTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.18, C:0.11, G:0.20, T:0.51
Consensus pattern (20 bp):
TTTCATGTTGCGATTTTAAG
Found at i:204421 original size:42 final size:42
Alignment explanation
Indices: 204357--204457 Score: 112
Period size: 42 Copynumber: 2.4 Consensus size: 42
204347 CTGTCATCGT
* * * *
204357 TCAAGAGGCCTCTCCTATCGTTCAAGAGGCCTCTATCATCCC
1 TCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTATCATCCC
* * **
204399 TCAAGAGTCCCCTCCCACCGTTCAAGAGGCCCCTGTCATCGT
1 TCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTATCATCCC
* *
204441 TGAAGAGGTCCCTCCCA
1 TCAAGAGGCCCCTCCCA
204458 ACATTCTATA
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.23
Consensus pattern (42 bp):
TCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTATCATCCC
Found at i:204441 original size:21 final size:21
Alignment explanation
Indices: 204346--204453 Score: 92
Period size: 21 Copynumber: 5.1 Consensus size: 21
204336 GCCCGACTCA
204346 CCTGTCATCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGCC
* *
204367 TCT-CCTATCGTTCAAGAGGCC
1 CCTGTC-ATCGTTCAAGAGGCC
* * ** *
204388 TCTATCATCCCTCAAGAGTCC
1 CCTGTCATCGTTCAAGAGGCC
** *
204409 CCTCCCACCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGCC
* *
204430 CCTGTCATCGTTGAAGAGGTC
1 CCTGTCATCGTTCAAGAGGCC
204451 CCT
1 CCT
204454 CCCAACATTC
Statistics
Matches: 67, Mismatches: 18, Indels: 4
0.75 0.20 0.04
Matches are distributed among these distances:
20 1 0.01
21 65 0.97
22 1 0.01
ACGTcount: A:0.19, C:0.36, G:0.19, T:0.25
Consensus pattern (21 bp):
CCTGTCATCGTTCAAGAGGCC
Found at i:205884 original size:25 final size:25
Alignment explanation
Indices: 205850--205900 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
205840 ATTTGTTTAA
*
205850 TTGATGTGTAAATAATTCTTATTTG
1 TTGATGTGTAAATAATTATTATTTG
205875 TTGATGTGTAAATAATTATTATTTG
1 TTGATGTGTAAATAATTATTATTTG
205900 T
1 T
205901 GCTTGTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.29, C:0.02, G:0.16, T:0.53
Consensus pattern (25 bp):
TTGATGTGTAAATAATTATTATTTG
Found at i:205987 original size:54 final size:55
Alignment explanation
Indices: 205874--205987 Score: 162
Period size: 54 Copynumber: 2.1 Consensus size: 55
205864 ATTCTTATTT
**
205874 GTTGATGTGTAAATAATTATTATTTGTGCTTGTTTAATTGATTAAAAGTTGATTA
1 GTTGATGTGTAAATAATTATTATTTGTGCTTGTTTAATTGATTAAAAGTTGAAAA
* *
205929 -TTGATGTGTAAATAATTCTTATTTGTGCTTGTTTAATTGATTGAAA--TGTAAAA
1 GTTGATGTGTAAATAATTATTATTTGTGCTTGTTTAATTGATTAAAAGTTG-AAAA
205982 GTTGAT
1 GTTGAT
205988 TTGTTGATTT
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
52 2 0.04
53 2 0.04
54 49 0.92
ACGTcount: A:0.31, C:0.03, G:0.18, T:0.48
Consensus pattern (55 bp):
GTTGATGTGTAAATAATTATTATTTGTGCTTGTTTAATTGATTAAAAGTTGAAAA
Found at i:206075 original size:20 final size:20
Alignment explanation
Indices: 206050--206307 Score: 133
Period size: 20 Copynumber: 13.8 Consensus size: 20
206040 GCAATTTTCT
*
206050 CGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCG
* *
206070 CGTTGCGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCG
*
206090 CGTTGCGATAGTC-ATTTCG
1 CGTTGCGATAGTCAAATTCG
*
206109 CGTTGCGAT--T---A-TCT
1 CGTTGCGATAGTCAAATTCG
* **
206123 CATTAAGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
206143 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
* *
206163 CATTGCGAT--T---A-TCC
1 CGTTGCGATAGTCAAATTCG
* *
206177 CGTTGTGATTGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* ** *
206197 TGTTGCGATAGTCATCTTCA
1 CGTTGCGATAGTCAAATTCG
* *
206217 CATTACGAT--T---A-TC-
1 CGTTGCGATAGTCAAATTCG
* *
206230 CAGTTGCGATATTCAAATTCA
1 C-GTTGCGATAGTCAAATTCG
* * *
206251 CATTGTGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
*
206271 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
206291 CGTTGCGATAGTCAAAT
1 CGTTGCGATAGTCAAAT
206308 GAATGTGTAA
Statistics
Matches: 176, Mismatches: 42, Indels: 40
0.68 0.16 0.16
Matches are distributed among these distances:
13 1 0.01
14 25 0.14
16 3 0.02
17 1 0.01
18 2 0.01
19 16 0.09
20 127 0.72
21 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:206191 original size:54 final size:54
Alignment explanation
Indices: 206067--206279 Score: 239
Period size: 54 Copynumber: 4.0 Consensus size: 54
206057 ATAGTCAAAT
* *
206067 TCCCGTTGCGATAATCAAATTCACGTTGCGATAGTCA-TTTCGCGTTGCGATTA
1 TCCCGTTGCGATAGTCAAATTCACGTTGCGATAGTCATTTTCGCATTGCGATTA
* * ** *
206120 TCTCATTAAGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTA
1 TCCCGTTGCGATAGTCAAATTCACGTTGCGATAGTCATTTTCGCATTGCGATTA
* * ** * * *
206174 TCCCGTTGTGATTGTCAAATTCGTGTTGCGATAGTCATCTTCACATTACGATTA
1 TCCCGTTGCGATAGTCAAATTCACGTTGCGATAGTCATTTTCGCATTGCGATTA
* * * * * *
206228 TCCAGTTGCGATATTCAAATTCACATTGTGATAGTCATATTCGCGTTGCGAT
1 TCCCGTTGCGATAGTCAAATTCACGTTGCGATAGTCATTTTCGCATTGCGAT
206280 AGTCATATTC
Statistics
Matches: 131, Mismatches: 28, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
53 31 0.24
54 100 0.76
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (54 bp):
TCCCGTTGCGATAGTCAAATTCACGTTGCGATAGTCATTTTCGCATTGCGATTA
Found at i:206505 original size:18 final size:18
Alignment explanation
Indices: 206482--206516 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
206472 AAGCCGGTTG
*
206482 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
206500 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
206517 GCCTTTTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:208564 original size:14 final size:14
Alignment explanation
Indices: 208545--208581 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
208535 TCCCGTGGTA
208545 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
*
208559 TTTTCTTCGGGGAT
1 TTTTCTTCGGGGAC
208573 TTCTTCTTC
1 TT-TTCTTC
208582 TTCTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.05, C:0.22, G:0.22, T:0.51
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:208805 original size:24 final size:24
Alignment explanation
Indices: 208771--208824 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
208761 CTGAAACATC
*
208771 ATCAAAATCCGATTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
208795 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
208819 ATCAAA
1 ATCAAA
208825 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:209707 original size:20 final size:20
Alignment explanation
Indices: 209678--209770 Score: 141
Period size: 20 Copynumber: 4.7 Consensus size: 20
209668 ATCACGTATT
* *
209678 ATCGCGTTGCGACAGTCTGA
1 ATCGCGTTGCGATAGTCAGA
**
209698 ATATCGTTGCGATAGTCAGA
1 ATCGCGTTGCGATAGTCAGA
*
209718 ATCGCGTTGCGATAGTCTGA
1 ATCGCGTTGCGATAGTCAGA
209738 ATCGCGTTGCGATAGTCAGA
1 ATCGCGTTGCGATAGTCAGA
209758 ATCGCGTTGCGAT
1 ATCGCGTTGCGAT
209771 CACGTGTTAT
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 65 1.00
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.28
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGA
Found at i:209769 original size:60 final size:61
Alignment explanation
Indices: 209644--209770 Score: 159
Period size: 60 Copynumber: 2.1 Consensus size: 61
209634 AATTCAGTGA
* * * *
209644 TGCGTTAGTCAGAATCACGTTGCGATCACGTATTATCGCGTTGCGACAGTCTGAATATCGT
1 TGCGATAGTCAGAATCACGTTGCGATCACGTATAATCGCGTTGCGACAGTCAGAATAGCGT
* * * *
209705 TGCGATAGTCAGAATCGCGTTGCGAT-A-GTCTGAATCGCGTTGCGATAGTCAGAATCGCGT
1 TGCGATAGTCAGAATCACGTTGCGATCACGTAT-AATCGCGTTGCGACAGTCAGAATAGCGT
209765 TGCGAT
1 TGCGAT
209771 CACGTGTTAT
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
59 3 0.05
60 30 0.53
61 24 0.42
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (61 bp):
TGCGATAGTCAGAATCACGTTGCGATCACGTATAATCGCGTTGCGACAGTCAGAATAGCGT
Found at i:209770 original size:40 final size:40
Alignment explanation
Indices: 209678--209770 Score: 159
Period size: 40 Copynumber: 2.3 Consensus size: 40
209668 ATCACGTATT
* *
209678 ATCGCGTTGCGACAGTCTGAATATCGTTGCGATAGTCAGA
1 ATCGCGTTGCGATAGTCTGAATAGCGTTGCGATAGTCAGA
*
209718 ATCGCGTTGCGATAGTCTGAATCGCGTTGCGATAGTCAGA
1 ATCGCGTTGCGATAGTCTGAATAGCGTTGCGATAGTCAGA
209758 ATCGCGTTGCGAT
1 ATCGCGTTGCGAT
209771 CACGTGTTAT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.28
Consensus pattern (40 bp):
ATCGCGTTGCGATAGTCTGAATAGCGTTGCGATAGTCAGA
Found at i:209812 original size:20 final size:20
Alignment explanation
Indices: 209789--209832 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
209779 ATCGCGTTGA
209789 GATTTACATATTCGCATTGC
1 GATTTACATATTCGCATTGC
209809 GATTTACATATTCGCATTGC
1 GATTTACATATTCGCATTGC
209829 GATT
1 GATT
209833 ATCTAAAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.41
Consensus pattern (20 bp):
GATTTACATATTCGCATTGC
Found at i:210963 original size:7 final size:8
Alignment explanation
Indices: 210952--211007 Score: 62
Period size: 8 Copynumber: 7.0 Consensus size: 8
210942 TATTTTATTA
210952 TATTTAA-
1 TATTTAAT
210959 TATTTAA-
1 TATTTAAT
210966 TATTTAATT
1 TATTTAA-T
*
210975 TATTTAAG
1 TATTTAAT
*
210983 TATTTAAG
1 TATTTAAT
210991 TATTTAAAT
1 TATTT-AAT
211000 TATTTAAT
1 TATTTAAT
211008 ATTGTATTTA
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
7 14 0.32
8 16 0.36
9 14 0.32
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (8 bp):
TATTTAAT
Found at i:210988 original size:8 final size:7
Alignment explanation
Indices: 210951--211010 Score: 66
Period size: 7 Copynumber: 7.7 Consensus size: 7
210941 ATATTTTATT
210951 ATATTTA
1 ATATTTA
210958 ATATTTA
1 ATATTTA
210965 ATATTTA
1 ATATTTA
210972 ATTTATTTA
1 A--TATTTA
210981 AGTATTTA
1 A-TATTTA
210989 AGTATTTAA
1 A-TATTT-A
210998 ATTATTTA
1 A-TATTTA
211006 ATATT
1 ATATT
211011 GTATTTAATT
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
7 19 0.40
8 15 0.31
9 14 0.29
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (7 bp):
ATATTTA
Found at i:210988 original size:17 final size:16
Alignment explanation
Indices: 210951--211007 Score: 57
Period size: 17 Copynumber: 3.6 Consensus size: 16
210941 ATATTTTATT
210951 ATATTTAA--TATTTA
1 ATATTTAATGTATTTA
*
210965 ATATTTAATTTATTTA
1 ATATTTAATGTATTTA
210981 AGTATTTAA-GTATTTAA
1 A-TATTTAATGTATTT-A
210998 ATTATTTAAT
1 A-TATTTAAT
211008 ATTGTATTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
14 8 0.22
16 12 0.33
17 16 0.44
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (16 bp):
ATATTTAATGTATTTA
Found at i:214885 original size:37 final size:37
Alignment explanation
Indices: 214807--214910 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 37
214797 CATTTTCGTC
214807 CTACTAAGATTTAAATTCCT-AAAATAGGATAAAATT
1 CTACTAAGATTTAAATTCCTAAAAATAGGATAAAATT
* * * * * * *
214843 TTACTAGGATTCAAACTCCTAAAAATATGATAGAGTT
1 CTACTAAGATTTAAATTCCTAAAAATAGGATAAAATT
*
214880 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAAGATTTAAATTCCTAAAAATAGGAT
214911 CCACAAACAT
Statistics
Matches: 54, Mismatches: 13, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
36 16 0.30
37 38 0.70
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (37 bp):
CTACTAAGATTTAAATTCCTAAAAATAGGATAAAATT
Found at i:215306 original size:18 final size:17
Alignment explanation
Indices: 215267--215309 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
215257 ATTATATGGA
215267 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
215283 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
215301 TATTATTAT
1 TATTATTAT
215310 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:215373 original size:2 final size:2
Alignment explanation
Indices: 215368--215394 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
215358 TATATTTTAT
215368 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 T
215395 TTCTTTAATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:215632 original size:21 final size:20
Alignment explanation
Indices: 215578--215633 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 20
215568 ACTTTATATA
* *
215578 TTTATATTATTTTTTATTAT
1 TTTATATTATTATTCATTAT
* *
215598 TTTCATTTTTTTATTCATTAT
1 TTT-ATATTATTATTCATTAT
215619 TATTATATTATTATT
1 T-TTATATTATTATT
215634 TTTTAAAAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
20 3 0.11
21 23 0.82
22 2 0.07
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTATATTATTATTCATTAT
Found at i:215916 original size:9 final size:9
Alignment explanation
Indices: 215899--215957 Score: 50
Period size: 9 Copynumber: 6.7 Consensus size: 9
215889 ATTTTTTTTC
215899 TTATCTTAT
1 TTATCTTAT
*
215908 TTATTTTAT
1 TTATCTTAT
215917 TTAT-TT-T
1 TTATCTTAT
215924 TGTATCTTAT
1 T-TATCTTAT
* * *
215934 TTGTTTTCT
1 TTATCTTAT
*
215943 TTACCTTAT
1 TTATCTTAT
215952 TTATCT
1 TTATCT
215958 AACACATTTC
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
7 2 0.05
8 5 0.13
9 29 0.76
10 2 0.05
ACGTcount: A:0.17, C:0.10, G:0.03, T:0.69
Consensus pattern (9 bp):
TTATCTTAT
Found at i:217869 original size:13 final size:13
Alignment explanation
Indices: 217851--217877 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
217841 TGTCGGTGCT
217851 ACCATCAAAGGGA
1 ACCATCAAAGGGA
217864 ACCATCAAAGGGA
1 ACCATCAAAGGGA
217877 A
1 A
217878 GTGTATGTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.22, G:0.22, T:0.07
Consensus pattern (13 bp):
ACCATCAAAGGGA
Found at i:227841 original size:39 final size:39
Alignment explanation
Indices: 227787--227862 Score: 125
Period size: 39 Copynumber: 1.9 Consensus size: 39
227777 GTTTTGTTCT
* * *
227787 TGTAATATACTACAAACAATTAGATTTTACATACATCTA
1 TGTAATATACTACAAACAAATAGATATTAAATACATCTA
227826 TGTAATATACTACAAACAAATAGATATTAAATACATC
1 TGTAATATACTACAAACAAATAGATATTAAATACATC
227863 GAGTCCCTCG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.47, C:0.14, G:0.05, T:0.33
Consensus pattern (39 bp):
TGTAATATACTACAAACAAATAGATATTAAATACATCTA
Found at i:234302 original size:145 final size:146
Alignment explanation
Indices: 234127--234416 Score: 573
Period size: 145 Copynumber: 2.0 Consensus size: 146
234117 CCATTGTGCT
234127 AAACAGAAAGGTCTGAATGCCAGACTTTGGAAGAATTTTTGTAGATAAGTTTACTCGGGAGATGA
1 AAACAGAAAGGTCTGAATGCCAGACTTTGGAAGAATTTTTGTAGATAAGTTTACTCGGGAGATGA
234192 ATCACGCTCATCTTTTTGTTCAACAGGTAAGAACTCATAAATATAACACAAGCTTAAGCATATCC
66 ATCACGCTCATCTTTTTGTTCAACAGGTAAGAACTCATAAATATAACACAAGCTTAAGCATATCC
234257 T-AAAAAATCAGCCTA
131 TAAAAAAATCAGCCTA
234272 AAACAGAAAGGTCTGAATGCCAGACTTTGGAAGAATTTTTGTAGATAAGTTTACTCGGGAGATGA
1 AAACAGAAAGGTCTGAATGCCAGACTTTGGAAGAATTTTTGTAGATAAGTTTACTCGGGAGATGA
234337 ATCACGCTCATCTTTTTGTTCAACAGGTAAGAACTCATAAATATAACACAAGCTTAAGCATATCC
66 ATCACGCTCATCTTTTTGTTCAACAGGTAAGAACTCATAAATATAACACAAGCTTAAGCATATCC
234402 TAAAAAAATCAGCCT
131 TAAAAAAATCAGCCT
234417 CAGAGCCATT
Statistics
Matches: 144, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
145 131 0.91
146 13 0.09
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (146 bp):
AAACAGAAAGGTCTGAATGCCAGACTTTGGAAGAATTTTTGTAGATAAGTTTACTCGGGAGATGA
ATCACGCTCATCTTTTTGTTCAACAGGTAAGAACTCATAAATATAACACAAGCTTAAGCATATCC
TAAAAAAATCAGCCTA
Found at i:236262 original size:6 final size:6
Alignment explanation
Indices: 236251--236275 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
236241 CTCTCCACAT
236251 CCGCAG CCGCAG CCGCAG CCGCAG C
1 CCGCAG CCGCAG CCGCAG CCGCAG C
236276 AACGGCAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.52, G:0.32, T:0.00
Consensus pattern (6 bp):
CCGCAG
Found at i:241509 original size:51 final size:51
Alignment explanation
Indices: 241393--241490 Score: 142
Period size: 51 Copynumber: 1.9 Consensus size: 51
241383 ATTCCCATAA
* ** * *
241393 AAAGGATCGACCCCTCGACCAAAGGGATCGATCCCAAAGTTTCTGTTCAGC
1 AAAGGATCGATCCCTCGACCAAAAAGATCGATCCCAAACTCTCTGTTCAGC
*
241444 AAATGATCGATCCCTCGACCAAAAAGATCGATCCCAAACTCTCTGTT
1 AAAGGATCGATCCCTCGACCAAAAAGATCGATCCCAAACTCTCTGTT
241491 GTGCCTAGGA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 41 1.00
ACGTcount: A:0.32, C:0.30, G:0.17, T:0.21
Consensus pattern (51 bp):
AAAGGATCGATCCCTCGACCAAAAAGATCGATCCCAAACTCTCTGTTCAGC
Found at i:243288 original size:14 final size:14
Alignment explanation
Indices: 243269--243298 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
243259 TTTAGATTTT
*
243269 TTAAAATTACATTA
1 TTAAAAATACATTA
243283 TTAAAAATACATTA
1 TTAAAAATACATTA
243297 TT
1 TT
243299 GATAATTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAAAATACATTA
Found at i:243404 original size:21 final size:21
Alignment explanation
Indices: 243380--243444 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
243370 ATGTGATAGT
243380 GTTTATGATTTAGTGTTTAGG
1 GTTTATGATTTAGTGTTTAGG
*
243401 GTTTATGATTTAAG-GTTTAAG
1 GTTTATGATTT-AGTGTTTAGG
* *
243422 GTTTATGGTTTAGTATTTAGG
1 GTTTATGATTTAGTGTTTAGG
243443 GT
1 GT
243445 CTAGGGTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.05
21 34 0.89
22 2 0.05
ACGTcount: A:0.22, C:0.00, G:0.28, T:0.51
Consensus pattern (21 bp):
GTTTATGATTTAGTGTTTAGG
Found at i:243405 original size:14 final size:14
Alignment explanation
Indices: 243376--243444 Score: 61
Period size: 14 Copynumber: 4.9 Consensus size: 14
243366 AATTATGTGA
* *
243376 TAGTGTTTATGATT
1 TAGTGTTTAGGGTT
243390 TAGTGTTTAGGGTT
1 TAGTGTTTAGGGTT
*
243404 TA-TGATTTAAGGTT
1 TAGTG-TTTAGGGTT
*
243418 TAAG-GTTTATGGTT
1 T-AGTGTTTAGGGTT
*
243432 TAGTATTTAGGGT
1 TAGTGTTTAGGGT
243445 CTAGGGTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
13 4 0.09
14 39 0.87
15 2 0.04
ACGTcount: A:0.22, C:0.00, G:0.28, T:0.51
Consensus pattern (14 bp):
TAGTGTTTAGGGTT
Found at i:245806 original size:11 final size:11
Alignment explanation
Indices: 245769--245842 Score: 67
Period size: 11 Copynumber: 6.7 Consensus size: 11
245759 TATTAATCCG
*
245769 TCGAGCTTGAA
1 TCGAGCTTGTA
* *
245780 TTGAGTTTGTA
1 TCGAGCTTGTA
245791 TCGAGCTTGTA
1 TCGAGCTTGTA
* *
245802 ACGAGCTTTTA
1 TCGAGCTTGTA
* *
245813 TTGAGTTTGTA
1 TCGAGCTTGTA
*
245824 TCGAGCTTGAA
1 TCGAGCTTGTA
*
245835 TTGAGCTT
1 TCGAGCTT
245843 TAGTTTTGAG
Statistics
Matches: 48, Mismatches: 15, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
11 48 1.00
ACGTcount: A:0.22, C:0.12, G:0.26, T:0.41
Consensus pattern (11 bp):
TCGAGCTTGTA
Found at i:245843 original size:33 final size:33
Alignment explanation
Indices: 245770--245832 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
245760 ATTAATCCGT
**
245770 CGAGCTTGAATTGAGTTTGTATCGAGCTTGTAA
1 CGAGCTTTTATTGAGTTTGTATCGAGCTTGTAA
245803 CGAGCTTTTATTGAGTTTGTATCGAGCTTG
1 CGAGCTTTTATTGAGTTTGTATCGAGCTTG
245833 AATTGAGCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.40
Consensus pattern (33 bp):
CGAGCTTTTATTGAGTTTGTATCGAGCTTGTAA
Found at i:246594 original size:19 final size:19
Alignment explanation
Indices: 246572--246609 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
246562 AACATAAATG
246572 AAAAACAAA-ACAAAATAAT
1 AAAAA-AAATACAAAATAAT
*
246591 AAAAAAAATAGAAAATAAT
1 AAAAAAAATACAAAATAAT
246610 TAAATGAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.79, C:0.05, G:0.03, T:0.13
Consensus pattern (19 bp):
AAAAAAAATACAAAATAAT
Found at i:247999 original size:16 final size:16
Alignment explanation
Indices: 247978--248015 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
247968 ATGATAATAT
*
247978 ATATATATATTAGATA
1 ATATATACATTAGATA
*
247994 ATATATACATTATATA
1 ATATATACATTAGATA
248010 AT-TATA
1 ATATATA
248016 ACTATAGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (16 bp):
ATATATACATTAGATA
Found at i:248800 original size:84 final size:83
Alignment explanation
Indices: 248553--249941 Score: 1411
Period size: 84 Copynumber: 16.5 Consensus size: 83
248543 ACTCGATAAT
* * * * * * * *
248553 TTTTGTTGACAGATAGCCCTTCTTGCTTTGAGTTATGCTGTAAATTTTATTTGCCTCTGAGTTGA
1 TTTTGTTGGCAGATAACCCTTC-TGCCTTGAGTTATGCTGCAAA--TGATGTGCCTTTGAGCTGA
* * *
248618 ATGAAATCGAACTCGAAGGTA
63 GTGTAATCGAACTCGAAGGTC
* * * * *
248639 TTTT-ATGACAGATAACCCTTCTCGCCTTGAGTTATGTTGTAAATTGGATATGCCTTTGAGCTGA
1 TTTTGTTGGCAGATAACCCTTCT-GCCTTGAGTTATGCTGCAAA-T-GATGTGCCTTTGAGCTGA
* *
248703 ATGTAATTGAACTCGAAGGTC
63 GTGTAATCGAACTCGAAGGTC
* * * *
248724 TTTTGTTGGCAGATAACCCTTCTCACCTTGAGCTATACTGCAAATGATGTGCCTTTGAGCTGAAT
1 TTTTGTTGGCAGATAACCCTTCT-GCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
*
248789 GTAATCAAACTCGAAGGTC
65 GTAATCGAACTCGAAGGTC
* * *
248808 -TTTGTTGTCAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTGCCTTTGAGCTGAGT
1 TTTTGTTGGCAGATAACCCTTCT-GCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
248872 GTAATCGAACTCGAAGGTC
65 GTAATCGAACTCGAAGGTC
* * * *
248891 TTTTATTGGCAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAAT-ATTGTGCCTTTGAACTGAG
1 TTTTGTTGGCAGATAACCCTTCT-GCCTTGAGTTATGCTGCAAATGA-TGTGCCTTTGAGCTGAG
*
248955 TGTAATCGAACTCGAAGGAC
64 TGTAATCGAACTCGAAGGTC
** * * *
248975 TTTTGTTAACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCCGAGC
1 TTTTGTTGGCAGATAACCCTTCT-GCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
* *
249040 GTAATCAAACTCAAAGGTC
65 GTAATCGAACTCGAAGGTC
* * * * * * * ** *
249059 TTTCGTTGGCAAATAGCCCTTCTTGCTTTGAGTCATGTTGTAAATGATGTATCTTTGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTC-TGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
* * * *
249124 GTAGTCAAACTTGAAGGTA
65 GTAATCGAACTCGAAGGTC
* * * * * *
249143 TTTGGTTGGCAGATAACCCTTCTAGCCTTAAGTTATGCTACAAATGATATGCTTTTGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCT-GCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
* * *
249208 GTAGTCGAACTCAAAGGTA
65 GTAATCGAACTCGAAGGTC
* * * * * * * * *
249227 TTTTGTTGACAAATAGCCCTTATTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGTTGAGC
1 TTTTGTTGGCAGATAACCCTT-CTGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
249292 GTAATCGAACTCGAAGGTC
65 GTAATCGAACTCGAAGGTC
* * * * *
249311 TTTTTGTTGGCAGATAGCCCTTATCGCCTTGAGTTATGCTGTAAATGTTGTGCCTTTAAGCTGAG
1 -TTTTGTTGGCAGATAACCCTTCT-GCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAG
249376 TGTAATCGAACTCGAAGGTC
64 TGTAATCGAACTCGAAGGTC
* ** ** * *
249396 TTTTATTGGCTTATAACCCTTCTAGCCTTGAGTTACACTGCAAATGATGTGCCTTGGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCT-GCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
*
249461 GTAGTCGAACTCGAAGGTC
65 GTAATCGAACTCGAAGGTC
* * * * * ** * *
249480 TTTTGTTGCCAAATATCCCTTATTGCCTTGAGCTATATTGCAAATGATGTG-CTTGGGACCTGAG
1 TTTTGTTGGCAGATAACCCTT-CTGCCTTGAGTTATGCTGCAAATGATGTGCCTT-TGAGCTGAG
* * *
249544 AGTAGTTGAACTCGAAGGTC
64 TGTAATCGAACTCGAAGGTC
* * * * *
249564 TTTGGTTGGAAGATAACCCTTCTAGCCTTGATTTATGCTGCAAATGATATGCCTTTGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCT-GCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
** * *
249629 GTAGCCAAACTCGAAGGAC
65 GTAATCGAACTCGAAGGTC
* * * * *
249648 TTTTGTTGGCAAATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGTTGAGT
1 TTTTGTTGGCAGATAACCCTTC-TGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
*
249713 GTAGTCGAACTCGAAGGTC
65 GTAATCGAACTCGAAGGTC
* * * * * *
249732 TTTTATTGGCAGATAACCCTTCTACCCTTGAGTTATGTTGCAAATGATATGCCTTGGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCT-GCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
*
249797 GTAGTCGAAACTCGAAGGTC
65 GTAATCG-AACTCGAAGGTC
* * *
249817 TTTTATTGGCAGATAGCCCTTCTCGCCTTGAGCTATGCTGCAAAT-ATTGTGCCTTTGAGCTGAG
1 TTTTGTTGGCAGATAACCCTTCT-GCCTTGAGTTATGCTGCAAATGA-TGTGCCTTTGAGCTGAG
*
249881 TGTAATGGAACTCGAAGGTC
64 TGTAATCGAACTCGAAGGTC
*
249901 TTTTGTTGGCAGATAATCCTTCTAGCCTTGAGTTATGCTGC
1 TTTTGTTGGCAGATAACCCTTCT-GCCTTGAGTTATGCTGC
249942 CAATAGTTTC
Statistics
Matches: 1095, Mismatches: 189, Indels: 40
0.83 0.14 0.03
Matches are distributed among these distances:
83 81 0.07
84 757 0.69
85 221 0.20
86 36 0.03
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (83 bp):
TTTTGTTGGCAGATAACCCTTCTGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTG
TAATCGAACTCGAAGGTC
Found at i:249471 original size:505 final size:504
Alignment explanation
Indices: 248647--249935 Score: 1636
Period size: 505 Copynumber: 2.6 Consensus size: 504
248637 TATTTTATGA
* * * * *
248647 CAGATAACCCTTCTCGCCTTGAGTTATGTTGTAAATTGGATATGCCTTTGAGCTGAATGTAATTG
1 CAGATAACCCTTCTAGCCTTGAGTTATGTTGCAAA-T-GATATGCCTTTGAGCTGAGTGTAGTCG
* **
248712 AACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCACCTTGAGCTATACTGCAAATGATGTGCC
64 AACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAACCTTGAGCTATGTTGCAAATGATGTGCC
* ** * * * *
248777 TTTGAGCTGAATGTAATCAAACTCGAAGGTC-TTTGTTGTCAGATAACCCTTCTAGCCTTGAGTT
129 TTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTCGCCTTGAGTT
* *
248841 ATGTTGTAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTATTGGCAGATA
194 ATGCTGTAAATGTTGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTATTGGCAGATA
* * ** * * *
248906 ACCCTTCTCGCCTTGAGCTATGCTGTAAATATTGTGCCTTTGAACTGAGTGTAATCGAACTCGAA
259 ACCCTTCTAGCCTTGAGTTACACTGCAAATATTGTGCCTTGGAACTGAGCGTAATCGAACTCGAA
* * * *
248971 GGACTTTTGTTAACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTT-GGAGC
324 GGACTTTTGTTAACAAATAACCCTTATAGCCTTGAGCTATACTGCAAATGATGTG-CTTGGGA-C
* * * * *
249035 C-GAGCGTAATCAAACTCAAAGGTCTTTCGTTGGCAA-ATAGCCCTTCTTGCTTTGAGTCATGTT
387 CTGAGAGTAATCAAACTCAAAGGTCTTTCGTTGG-AAGATAACCCTTCTAGCCTTGAGTCATGCT
* * * * *
249098 GTAAATGATGTATCTTTGAGCTGAGCGTAGTCAAACTTGAAGGTA-TTTGGTTGG
451 GCAAATGATATACCTTTGAGCTGAGCGTAGCCAAACTCGAAGG-ACTTTGGTTGG
* * * * *
249152 CAGATAACCCTTCTAGCCTTAAGTTATGCTACAAATGATATGCTTTTGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGTTATGTTGCAAATGATATGCCTTTGAGCTGAGTGTAGTCGAA
* * * * * * **
249217 CTCAAAGGTATTTTGTTGACAAATAGCCCTTATTGCCTTGAGCTATGTTGCAAATGATGTGCCTT
66 CTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAACCTTGAGCTATGTTGCAAATGATGTGCCTT
* *
249282 GGAGTTGAGCGTAATCGAACTCGAAGGTCTTTTTGTTGGCAGATAGCCCTTATCGCCTTGAGTTA
131 GGAGCTGAGCGTAATCGAACTCGAAGGTC-TTTTGTTGGCAGATAGCCCTTCTCGCCTTGAGTTA
* **
249347 TGCTGTAAATGTTGTGCCTTTAAGCTGAGTGTAATCGAACTCGAAGGTCTTTTATTGGCTTATAA
195 TGCTGTAAATGTTGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTATTGGCAGATAA
* *
249412 CCCTTCTAGCCTTGAGTTACACTGCAAATGA-TGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAA
260 CCCTTCTAGCCTTGAGTTACACTGCAAAT-ATTGTGCCTTGGAACTGAGCGTAATCGAACTCGAA
* ** * * *
249476 GGTCTTTTGTTGCCAAATATCCCTTATTGCCTTGAGCTATATTGCAAATGATGTGCTTGGGACCT
324 GGACTTTTGTTAACAAATAACCCTTATAGCCTTGAGCTATACTGCAAATGATGTGCTTGGGACCT
* ** * * * *
249541 GAGAGTAGTTGAACTCGAAGGTCTTTGGTTGGAAGATAACCCTTCTAGCCTTGATTTATGCTGCA
389 GAGAGTAATCAAACTCAAAGGTCTTTCGTTGGAAGATAACCCTTCTAGCCTTGAGTCATGCTGCA
* *
249606 AATGATATGCCTTTGAGCTGAGCGTAGCCAAACTCGAAGGACTTTTGTTGG
454 AATGATATACCTTTGAGCTGAGCGTAGCCAAACTCGAAGGACTTTGGTTGG
* * * * * *
249657 CAAATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGTTGAGTGTAGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGTTATGTTGCAAATGATATGCCTTTGAGCTGAGTGTAGTCGAA
* * * *
249722 CTCGAAGGTCTTTTATTGGCAGATAACCCTTCTACCCTTGAGTTATGTTGCAAATGATATGCCTT
66 CTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAACCTTGAGCTATGTTGCAAATGATGTGCCTT
* * *
249787 GGAGCTGAGCGTAGTCGAAACTCGAAGGTCTTTTATTGGCAGATAGCCCTTCTCGCCTTGAGCTA
131 GGAGCTGAGCGTAATCG-AACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTCGCCTTGAGTTA
* * * *
249852 TGCTGCAAATATTGTGCCTTTGAGCTGAGTGTAATGGAACTCGAAGGTCTTTTGTTGGCAGATAA
195 TGCTGTAAATGTTGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTATTGGCAGATAA
*
249917 TCCTTCTAGCCTTGAGTTA
260 CCCTTCTAGCCTTGAGTTA
249936 TGCTGCCAAT
Statistics
Matches: 669, Mismatches: 107, Indels: 16
0.84 0.14 0.02
Matches are distributed among these distances:
503 103 0.15
504 9 0.01
505 544 0.81
506 13 0.02
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (504 bp):
CAGATAACCCTTCTAGCCTTGAGTTATGTTGCAAATGATATGCCTTTGAGCTGAGTGTAGTCGAA
CTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAACCTTGAGCTATGTTGCAAATGATGTGCCTT
GGAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTCGCCTTGAGTTAT
GCTGTAAATGTTGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTATTGGCAGATAAC
CCTTCTAGCCTTGAGTTACACTGCAAATATTGTGCCTTGGAACTGAGCGTAATCGAACTCGAAGG
ACTTTTGTTAACAAATAACCCTTATAGCCTTGAGCTATACTGCAAATGATGTGCTTGGGACCTGA
GAGTAATCAAACTCAAAGGTCTTTCGTTGGAAGATAACCCTTCTAGCCTTGAGTCATGCTGCAAA
TGATATACCTTTGAGCTGAGCGTAGCCAAACTCGAAGGACTTTGGTTGG
Found at i:251283 original size:95 final size:94
Alignment explanation
Indices: 251072--251322 Score: 360
Period size: 95 Copynumber: 2.6 Consensus size: 94
251062 GGCTAGCTGA
* **
251072 ATCCATAAAGTCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAA-TATCGTTGTAGATAT
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGT-TTATTGT--ATAT
*
251136 TATAATCACCTTTATCAGACTAGCTGAATATT
63 TATAATCACCTTTATCAGACTAGCTAAATATT
* * *
251168 ATCCATTAAGCAGGGACGTTTAACCAATTGCTCTAGAGGGACAACTCAAGGTTTATTGTATATTA
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAA-GTTTATTGTATATTA
* *
251233 TAATCACCTTTATCAGGCTAGCTAAATCTT
65 TAATCACCTTTATCAGACTAGCTAAATATT
*
251263 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAAATCAAGCTTTATTGTA
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAG-TTTATTGTA
251323 GATATATATA
Statistics
Matches: 139, Mismatches: 13, Indels: 7
0.87 0.08 0.04
Matches are distributed among these distances:
94 1 0.01
95 87 0.63
96 45 0.32
97 5 0.04
98 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (94 bp):
ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGTTTATTGTATATTAT
AATCACCTTTATCAGACTAGCTAAATATT
Found at i:252840 original size:17 final size:16
Alignment explanation
Indices: 252820--252858 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
252810 AAATGATTAA
252820 AAAAAACAAATTAAAAG
1 AAAAAA-AAATTAAAAG
*
252837 AAAATAAAAATTAAAGG
1 AAAA-AAAAATTAAAAG
252854 AAAAA
1 AAAAA
252859 GGTTAGTAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 17 0.85
18 2 0.10
ACGTcount: A:0.77, C:0.03, G:0.08, T:0.13
Consensus pattern (16 bp):
AAAAAAAAATTAAAAG
Found at i:254256 original size:15 final size:15
Alignment explanation
Indices: 254233--254267 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
254223 ATTAAATAAA
*
254233 AAAACAATAACAAAT
1 AAAATAATAACAAAT
254248 AAAATAATAACAAAT
1 AAAATAATAACAAAT
254263 AAAAT
1 AAAAT
254268 GAAAGAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.17
Consensus pattern (15 bp):
AAAATAATAACAAAT
Found at i:254281 original size:17 final size:17
Alignment explanation
Indices: 254259--254297 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
254249 AAATAATAAC
254259 AAATAAAATGAAAGAAA
1 AAATAAAATGAAAGAAA
254276 AAATAAAATGAAAGAAA
1 AAATAAAATGAAAGAAA
254293 AAATA
1 AAATA
254298 GACTATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (17 bp):
AAATAAAATGAAAGAAA
Found at i:254341 original size:2 final size:2
Alignment explanation
Indices: 254334--254366 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
254324 ATAAAAAGGA
254334 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
254367 AAGTATAGCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:256010 original size:31 final size:31
Alignment explanation
Indices: 255963--256027 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
255953 AGGGAGAATG
* * *
255963 GTCCCTAATATTATCGATCTGTTCGATTTTA
1 GTCCATAACATTATCGATCTATTCGATTTTA
*
255994 GTCCATAACATTATCGATTTATTCGATTTTA
1 GTCCATAACATTATCGATCTATTCGATTTTA
256025 GTC
1 GTC
256028 TCTCAATTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.45
Consensus pattern (31 bp):
GTCCATAACATTATCGATCTATTCGATTTTA
Found at i:256428 original size:26 final size:26
Alignment explanation
Indices: 256398--256456 Score: 118
Period size: 26 Copynumber: 2.3 Consensus size: 26
256388 CGGTCATGTT
256398 ACCGGTTCATTGGTTCAACCGGTCGA
1 ACCGGTTCATTGGTTCAACCGGTCGA
256424 ACCGGTTCATTGGTTCAACCGGTCGA
1 ACCGGTTCATTGGTTCAACCGGTCGA
256450 ACCGGTT
1 ACCGGTT
256457 TGACCGGTCG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (26 bp):
ACCGGTTCATTGGTTCAACCGGTCGA
Found at i:259108 original size:14 final size:15
Alignment explanation
Indices: 259070--259112 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
259060 TTGGTTTTTC
*
259070 GGAAAATGAATTATT
1 GGAAAATGAATTACT
**
259085 GGAATTTGAATT-CT
1 GGAAAATGAATTACT
259099 GGAAAATGAATTAC
1 GGAAAATGAATTAC
259113 ATTTCTGTAA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
14 11 0.50
15 11 0.50
ACGTcount: A:0.42, C:0.05, G:0.21, T:0.33
Consensus pattern (15 bp):
GGAAAATGAATTACT
Found at i:259428 original size:11 final size:12
Alignment explanation
Indices: 259389--259480 Score: 57
Period size: 12 Copynumber: 7.4 Consensus size: 12
259379 AGTCTTATAT
259389 TATATT-TTAAA
1 TATATTATTAAA
* *
259400 AATATTAATT-AG
1 TATATT-ATTAAA
259412 TATATT-TTAAA
1 TATATTATTAAA
259423 TATATTTATTAAA
1 TATA-TTATTAAA
259436 -ATATTATCTAAA
1 TATATTAT-TAAA
* *
259448 TATATAAATAATA
1 TATATTATTAA-A
259461 TTATTCATTATTAAA
1 -TA-T-ATTATTAAA
259476 TATAT
1 TATAT
259481 AAATTTTTTA
Statistics
Matches: 62, Mismatches: 8, Indels: 21
0.68 0.09 0.23
Matches are distributed among these distances:
10 2 0.03
11 14 0.23
12 20 0.32
13 14 0.23
14 4 0.06
15 2 0.03
16 6 0.10
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (12 bp):
TATATTATTAAA
Found at i:259439 original size:23 final size:23
Alignment explanation
Indices: 259390--259452 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
259380 GTCTTATATT
* **
259390 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAATATATTAATTAAA
*
259413 ATATTTTAAATATATTTATTAAA
1 ATATTTTAAATATATTAATTAAA
259436 ATATTATCTAAATATAT
1 ATATT-T-TAAATATAT
259453 AAATAATATT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 24 0.71
24 1 0.03
25 9 0.26
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (23 bp):
ATATTTTAAATATATTAATTAAA
Found at i:259493 original size:30 final size:29
Alignment explanation
Indices: 259436--259603 Score: 113
Period size: 28 Copynumber: 5.9 Consensus size: 29
259426 ATTTATTAAA
259436 ATATTATCTAAATATATAAA-TAATATTAT
1 ATATTAT-TAAATATATAAATTAATATTAT
**
259465 -TCATTATTAAATATATAAATTTTTTATTAT
1 AT-ATTATTAAATATATAAA-TTAATATTAT
*
259495 ATATTATTAAA-ATA-AAAATAATATCT-T
1 ATATTATTAAATATATAAATTAATAT-TAT
** *
259522 ATATTATTATAATATATTGATT-ATTTTAT
1 ATATTATTA-AATATATAAATTAATATTAT
* * *
259551 ATA-TATTAAAAATATTATATTATTATTAT
1 ATATTATTAAATATA-TAAATTAATATTAT
* *
259580 A-AATATT-AATAAATAAA-TAATATT
1 ATATTATTAAATATATAAATTAATATT
259604 CTGATGAAAA
Statistics
Matches: 109, Mismatches: 18, Indels: 27
0.71 0.12 0.18
Matches are distributed among these distances:
26 6 0.06
27 22 0.20
28 34 0.31
29 28 0.26
30 18 0.17
31 1 0.01
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.49
Consensus pattern (29 bp):
ATATTATTAAATATATAAATTAATATTAT
Found at i:259603 original size:29 final size:28
Alignment explanation
Indices: 259543--259603 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 28
259533 ATATATTGAT
* * *
259543 TATTTTATATATATTAAAAATATTATAT
1 TATTTTATAAATATTAAAAATATAATAA
259571 TATTATTATAAATATTAATAAATA-AATAA
1 TATT-TTATAAATATTAA-AAATATAATAA
259600 TATT
1 TATT
259604 CTGATGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 4 0.14
29 19 0.68
30 5 0.18
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (28 bp):
TATTTTATAAATATTAAAAATATAATAA
Found at i:259844 original size:42 final size:41
Alignment explanation
Indices: 259780--259893 Score: 176
Period size: 42 Copynumber: 2.7 Consensus size: 41
259770 AATTACATTC
* *
259780 CGGAAAATC-AATTACGTAAAACAAACACGGGAAAATATTTTT
1 CGGAAAA-CGAATTACGTGAAACAAACACGGGAAAACA-TTTT
259822 CGGAAAACGAATTACGTGAAACAAACACGGGAAAACATTTT
1 CGGAAAACGAATTACGTGAAACAAACACGGGAAAACATTTT
259863 CTGGAAAACGAATTACGTGAAACAAACACGG
1 C-GGAAAACGAATTACGTGAAACAAACACGG
259894 TAATTCGGGG
Statistics
Matches: 68, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
41 6 0.09
42 62 0.91
ACGTcount: A:0.46, C:0.17, G:0.18, T:0.18
Consensus pattern (41 bp):
CGGAAAACGAATTACGTGAAACAAACACGGGAAAACATTTT
Found at i:260257 original size:18 final size:18
Alignment explanation
Indices: 260234--260268 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
260224 TTAAGAATTA
*
260234 TTTTTAGGAATTCTCTTG
1 TTTTTAGGAATTATCTTG
260252 TTTTTAGGAATTATCTT
1 TTTTTAGGAATTATCTT
260269 TTAGGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.09, G:0.14, T:0.57
Consensus pattern (18 bp):
TTTTTAGGAATTATCTTG
Found at i:260934 original size:21 final size:21
Alignment explanation
Indices: 260910--260959 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
260900 TTTTAAACTT
260910 TCTT-TTTAAATATCTTTTTAA
1 TCTTCTTTAAA-ATCTTTTTAA
* *
260931 TCTTCTTTGAAATCTTTTTAT
1 TCTTCTTTAAAATCTTTTTAA
*
260952 TTTTCTTT
1 TCTTCTTT
260960 CTTTTATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 20 0.80
22 5 0.20
ACGTcount: A:0.20, C:0.12, G:0.02, T:0.66
Consensus pattern (21 bp):
TCTTCTTTAAAATCTTTTTAA
Found at i:267712 original size:19 final size:20
Alignment explanation
Indices: 267676--267716 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
267666 CTCAGGTAGG
*
267676 GTATCGATACTTAAGTGAAA
1 GTATCGATACTCAAGTGAAA
267696 GTATCGATAC-CAAGTGAAA
1 GTATCGATACTCAAGTGAAA
267715 GT
1 GT
267717 TTGATCTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.39, C:0.12, G:0.22, T:0.27
Consensus pattern (20 bp):
GTATCGATACTCAAGTGAAA
Found at i:268918 original size:96 final size:96
Alignment explanation
Indices: 268754--268946 Score: 377
Period size: 96 Copynumber: 2.0 Consensus size: 96
268744 TCACGCTCTC
*
268754 TTTCCACTACCAGTCGAATCACTTTAGCTAAATCGATTCTGCCTTCTATTCCGATCTATTTCATG
1 TTTCCACTACCAGTCGAATCACTTTAGCTAAATCGATTCTGACTTCTATTCCGATCTATTTCATG
268819 CAAACAACCATGTTTCCTATTGGGTCAGTAA
66 CAAACAACCATGTTTCCTATTGGGTCAGTAA
268850 TTTCCACTACCAGTCGAATCACTTTAGCTAAATCGATTCTGACTTCTATTCCGATCTATTTCATG
1 TTTCCACTACCAGTCGAATCACTTTAGCTAAATCGATTCTGACTTCTATTCCGATCTATTTCATG
268915 CAAACAACCATGTTTCCTATTGGGTCAGTAA
66 CAAACAACCATGTTTCCTATTGGGTCAGTAA
268946 T
1 T
268947 GAAATTTAAC
Statistics
Matches: 96, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
96 96 1.00
ACGTcount: A:0.26, C:0.25, G:0.12, T:0.36
Consensus pattern (96 bp):
TTTCCACTACCAGTCGAATCACTTTAGCTAAATCGATTCTGACTTCTATTCCGATCTATTTCATG
CAAACAACCATGTTTCCTATTGGGTCAGTAA
Found at i:270212 original size:33 final size:33
Alignment explanation
Indices: 270164--270232 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
270154 CCTAACTGCA
* *
270164 CAACACCACATGAGCTATAACTGTAGCTTACTT
1 CAACACCACATGAGCTACAACTGCAGCTTACTT
*
270197 CAACACCACGA-GAGCTACAACTGCAGGTTACTT
1 CAACACCAC-ATGAGCTACAACTGCAGCTTACTT
270230 CAA
1 CAA
270233 TATTCTTCCT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 31 0.97
34 1 0.03
ACGTcount: A:0.35, C:0.29, G:0.14, T:0.22
Consensus pattern (33 bp):
CAACACCACATGAGCTACAACTGCAGCTTACTT
Found at i:279727 original size:30 final size:30
Alignment explanation
Indices: 279686--279771 Score: 93
Period size: 30 Copynumber: 2.8 Consensus size: 30
279676 ACCACTATCT
*
279686 ATATGTTCCGAAGAACATAGGTAACTGTCC
1 ATATGTCCCGAAGAACATAGGTAACTGTCC
* * *
279716 ATATGTCCCGAAGGATATAGGGAAACTGTCC
1 ATATGTCCCGAAGAACATA-GGTAACTGTCC
* *
279747 ATATGTCTC-AAAAGACATAGGTAAC
1 ATATGTCCCGAAGA-ACATAGGTAAC
279772 CCTCGATTAT
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
30 23 0.51
31 22 0.49
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (30 bp):
ATATGTCCCGAAGAACATAGGTAACTGTCC
Found at i:279746 original size:31 final size:30
Alignment explanation
Indices: 279686--279753 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 30
279676 ACCACTATCT
* *
279686 ATATGTTCCGAAGAACATAGGTAACTGTCC
1 ATATGTCCCGAAGAACATAGGAAACTGTCC
* *
279716 ATATGTCCCGAAGGATATAGGGAAACTGTCC
1 ATATGTCCCGAAGAACATA-GGAAACTGTCC
279747 ATATGTC
1 ATATGTC
279754 TCAAAAGACA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
30 16 0.48
31 17 0.52
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.26
Consensus pattern (30 bp):
ATATGTCCCGAAGAACATAGGAAACTGTCC
Found at i:279767 original size:31 final size:31
Alignment explanation
Indices: 279700--279767 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
279690 GTTCCGAAGA
* * *
279700 ACATA-GGTAACTGTCCATATGTCCCGAAGG
1 ACATAGGGAAACTGTCCATATGTCCCAAAAG
* *
279730 ATATAGGGAAACTGTCCATATGTCTCAAAAG
1 ACATAGGGAAACTGTCCATATGTCCCAAAAG
279761 ACATAGG
1 ACATAGG
279768 TAACCCTCGA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (31 bp):
ACATAGGGAAACTGTCCATATGTCCCAAAAG
Found at i:281496 original size:21 final size:22
Alignment explanation
Indices: 281470--281510 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
281460 GCTAAATTTA
*
281470 CCATAA-TACCCTTTAATCCTT
1 CCATAATTACCATTTAATCCTT
281491 CCATAATTACCATTTAATCC
1 CCATAATTACCATTTAATCC
281511 AATACCAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.37
Consensus pattern (22 bp):
CCATAATTACCATTTAATCCTT
Found at i:286027 original size:22 final size:22
Alignment explanation
Indices: 285992--286038 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
285982 TCCTTTAAGC
*
285992 TAAATTTACCATAA-TATCCTT
1 TAAATTTACCATAATTATCATT
*
286013 TAAATTCTTCCATAATTATCATT
1 TAAATT-TACCATAATTATCATT
286036 TAA
1 TAA
286039 TCCAATACCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 6 0.27
22 7 0.32
23 9 0.41
ACGTcount: A:0.38, C:0.17, G:0.00, T:0.45
Consensus pattern (22 bp):
TAAATTTACCATAATTATCATT
Found at i:299818 original size:84 final size:85
Alignment explanation
Indices: 299651--299894 Score: 241
Period size: 84 Copynumber: 2.9 Consensus size: 85
299641 ATCAGATCGA
* * * *
299651 GGAGTTCAATCCTCCGA-GCTGCC-AGGGAACAAATCAGATAGTGCAGTTCAACCACCGAGGCTC
1 GGAGTTCAATCC-CCAAGGCT-CCTAGTGAACAAATCAGATAGTGCATTTCAATCACCGAGGCTC
*
299714 TCGAAGG-CAAA-ATCATATAGG
64 TCGAAGGACAAACA-CAGATAGG
* ** * ** * *
299735 GGAGTT-ATATTCTCCGGGGC-CCTGGTGAACATGTCAGAAAGTGCATTTCAATCACCAAGGCTC
1 GGAGTTCA-A-TCCCCAAGGCTCCTAGTGAACAAATCAGATAGTGCATTTCAATCACCGAGGCTC
*
299798 TTGAAGGACAAACA-AGATAGG
64 TCGAAGGACAAACACAGATAGG
* * *
299819 GGAGTTCAATCCCCAAGGCTCCTAGTGAGCAAATCAGATAGTGCATTTCATTCACTGAGGCTCTC
1 GGAGTTCAATCCCCAAGGCTCCTAGTGAACAAATCAGATAGTGCATTTCAATCACCGAGGCTCTC
299884 GAAGGACAAAC
66 GAAGGACAAAC
299895 CGGATACTGA
Statistics
Matches: 128, Mismatches: 24, Indels: 16
0.76 0.14 0.10
Matches are distributed among these distances:
83 10 0.08
84 108 0.84
85 9 0.07
86 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.25, T:0.21
Consensus pattern (85 bp):
GGAGTTCAATCCCCAAGGCTCCTAGTGAACAAATCAGATAGTGCATTTCAATCACCGAGGCTCTC
GAAGGACAAACACAGATAGG
Found at i:304629 original size:15 final size:13
Alignment explanation
Indices: 304598--304624 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
304588 GTTTAAGTAG
304598 TTTAGGATTTATC
1 TTTAGGATTTATC
304611 TTTAGGATTTATC
1 TTTAGGATTTATC
304624 T
1 T
304625 CTTTATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.07, G:0.15, T:0.56
Consensus pattern (13 bp):
TTTAGGATTTATC
Found at i:304629 original size:21 final size:20
Alignment explanation
Indices: 304605--304653 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 20
304595 TAGTTTAGGA
*
304605 TTTATCTTTAGGATTTATCTC
1 TTTAT-TTTAGGAATTATCTC
304626 TTTATTTTAGGAATTATCT-
1 TTTATTTTAGGAATTATCTC
304645 TTTCATTTT
1 TTT-ATTTT
304654 GAATGCTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 3 0.12
20 18 0.69
21 5 0.19
ACGTcount: A:0.20, C:0.10, G:0.08, T:0.61
Consensus pattern (20 bp):
TTTATTTTAGGAATTATCTC
Found at i:306684 original size:45 final size:45
Alignment explanation
Indices: 306626--306712 Score: 174
Period size: 45 Copynumber: 1.9 Consensus size: 45
306616 ATAATACAAA
306626 AAAAAAAATGGTTGTCCCTTGTTCCCATATGTAATGGGGTAATAC
1 AAAAAAAATGGTTGTCCCTTGTTCCCATATGTAATGGGGTAATAC
306671 AAAAAAAATGGTTGTCCCTTGTTCCCATATGTAATGGGGTAA
1 AAAAAAAATGGTTGTCCCTTGTTCCCATATGTAATGGGGTAA
306713 GGGGGAGGTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (45 bp):
AAAAAAAATGGTTGTCCCTTGTTCCCATATGTAATGGGGTAATAC
Found at i:321814 original size:123 final size:125
Alignment explanation
Indices: 321668--321986 Score: 432
Period size: 125 Copynumber: 2.6 Consensus size: 125
321658 CTCTTATTAC
* * * *
321668 TCGATCTTGTGGTGA-TCTGATCCGGGATAAGATCCACATTATTATGGTTTGGACTCTGCTAAAC
1 TCGACCTTGTGGTGACTC-AATCCGGGGTAAGATCCACATTATTATGGTTCGGACTCTGCTAAAC
* *
321732 ACTAACTTTTTTATTTTATTTA-TTTA-TTTATTTTTATAT-TTCCATTTGCATTATTCTAT
65 ACTAACTTTTTCATTTTATTTATTTTATTTTATTTTTATATATT-CATTTGCATTATTCGAT
* * *
321791 TCGACCTTGTGGTGACTCAATCCGGGGTAAAATCTACATTATTATGGTTCAGACTCTGCT-AACT
1 TCGACCTTGTGGTGACTCAATCCGGGGTAAGATCCACATTATTATGGTTCGGACTCTGCTAAAC-
*
321855 ACTAACTTTTTCATTTTATTTATTTTATTTTATTTTTATATATTCGTTTGCATTATTCGAT
65 ACTAACTTTTTCATTTTATTTATTTTATTTTATTTTTATATATTCATTTGCATTATTCGAT
* * * * * *
321916 TTGACCTTGTGGTGACCCAATTCGGGGTAAGATTCACATTATTATGGTTCGGACTCTACTAACCA
1 TCGACCTTGTGGTGACTCAATCCGGGGTAAGATCCACATTATTATGGTTCGGACTCTGCTAAACA
321981 CTAACT
66 CTAACT
321987 GCTAACTTTT
Statistics
Matches: 171, Mismatches: 19, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
122 3 0.02
123 71 0.42
124 6 0.04
125 87 0.51
126 4 0.02
ACGTcount: A:0.24, C:0.17, G:0.14, T:0.45
Consensus pattern (125 bp):
TCGACCTTGTGGTGACTCAATCCGGGGTAAGATCCACATTATTATGGTTCGGACTCTGCTAAACA
CTAACTTTTTCATTTTATTTATTTTATTTTATTTTTATATATTCATTTGCATTATTCGAT
Found at i:322039 original size:32 final size:34
Alignment explanation
Indices: 322003--322076 Score: 125
Period size: 34 Copynumber: 2.2 Consensus size: 34
321993 TTTTCTAACT
322003 TACTAACATTCTAAC-TTTTA-TTTTATTGTTCA
1 TACTAACATTCTAACTTTTTATTTTTATTGTTCA
*
322035 TACTAACATTCTAACTTTTTATTTTTATTGTTCT
1 TACTAACATTCTAACTTTTTATTTTTATTGTTCA
322069 TACTAACA
1 TACTAACA
322077 CTTTATTCTA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
32 15 0.38
33 5 0.13
34 19 0.49
ACGTcount: A:0.28, C:0.16, G:0.03, T:0.53
Consensus pattern (34 bp):
TACTAACATTCTAACTTTTTATTTTTATTGTTCA
Found at i:322147 original size:15 final size:14
Alignment explanation
Indices: 322125--322156 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
322115 ATTTATGCAA
322125 TTTATTTATTTATT
1 TTTATTTATTTATT
322139 TTTATTTTATTTATT
1 TTTA-TTTATTTATT
322154 TTT
1 TTT
322157 CCAGCACTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTATTTATTTATT
Found at i:322233 original size:29 final size:30
Alignment explanation
Indices: 322185--322246 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
322175 ATTCTTTATT
* *
322185 TTTCTGTCCCTTTAATTTTCCTA-CATTTTA
1 TTTCAGTCCCTTTAATTTT-CTAGCATTTAA
*
322215 TTTCAGTCCTTTTAA-TTTCTAGCATTTAA
1 TTTCAGTCCCTTTAATTTTCTAGCATTTAA
322244 TTT
1 TTT
322247 TTTGCATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 3 0.11
29 12 0.43
30 13 0.46
ACGTcount: A:0.19, C:0.19, G:0.05, T:0.56
Consensus pattern (30 bp):
TTTCAGTCCCTTTAATTTTCTAGCATTTAA
Found at i:322568 original size:17 final size:18
Alignment explanation
Indices: 322529--322574 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
322519 TGAGGTAATG
322529 TGTTTTATTTTTTCACAT
1 TGTTTTATTTTTTCACAT
* **
322547 CGTTTTATTTTTT-ATTT
1 TGTTTTATTTTTTCACAT
322564 TGTTTTATTTT
1 TGTTTTATTTT
322575 ATTTTTATCT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 12 0.50
18 12 0.50
ACGTcount: A:0.13, C:0.07, G:0.07, T:0.74
Consensus pattern (18 bp):
TGTTTTATTTTTTCACAT
Found at i:326425 original size:21 final size:20
Alignment explanation
Indices: 326401--326442 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
326391 GTCATACAAC
*
326401 TAATAATAGTTGTATAATGCA
1 TAATAATAGTT-CATAATGCA
*
326422 TAATAATGGTTCATAATGCA
1 TAATAATAGTTCATAATGCA
326442 T
1 T
326443 TGTAAGTTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.38
Consensus pattern (20 bp):
TAATAATAGTTCATAATGCA
Found at i:331100 original size:21 final size:20
Alignment explanation
Indices: 331076--331117 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
331066 GTCATACAAC
*
331076 TAATAATAGTTGTATAATGCA
1 TAATAATAGTT-CATAATGCA
*
331097 TAATAATGGTTCATAATGCA
1 TAATAATAGTTCATAATGCA
331117 T
1 T
331118 TGTAAGTTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.38
Consensus pattern (20 bp):
TAATAATAGTTCATAATGCA
Found at i:342131 original size:23 final size:21
Alignment explanation
Indices: 342105--342149 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 21
342095 TTTCACTTGT
342105 ATCATCTG-CACTATCATCACAGA
1 ATCA-CTGTCACTATC-TC-CAGA
342128 ATCACTGTCACTATCTCCAGA
1 ATCACTGTCACTATCTCCAGA
342149 A
1 A
342150 GAATCCTTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 5 0.24
22 5 0.24
23 11 0.52
ACGTcount: A:0.33, C:0.31, G:0.09, T:0.27
Consensus pattern (21 bp):
ATCACTGTCACTATCTCCAGA
Found at i:344547 original size:11 final size:11
Alignment explanation
Indices: 344511--344553 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
344501 TTACCCTTTA
*
344511 TTTTAAATAAT
1 TTTTAATTAAT
* *
344522 TTATCATTAAAT
1 TTTTAATT-AAT
344534 TTTTAATTAAT
1 TTTTAATTAAT
344545 TTTTAATTA
1 TTTTAATTA
344554 TACGTTGAGT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 17 0.65
12 9 0.35
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (11 bp):
TTTTAATTAAT
Found at i:345043 original size:21 final size:20
Alignment explanation
Indices: 345019--345060 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
345009 GTCATACAAC
*
345019 TAATAATAGTTGTATAATGCA
1 TAATAATAGTT-CATAATGCA
*
345040 TAATAATGGTTCATAATGCA
1 TAATAATAGTTCATAATGCA
345060 T
1 T
345061 TGTAAGTTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.38
Consensus pattern (20 bp):
TAATAATAGTTCATAATGCA
Found at i:349132 original size:25 final size:25
Alignment explanation
Indices: 349104--349155 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
349094 GAAAAAGAAT
349104 GTTTATTTGTGGAATTTTATGGTGA
1 GTTTATTTGTGGAATTTTATGGTGA
349129 GTTTATTTGTGGAATTTTATGGTGA
1 GTTTATTTGTGGAATTTTATGGTGA
349154 GT
1 GT
349156 GAGTACGCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.19, C:0.00, G:0.29, T:0.52
Consensus pattern (25 bp):
GTTTATTTGTGGAATTTTATGGTGA
Found at i:362745 original size:2 final size:2
Alignment explanation
Indices: 362738--362770 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
362728 TGAAGTAAAA
*
362738 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
362771 AGCATGATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 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):
AT
Found at i:363045 original size:11 final size:11
Alignment explanation
Indices: 363029--363094 Score: 53
Period size: 11 Copynumber: 5.5 Consensus size: 11
363019 TATGACTAAG
363029 ATAATAATAAA
1 ATAATAATAAA
363040 ATAATAATGAAA
1 ATAATAAT-AAA
*
363052 GTAATAATTTAAAA
1 ATAATAA--T-AAA
363066 ATATATCAA-AAA
1 ATA-AT-AATAAA
*
363078 GTAATAATAAA
1 ATAATAATAAA
363089 ATAATA
1 ATAATA
363095 TTGCAAATAA
Statistics
Matches: 44, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
10 2 0.05
11 18 0.41
12 14 0.32
14 6 0.14
15 2 0.05
16 2 0.05
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.29
Consensus pattern (11 bp):
ATAATAATAAA
Found at i:363101 original size:26 final size:26
Alignment explanation
Indices: 363030--363120 Score: 75
Period size: 26 Copynumber: 3.5 Consensus size: 26
363020 ATGACTAAGA
*
363030 TAATAATAAAATAATAATG---AAAG
1 TAATAATAAAATAATATTGCAAAAAG
*
363053 TAATAATTTAAA-AATATAT-CAAAAAG
1 TAATAA-TAAAATAATAT-TGCAAAAAG
*
363079 TAATAATAAAATAATATTGCAAATAAT
1 TAATAATAAAATAATATTGCAAA-AAG
*
363106 TAATGATCAAAATAA
1 TAATAAT-AAAATAA
363121 AAGAAATTAA
Statistics
Matches: 54, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
23 10 0.19
24 5 0.09
25 5 0.09
26 19 0.35
27 8 0.15
28 7 0.13
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (26 bp):
TAATAATAAAATAATATTGCAAAAAG
Found at i:364503 original size:3 final size:3
Alignment explanation
Indices: 364495--364549 Score: 92
Period size: 3 Copynumber: 18.0 Consensus size: 3
364485 TATTTGTAAT
364495 TAA TAA TAA TAA TAA TAA TAA TAA TAA TATA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA
*
364541 TAT TAA TAA
1 TAA TAA TAA
364550 GATTAAAAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 46 0.94
4 3 0.06
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:364554 original size:9 final size:9
Alignment explanation
Indices: 364498--364563 Score: 73
Period size: 9 Copynumber: 7.4 Consensus size: 9
364488 TTGTAATTAA
*
364498 TAATAATAA
1 TAATAATAT
*
364507 TAATAATAA
1 TAATAATAT
364516 TAATAATAT
1 TAATAATAT
*
364525 ATAATAATAA
1 -TAATAATAT
364535 TAATAATAT
1 TAATAATAT
*
364544 TAATAAGAT
1 TAATAATAT
364553 TAA-AA-AT
1 TAATAATAT
364560 TAAT
1 TAAT
364564 GTCTACAGTT
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
7 5 0.10
8 2 0.04
9 36 0.71
10 8 0.16
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (9 bp):
TAATAATAT
Found at i:364789 original size:45 final size:45
Alignment explanation
Indices: 364737--364840 Score: 163
Period size: 45 Copynumber: 2.3 Consensus size: 45
364727 CACTGGAGGT
* * *
364737 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCAAAGG
*
364782 TTTTGAAAACATCATGTACTGAAGGGCTTACAGATGACCCAAAGG
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCAAAGG
*
364827 CTTTGAAAACATCA
1 TTTTGAAAACATCA
364841 AAAAGCTCCC
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 54 1.00
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (45 bp):
TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCAAAGG
Found at i:364908 original size:76 final size:76
Alignment explanation
Indices: 364774--364992 Score: 316
Period size: 76 Copynumber: 2.9 Consensus size: 76
364764 TTACAGATGA
* * * * ** * *
364774 CCCGAAGG--TTTTGAAAACATCATGTACTGAAGGGCTTACAGATGACCCAAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAAC
364837 ATCAAAAAGCT
66 ATCAAAAAGCT
*
364848 CCCGAAGGCTTTTTGAAAACATCCTGCATTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAAC
1 CCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAAC
364913 ATCAAAAAGCT
66 ATCAAAAAGCT
* * *
364924 CTCGAAGGCTTTTTGAAAACATCCTACACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAGAAC
1 CCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAAC
364989 ATCA
66 ATCA
364993 TGCACTGAAG
Statistics
Matches: 130, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
74 8 0.06
76 122 0.94
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (76 bp):
CCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAAC
ATCAAAAAGCT
Found at i:364983 original size:121 final size:121
Alignment explanation
Indices: 364848--365507 Score: 574
Period size: 121 Copynumber: 5.6 Consensus size: 121
364838 TCAAAAAGCT
* * * **
364848 CCCGAAGGCTTTTTGAAAACATCCTGCATTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAAC
1 CCCGAAGG--TTTTGAAAACATCATGCATTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAAC
* *
364913 ATCAAAAAGCTCTCGAAGGCTTTTTGAAAACATCCTACACTGTAGGTCTTATGGATGA
64 ATCAAAAAGCTCTCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTATGGATGA
* * *
364971 CCCGAAGGTTTTGAGAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACAT
1 CCCGAAGGTTTTGAAAACATCATGCATTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACAT
* * * * *
365036 CAAAAATCTCCCAAAGGCTTTTTGAAAACATCTTGCACTGTAGATCTTATGGATGA
66 CAAAAAGCTCTCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTATGGATGA
* * * *
365092 CCCGAAGGCTTTGAAAACATCATGCATTGAAGGGCTTACAGATGACCTGAAGGTTTTAAAAATAT
1 CCCGAAGGTTTTGAAAACATCATGCATTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACAT
**
365157 CAAAAAGCTCTCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGA
66 CAAAAAGCTCTCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTATGGATGA
** * *** ** * * ***
365213 CCCGAAGGTTTTGAAAACATCAAAATGC-TCCCAAAGGCTTTTTGAAAACATC--ATGCAATGAA
1 CCCGAAGGTTTTGAAAACATC---ATGCAT-TGAAGGGCTTACAGATGAC-CCGAAGGTTTTGAA
* * * * * * *
365275 TAGC-TTACAGATG-ACTCGAAGGC--TTTGAAAACATCA---A----A------A-AGCT--
61 -AACATCA-AAAAGCTCTCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTATGGATGA
* * * * ** *
365318 CCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTAAAAAC
1 CCCGAAGG--TTTTGAAAACATCATGCATTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAAC
* *
365383 ATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGA
64 ATCAAAAAGCTCTCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTATGGATGA
* * * *
365441 CCCTAAGGCTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACAT
1 CCCGAAGGTTTTGAAAACATCATGCATTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACAT
365506 CA
66 CA
365508 TGCACTGAAG
Statistics
Matches: 419, Mismatches: 86, Indels: 66
0.73 0.15 0.12
Matches are distributed among these distances:
103 1 0.00
104 18 0.04
105 23 0.05
107 28 0.07
108 1 0.00
110 1 0.00
114 2 0.00
118 1 0.00
120 1 0.00
121 292 0.70
123 32 0.08
124 19 0.05
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.26
Consensus pattern (121 bp):
CCCGAAGGTTTTGAAAACATCATGCATTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACAT
CAAAAAGCTCTCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTATGGATGA
Found at i:364999 original size:45 final size:45
Alignment explanation
Indices: 364934--365037 Score: 136
Period size: 45 Copynumber: 2.3 Consensus size: 45
364924 CTCGAAGGCT
* * * **
364934 TTTTGAAAACATCCTACACTGTAGGTCTTATGGATGACCCGAAGG
1 TTTTGAAAACATCATACACTGAAGGGCTTACAGATGACCCGAAGG
* *
364979 TTTTGAGAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
1 TTTTGAAAACATCATACACTGAAGGGCTTACAGATGACCCGAAGG
*
365024 CTTTGAAAACATCA
1 TTTTGAAAACATCA
365038 AAAATCTCCC
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 50 1.00
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (45 bp):
TTTTGAAAACATCATACACTGAAGGGCTTACAGATGACCCGAAGG
Found at i:365086 original size:197 final size:197
Alignment explanation
Indices: 364736--365386 Score: 745
Period size: 197 Copynumber: 3.3 Consensus size: 197
364726 ACACTGGAGG
* * ** *
364736 TTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCGAAGGTTTTGAAAACATCATGTAC
1 TTTTTGAAAACATCCTACACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAACATCATGCAC
* * *
364801 TGAAGGGCTTACAGATGACCCAAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAA
66 TGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAATCTCCCAAAGGCTTTTTGAAA
* * * *
364866 ACATCCTGCATTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCTCGAAG
131 ACATCATGCAATGTAGATCTTATGGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCTCGAAG
364931 GC
196 GC
*
364933 TTTTTGAAAACATCCTACACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAGAACATCATGCAC
1 TTTTTGAAAACATCCTACACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAACATCATGCAC
364998 TGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAATCTCCCAAAGGCTTTTTGAAA
66 TGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAATCTCCCAAAGGCTTTTTGAAA
* * *
365063 ACATCTTGCACTGTAGATCTTATGGATGACCCGAAGGCTTTGAAAACATC---ATGCAT-T-GAA
131 ACATCATGCAATGTAGATCTTATGGATGACCCGAAGGCTTTGAAAACATCAAAAAGC-TCTCGAA
365123 GGGC
195 -GGC
* * * * * ** **
365127 ---TT--ACAGAT--GAC-CTGAAGGTTTTAAAAATATCAAAAAGCTCTCGAAGGCTTTTTGAAA
1 TTTTTGAAAACATCCTACACTGTAGG-TCT-----TATGGATGA-C-C-CGAAGG--TTTTGAAA
* * *
365184 ACATCATGCACTGTAGGTCTTACAGATGACCCGAAGGTTTTGAAAACATC-AAAATGCTCCCAAA
55 ACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAT-CTCCCAAA
* * * ** *
365248 GGCTTTTTGAAAACATCATGCAATGAATAGCTTACAGATGACTCGAAGGCTTTGAAAACATCAAA
119 GGCTTTTTGAAAACATCATGCAATGTAGATCTTATGGATGACCCGAAGGCTTTGAAAACATCAAA
*
365313 AAGCTCCCGAAGGC
184 AAGCTCTCGAAGGC
* *
365327 TTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTAAAAACATCA
1 TTTTTGAAAACATCCTACACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAACATCA
365387 AAAAGCTCCC
Statistics
Matches: 379, Mismatches: 48, Indels: 54
0.79 0.10 0.11
Matches are distributed among these distances:
186 6 0.02
187 4 0.01
189 4 0.01
191 2 0.01
192 5 0.01
193 4 0.01
194 8 0.02
195 7 0.02
196 5 0.01
197 296 0.78
199 7 0.02
200 7 0.02
201 4 0.01
202 5 0.01
203 2 0.01
205 4 0.01
207 3 0.01
208 6 0.02
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (197 bp):
TTTTTGAAAACATCCTACACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAACATCATGCAC
TGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAATCTCCCAAAGGCTTTTTGAAA
ACATCATGCAATGTAGATCTTATGGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCTCGAAG
GC
Found at i:365181 original size:76 final size:76
Alignment explanation
Indices: 365092--365462 Score: 476
Period size: 76 Copynumber: 4.9 Consensus size: 76
365082 TTATGGATGA
* * *
365092 CCCGAAGGC--TTTGAAAACATCATGCATTGAAGGGCTTACAGATGACCTGAAGGTTTTAAAAAT
1 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTAAAAAC
365155 ATCAAAAAGCT
66 ATCAAAAAGCT
* * * *
365166 CTCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCGAAGGTTTTGAAAAC
1 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTAAAAAC
*
365231 ATCAAAATGCT
66 ATCAAAAAGCT
* * ** * * *
365242 CCCAAAGGCTTTTTGAAAACATCATGCAATGAATAGCTTACAGATGACTCGAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTAAAAAC
365307 ATCAAAAAGCT
66 ATCAAAAAGCT
* * * **
365318 CCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTAAAAAC
1 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTAAAAAC
365383 ATCAAAAAGCT
66 ATCAAAAAGCT
* * * ** * * *
365394 CCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCTAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTAAAAAC
365459 ATCA
66 ATCA
365463 TGCACTGAAG
Statistics
Matches: 262, Mismatches: 33, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
74 8 0.03
76 254 0.97
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (76 bp):
CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTAAAAAC
ATCAAAAAGCT
Found at i:365467 original size:45 final size:45
Alignment explanation
Indices: 365394--365552 Score: 228
Period size: 45 Copynumber: 3.5 Consensus size: 45
365384 TCAAAAAGCT
* * * **
365394 CCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGA
1 CCCGAAGGC--TTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
*
365441 CCCTAAGGCTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGCTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
365486 CCCGAAGGCTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGCTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
* *
365531 CCCGAAGGTTTTGAAAATATCA
1 CCCGAAGGCTTTGAAAACATCA
365553 AAAAGCTCCC
Statistics
Matches: 103, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
45 95 0.92
47 8 0.08
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (45 bp):
CCCGAAGGCTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
Found at i:365510 original size:394 final size:392
Alignment explanation
Indices: 364782--365751 Score: 1261
Period size: 394 Copynumber: 2.5 Consensus size: 392
364772 GACCCGAAGG
* * * * *
364782 TTTTGAAAACATCATGTACTGAAGGGCTTACAGATGACCCAAAGGCTTTGAAAACATCAAAAAGC
1 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGC
* * ** * *
364847 TCCCGAAGGCTTTTTGAAAACATCCTGCATTG--TAGGTCTTATGGATGACCCGAAGGTTTTGAA
66 TCCCGAAGGCTTTTTGAAAACATCATGCAATGAATA-G-CTTACAGATGACTCGAAGGCTTTGAA
* *
364910 AACATCAAAAAGCTCTCGAAGGCTTTTTGAAAACATCCTACACTGTAGGTCTTATGGATGACCCG
129 AACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCG
* * * * ** *
364975 AAGGTTTTGAGAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAA
194 AAGGTTTTAAAAACATCAAGCACCGAAGGGCTTACAGAAAACCCGAA-GCTGTGAAAACATCAAA
* * * * **
365040 AATCTCCCAAAGGCTTTTTGAAAACATCTTGCACTGTAGATCTTATGGATGACCCGAAGGCTTTG
258 AATCACCCAAAGGC-TTTTGAAAACATCATGCACTGAAGAGCTTACAGATGACCCGAAGGCTTTG
* * * *
365105 AAAACATCATGCATTGAAGGGCTTACAGATGACCTGAAGGTTTTAAAAATATCAAAAAGCTCTCG
322 AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTAAAAATATCAAAAAGCTCCCA
365170 AAGGCT
387 AAGGCT
*
365176 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAATGC
1 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGC
*
365241 TCCCAAAGGCTTTTTGAAAACATCATGCAATGAATAGCTTACAGATGACTCGAAGGCTTTGAAAA
66 TCCCGAAGGCTTTTTGAAAACATCATGCAATGAATAGCTTACAGATGACTCGAAGGCTTTGAAAA
365306 CATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAA
131 CATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAA
* *** * ***
365371 GGTTTTAAAAACATCAAAAAGCTCCCGAA-GGCTTTTTGAAAACATCCTGCA-CTGT-AGGTC-T
196 GGTTTTAAAAACATC---AAGC-ACCGAAGGGCTTACAGAAAAC--CC-GAAGCTGTGAAAACAT
* *** * * *
365432 TATGGATGACCCTAAGGC-TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCT
254 CAAAAATCACCCAAAGGCTTTTGAAAACATCATGCACTGAAGAGCTTACAGATGACCCGAAGGCT
*
365496 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAATATCAAAAAGCTC
319 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTAAAAATATCAAAAAGCTC
365561 CCAAAGGCT
384 CCAAAGGCT
* *
365570 TTTTGAAAACATCCTGCACTGTAGGTCTTACAGATGACCCGAAGGTTTTGAAAGCATCAAAAAGC
1 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGC
* ** *
365635 TCCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACTCGAAGGCCTTGAAAA
66 TCCCGAAGGCTTTTTGAAAACATCATGCAATGAATAGCTTACAGATGACTCGAAGGCTTTGAAAA
* * * * *
365700 CATCGAAAAGCTCCCGAAGGCTTTTTGAGAACATCATGCACTGAAGGGCTTA
131 CATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTA
365752 CAGATGTGGG
Statistics
Matches: 506, Mismatches: 61, Indels: 18
0.86 0.10 0.03
Matches are distributed among these distances:
394 466 0.92
395 1 0.00
396 14 0.03
397 14 0.03
398 7 0.01
399 2 0.00
400 2 0.00
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (392 bp):
TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGC
TCCCGAAGGCTTTTTGAAAACATCATGCAATGAATAGCTTACAGATGACTCGAAGGCTTTGAAAA
CATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAA
GGTTTTAAAAACATCAAGCACCGAAGGGCTTACAGAAAACCCGAAGCTGTGAAAACATCAAAAAT
CACCCAAAGGCTTTTGAAAACATCATGCACTGAAGAGCTTACAGATGACCCGAAGGCTTTGAAAA
CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTAAAAATATCAAAAAGCTCCCAAAGG
CT
Found at i:365588 original size:76 final size:76
Alignment explanation
Indices: 365486--365757 Score: 431
Period size: 76 Copynumber: 3.6 Consensus size: 76
365476 TTACAGATGA
*
365486 CCCGAAGGC--TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAAT
1 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAAC
365549 ATCAAAAAGCT
66 ATCAAAAAGCT
* * * * *
365560 CCCAAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTACAGATGACCCGAAGGTTTTGAAAGC
1 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAAC
365625 ATCAAAAAGCT
66 ATCAAAAAGCT
* **
365636 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACTCGAAGGCCTTGAAAAC
1 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAAC
*
365701 ATCGAAAAGCT
66 ATCAAAAAGCT
*
365712 CCCGAAGGCTTTTTGAGAACATCATGCACTGAAGGGCTTACAGATG
1 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATG
365758 TGGGAAATAG
Statistics
Matches: 180, Mismatches: 16, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
74 8 0.04
76 172 0.96
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.23
Consensus pattern (76 bp):
CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAAC
ATCAAAAAGCT
Found at i:365662 original size:470 final size:468
Alignment explanation
Indices: 364782--365757 Score: 1368
Period size: 470 Copynumber: 2.1 Consensus size: 468
364772 GACCCGAAGG
*
364782 TTTTGAAAACATCATGTACTGAAGGGCTTACAGATGACCCAAAGGCTTTGAAAACATCAAAAAGC
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCAAAGGCTTTGAAAACATCAAAAAGC
* *
364847 TCCCGAAGGCTTTTTGAAAACATCCTGCATTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAA
66 TCCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTAAAAA
*
364912 CATCAAAAAGCTCTCGAAGGCTTTTTGAAAACATCCTACACTGTAGGTCTTATGGATGACCCGAA
131 CATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCCTACACTGTAGGTCTTATGGATGACCCGAA
* *
364977 GGTTTTGAGAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAA
196 GGCTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAA
*** * * *** ** * *
365042 TCTCCCAAAGGCTTTTTGAAAACATCTTGCACTGTAGATCTTATGGATGACCCGAAGGCTTTGAA
261 TCT-CCAAAGGCTTACAGAAAACA-CTCGAACTGTAGAAAATATAAAAGACCCAAAGGCTTTGAA
* * * *
365107 AACATCATGCATTGAAGGGCTTACAGATGACCTGAAGGTTTTAAAAATATCAAAAAGCTCTCGAA
324 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTAAAAACATCAAAAAGCTCCCGAA
* * **
365172 GGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCGAAGGTTTTGAAAACATC-AA
389 GGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCCTTGAAAACATCGAA
365236 AATGCTCCCAAAGGCT
454 AA-GCTCCCAAAGGCT
* ** * *
365252 TTTTGAAAACATCATGCAATGAATAGCTTACAGATGACTCGAAGGCTTTGAAAACATCAAAAAGC
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCAAAGGCTTTGAAAACATCAAAAAGC
365317 TCCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTAAAAA
66 TCCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTAAAAA
* *
365382 CATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCTAA
131 CATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCCTACACTGTAGGTCTTATGGATGACCCGAA
***
365447 GGCTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCATGCA
196 GGCTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAA
* * ** * * * *
365512 -CT-GAAGGGCTTACAGATGAC-C-CGAAGGTTTTGAAAATATCAAAAAGCTCCCAAAGGCTTTT
261 TCTCCAAAGGCTTACAGAAAACACTCGAA-CTGTAGAAAATAT--AAAAG-ACCCAAAGGC--TT
* * * * *
365573 TGAAAACATCCTGCACTGTAGGTCTTACAGATGACCCGAAGGTTTTGAAAGCATCAAAAAGCTCC
320 TGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTAAAAACATCAAAAAGCTCC
*
365638 CGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACTCGAAGGCCTTGAAAACAT
385 CGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCCTTGAAAACAT
*
365703 CGAAAAGCTCCCGAAGGCT
450 CGAAAAGCTCCCAAAGGCT
*
365722 TTTTGAGAACATCATGCACTGAAGGGCTTACAGATG
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATG
365758 TGGGAAATAG
Statistics
Matches: 444, Mismatches: 55, Indels: 14
0.87 0.11 0.03
Matches are distributed among these distances:
464 2 0.00
465 8 0.02
467 13 0.03
468 8 0.02
469 2 0.00
470 407 0.92
471 4 0.01
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (468 bp):
TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCAAAGGCTTTGAAAACATCAAAAAGC
TCCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTAAAAA
CATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCCTACACTGTAGGTCTTATGGATGACCCGAA
GGCTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAA
TCTCCAAAGGCTTACAGAAAACACTCGAACTGTAGAAAATATAAAAGACCCAAAGGCTTTGAAAA
CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTAAAAACATCAAAAAGCTCCCGAAGG
CTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCCTTGAAAACATCGAAAA
GCTCCCAAAGGCT
Found at i:365699 original size:242 final size:242
Alignment explanation
Indices: 365253--365703 Score: 731
Period size: 242 Copynumber: 1.9 Consensus size: 242
365243 CCAAAGGCTT
* *
365253 TTTGAAAACATCATGCAATGAATAGCTTACAGATGACTCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGAAAACATCATGCAATGAAGAGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
* **
365318 CCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTAAAAAC
66 CCCAAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTACAGATGACCCGAAGGTTTTAAAAAC
* * * ** *
365383 ATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCTAAG
131 ATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAG
*
365448 GCTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGC
196 GCCTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGC
* * * *
365495 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAATATCAAAAAGCT
1 TTTGAAAACATCATGCAATGAAGAGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
* *
365560 CCCAAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTACAGATGACCCGAAGGTTTTGAAAGC
66 CCCAAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTACAGATGACCCGAAGGTTTTAAAAAC
*
365625 ATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACTCGAAG
131 ATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAG
365690 GCCTTGAAAACATC
196 GCCTTGAAAACATC
365704 GAAAAGCTCC
Statistics
Matches: 190, Mismatches: 19, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
242 190 1.00
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (242 bp):
TTTGAAAACATCATGCAATGAAGAGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
CCCAAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTACAGATGACCCGAAGGTTTTAAAAAC
ATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAG
GCCTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGC
Found at i:365702 original size:318 final size:318
Alignment explanation
Indices: 365168--365751 Score: 911
Period size: 318 Copynumber: 1.8 Consensus size: 318
365158 AAAAAGCTCT
* *
365168 CGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCGAAGGTTTTGAAAACAT
1 CGAAGGC-TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACAT
* *
365233 CAAAATGCTCCCAAAGGCTTTTTGAAAACATCATGCAATGAATAGCTTACAGATGACTCGAAGGC
65 CAAAAAGCTCCCAAAGGCTTTTTGAAAACATCATGCAATG-ATAGCTTACAGATGACCCGAAGGC
* * * **
365298 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGAT
129 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGAT
** * *
365363 GACCCGAAGGTTTTAAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCCTGCACTGTAG
194 GACCCGAAGGCCTTAAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGAAG
*
365428 GTCTTATGGATGACCCTAAGGCTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACC
259 GGCTTATGGATGACCCTAAGGCTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACC
*
365488 CGAAGGC-TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAATATC
1 CGAAGGCTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATC
* * *
365552 AAAAAGCTCCCAAAGGCTTTTTGAAAACATCCTGCACTG-TAGGTCTTACAGATGACCCGAAGGT
66 AAAAAGCTCCCAAAGGCTTTTTGAAAACATCATGCAATGATA-G-CTTACAGATGACCCGAAGGC
*
365616 TTTGAAAGCATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGAT
129 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGAT
* * * *
365681 GACTCGAAGGCCTTGAAAACATCGAAAAGCTCCCGAAGGCTTTTTGAGAACATCATGCACTGAAG
194 GACCCGAAGGCCTTAAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGAAG
365746 GGCTTA
259 GGCTTA
365752 CAGATGTGGG
Statistics
Matches: 239, Mismatches: 23, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
316 2 0.01
317 1 0.00
318 229 0.96
320 7 0.03
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (318 bp):
CGAAGGCTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATC
AAAAAGCTCCCAAAGGCTTTTTGAAAACATCATGCAATGATAGCTTACAGATGACCCGAAGGCTT
TGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
CCCGAAGGCCTTAAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGG
CTTATGGATGACCCTAAGGCTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACC
Found at i:366923 original size:54 final size:54
Alignment explanation
Indices: 366840--367001 Score: 261
Period size: 54 Copynumber: 3.0 Consensus size: 54
366830 TATAATCACT
* * * *
366840 GGTTCGTAAAACATTTGACAACTCGTTCATCGTTTCCTGTGGCTTCTGTCCAGA
1 GGTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCCCAGA
366894 GGTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCCCAGA
1 GGTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCCCAGA
* * *
366948 TGTTTGTAAAACATTTGACAATACATTCATCCTTTCCTGTGGCTTCTGCCCAGA
1 GGTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCCCAGA
367002 TTTCTCAATC
Statistics
Matches: 101, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 101 1.00
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Consensus pattern (54 bp):
GGTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCCCAGA
Found at i:376818 original size:16 final size:18
Alignment explanation
Indices: 376791--376837 Score: 59
Period size: 16 Copynumber: 2.9 Consensus size: 18
376781 ATTCAAAATA
376791 CTTTAGGA-ATTATTTAT
1 CTTTAGGATATTATTTAT
376808 -TTTA-GATATTA-TTAT
1 CTTTAGGATATTATTTAT
376823 CTTTAGGAT-TTATTT
1 CTTTAGGATATTATTT
376838 TGGATTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
15 6 0.23
16 15 0.58
17 5 0.19
ACGTcount: A:0.28, C:0.04, G:0.11, T:0.57
Consensus pattern (18 bp):
CTTTAGGATATTATTTAT
Found at i:378717 original size:14 final size:14
Alignment explanation
Indices: 378691--378728 Score: 67
Period size: 14 Copynumber: 2.6 Consensus size: 14
378681 TTATAACATG
378691 AATTATATTTTTTAA
1 AATTAT-TTTTTTAA
378706 AATTATTTTTTTAA
1 AATTATTTTTTTAA
378720 AATTATTTT
1 AATTATTTT
378729 ATGATGTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 17 0.74
15 6 0.26
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
AATTATTTTTTTAA
Found at i:378852 original size:20 final size:20
Alignment explanation
Indices: 378814--378852 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
378804 CAAATACAGT
*
378814 AAATAATATTATTTATTAAC
1 AAATAATATAATTTATTAAC
378834 AAATAATAATAATTT-TTAA
1 AAATAAT-ATAATTTATTAA
378853 ATATTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (20 bp):
AAATAATATAATTTATTAAC
Found at i:378880 original size:13 final size:13
Alignment explanation
Indices: 378860--378906 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
378850 TAAATATTAA
378860 AATA-TATTATTT
1 AATATTATTATTT
*
378872 AATATTATTATGT
1 AATATTATTATTT
* *
378885 CATATTATTATTAA
1 AATATTATTATT-T
378899 AATATTAT
1 AATATTAT
378907 ATCTACAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
12 4 0.14
13 17 0.61
14 7 0.25
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (13 bp):
AATATTATTATTT
Found at i:378958 original size:21 final size:21
Alignment explanation
Indices: 378934--378999 Score: 50
Period size: 23 Copynumber: 3.2 Consensus size: 21
378924 TAAAAATATG
378934 ATTAAAATAAAATTATTATAA
1 ATTAAAATAAAATTATTATAA
378955 ATTATAGTAAT-AAATTATTA-AA
1 ATTA-A--AATAAAATTATTATAA
* * *
378977 A-TAAGATAATA-TATTATTA
1 ATTAAAATAAAATTATTATAA
378996 ATTA
1 ATTA
379000 TATTAATTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 13
0.69 0.06 0.25
Matches are distributed among these distances:
18 7 0.19
19 4 0.11
20 3 0.08
21 6 0.17
22 4 0.11
23 9 0.25
24 3 0.08
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (21 bp):
ATTAAAATAAAATTATTATAA
Found at i:378979 original size:37 final size:37
Alignment explanation
Indices: 378934--379034 Score: 96
Period size: 41 Copynumber: 2.6 Consensus size: 37
378924 TAAAAATATG
378934 ATTAAAATAAAATTATTATAAATTATAGTAATAAATT
1 ATTAAAATAAAATTATTATAAATTATAGTAATAAATT
* * ***
378971 ATTAAAATAAGATAATATATTATTAATTATATTAATTTTTT
1 ATTAAAAT-A-A-AAT-TATTATAAATTATAGTAATAAATT
* *
379012 ATTAAAATAATATTGTTA-AAATT
1 ATTAAAATAAAATTATTATAAATT
379035 TGAAAATTAT
Statistics
Matches: 52, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
36 4 0.08
37 12 0.23
38 3 0.06
39 2 0.04
40 4 0.08
41 27 0.52
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (37 bp):
ATTAAAATAAAATTATTATAAATTATAGTAATAAATT
Found at i:379219 original size:9 final size:8
Alignment explanation
Indices: 379176--379241 Score: 62
Period size: 9 Copynumber: 7.9 Consensus size: 8
379166 AAAATAAAAG
379176 TATAATAT
1 TATAATAT
379184 TAT-ATAT
1 TATAATAT
*
379191 TATAATAA
1 TATAATAT
379199 TATAATTAT
1 TATAA-TAT
*
379208 AATAATAT
1 TATAATAT
379216 TAATAATAT
1 T-ATAATAT
*
379225 TATTAAAAT
1 TA-TAATAT
379234 TATCAATA
1 TAT-AATA
379242 AATATAATTT
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
7 7 0.15
8 16 0.34
9 24 0.51
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (8 bp):
TATAATAT
Found at i:379303 original size:40 final size:42
Alignment explanation
Indices: 379209--379292 Score: 102
Period size: 42 Copynumber: 2.1 Consensus size: 42
379199 TATAATTATA
* * *
379209 ATAATA-TTAATAATATTATTAAAATTATCAATAAATATAAT
1 ATAATACTTAATATTTTTATTAAAATGATCAATAAATATAAT
* *
379250 TTAATACTTAATATTTTTATTAAAATGAT-ACTAAA-ATAAT
1 ATAATACTTAATATTTTTATTAAAATGATCAATAAATATAAT
379290 ATA
1 ATA
379293 GTATTAAATA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
40 7 0.19
41 10 0.28
42 19 0.53
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (42 bp):
ATAATACTTAATATTTTTATTAAAATGATCAATAAATATAAT
Found at i:379314 original size:24 final size:27
Alignment explanation
Indices: 379267--379316 Score: 70
Period size: 24 Copynumber: 2.0 Consensus size: 27
379257 TTAATATTTT
*
379267 TATTAAAATGATACTAAAATAATATAG
1 TATTAAAATGATACTAAAACAATATAG
379294 TATT-AAAT-ATA-TAAAACAATATA
1 TATTAAAATGATACTAAAACAATATA
379317 TTTTGAGTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 11 0.50
25 3 0.14
26 4 0.18
27 4 0.18
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.34
Consensus pattern (27 bp):
TATTAAAATGATACTAAAACAATATAG
Found at i:387343 original size:175 final size:178
Alignment explanation
Indices: 386848--387788 Score: 1109
Period size: 177 Copynumber: 5.4 Consensus size: 178
386838 AAAAATGTAT
* * * * * *
386848 CGATCCATATCAATATAACAGGTAAAAATATGATAAAACCGGTGTC-ATTATGATAAAACCGGTA
1 CGAT-CATAGCAATATAACAGGTAATAATATGACAAAACAGGTCTCGA-AATGATAAAACCGGTA
** *
386912 AACCGCTACCTGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTTTTGTAATTTA
64 AAAAGCTA-CGGATATATTGAAAGTGTCGATAAATTAATA-AAGTATCGACACTTTTGTAATTTA
* * **
386977 AAAGAGAAGAAGATATAGCGCCTATAAAGTGTATATAC-TT-T-CAAAGTAT-
127 AAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATACAAA-TATA
* * * *
387026 CGCATTC-TAGCAATAT-ACAGGTAATAATATGACAAAACCGGTGTC-ATTATGATAAAAACCGA
1 CG-A-TCATAGCAATATAACAGGTAATAATATGACAAAACAGGTCTCGA-AATGAT-AAAACCGG
** *
387088 TAAACCGCTACCGGATATATTGAAAGTGTCGATAAA-TAATATAAGTATCAACAC-TTTGTAATT
62 TAAAAAGCTA-CGGATATATTGAAAGTGTCGATAAATTAATA-AAGTATCGACACTTTTGTAATT
*
387151 T-AAAGAGAATAAGTTATAGCGCCT-AAAAGTGTCGATACTTTATACAAATATA
125 TAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATACAAATATA
* * *
387203 CGATCCATAGCAA-AT-ATAGGTAAT-ATATGACAAAACAAGTCTTGAAATGATAAAACCGGTAA
1 CGAT-CATAGCAATATAACAGGTAATAATATGACAAAACAGGTCTCGAAATGATAAAACCGGTAA
*
387265 AAAGTTATCGGATATATTGAAAGTGTCGAT-AATTAATAAAGTATCGACACTTTTG-ATATTTAA
65 AAAGCTA-CGGATATATTGAAAGTGTCGATAAATTAATAAAGTATCGACACTTTTGTA-ATTTAA
* * *
387328 AAGAGAAGAAGTTATAGCACCTAAAAAGTGCCGATACTTTATACAAATGTA
128 AAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATACAAATATA
* * *
387379 TCGATCCTATCAATATAACAGGTAATAATATGACAAAACAGGTCTCGAAATGATAAAATCGGTAA
1 -CGATCATAGCAATATAACAGGTAATAATATGACAAAACAGGTCTCGAAATGATAAAACCGGTAA
* *
387444 AAAGCTACGGATATATTGAAAGTGTCGATAAATTAATATATTATCGACACTTTT-T-ATTTAAAA
65 AAAGCTACGGATATATTGAAAGTGTCGATAAATTAATAAAGTATCGACACTTTTGTAATTTAAAA
*
387507 GAGAAGAAGTTATAGCGCCTAAAAAGTG-CGATATTTTATACAAATATA
130 GAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATACAAATATA
387555 TCGAT-ATAGCAATATAACAGGTAATAATATGACAAAACAGGTCTCG-AATGAT-AAACCGGT-A
1 -CGATCATAGCAATATAACAGGTAATAATATGACAAAACAGGTCTCGAAATGATAAAACCGGTAA
* *
387616 AAAGCTACGGA-ATATTGAAAGTGTCGATAAATTAATATAGTATCGACACTTTCGTAATTTAAAA
65 AAAGCTACGGATATATTGAAAGTGTCGATAAATTAATAAAGTATCGACACTTTTGTAATTTAAAA
* * *
387680 GAGAATACA--TATAGCGCCTAAAAAGTGTCGATACTTTAT--GAATGTA
130 GAGAAGA-AGTTATAGCGCCTAAAAAGTGTCGATACTTTATACAAATATA
* * * *
387726 CGATCATAACAATATAATAGGTAA-AATATGACAAAACTGGTATCGAAAT-A-ACAAACCGGTAA
1 CGATCATAGCAATATAACAGGTAATAATATGACAAAACAGGTCTCGAAATGATA-AAACCGGTAA
387788 A
65 A
387789 GCGCTATCGG
Statistics
Matches: 681, Mismatches: 52, Indels: 66
0.85 0.07 0.08
Matches are distributed among these distances:
170 24 0.04
171 73 0.11
172 33 0.05
173 45 0.07
174 67 0.10
175 104 0.15
176 82 0.12
177 105 0.15
178 82 0.12
179 65 0.10
180 1 0.00
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (178 bp):
CGATCATAGCAATATAACAGGTAATAATATGACAAAACAGGTCTCGAAATGATAAAACCGGTAAA
AAGCTACGGATATATTGAAAGTGTCGATAAATTAATAAAGTATCGACACTTTTGTAATTTAAAAG
AGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATACAAATATA
Found at i:387547 original size:352 final size:353
Alignment explanation
Indices: 386840--387774 Score: 1144
Period size: 352 Copynumber: 2.7 Consensus size: 353
386830 TACAAATGAA
* * * * ** *
386840 AAATGTATCGATCCATATCAATATAACAGGTAAAAATATGATAAAACCGGTGTC-ATTATGATAA
1 AAATATATCGAT--ATAGCAATATAACAGGTAATAATATGACAAAACAAGTCTCGA--ATGATAA
** *
386904 AACCGGTAAACCGCTACCTGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTTTT
62 AACCGGTAAAAAGCTA-CGGATATATTGAAAGTGTCGATAAATTAATA-AAGTATCGACACTTTT
* **
386969 GTAATTTAAAAGAGAAGAAGATATAGCGCCTATAAAGTGTATATAC-TT-TCAAA-GTATCGCAT
125 GTAATTTAAAAGAGAAGAAG-TATAGCGCCTAAAAAGTGTCGATACTTTATCAAATGTATCG-AT
* * * * * **
387031 TCTAGCAATAT-ACAGGTAATAATATGACAAAACCGGTGTC-ATTATGATAAAAACCGATAAACC
188 CCTAACAATATAACAGGTAATAATATGACAAAACAGGTATCGA-AATGATAAAAACCGATAAAAA
387094 GCTACCGGATATATTGAAAGTGTCGATAAATAATATAAGTATCAACACTTTGTAATTTAAAGAGA
252 GCTACCGGATATATTGAAAGTGTCGATAAATAATATAAGTATCAACACTTTGTAATTTAAAGAGA
*
387159 ATAAGTTATAGCGCCTAAAAGTGTCGATACTTTATAC
317 AGAAGTTATAGCGCCTAAAAGTGTCGATACTTTATAC
* *
387196 AAATATA-CGATCCATAGCAA-AT-ATAGGTAAT-ATATGACAAAACAAGTCTTGAAATGATAAA
1 AAATATATCGAT--ATAGCAATATAACAGGTAATAATATGACAAAACAAGTCTCG-AATGATAAA
*
387257 ACCGGTAAAAAGTTATCGGATATATTGAAAGTGTCGAT-AATTAATAAAGTATCGACACTTTTG-
63 ACCGGTAAAAAGCTA-CGGATATATTGAAAGTGTCGATAAATTAATAAAGTATCGACACTTTTGT
* *
387320 ATATTTAAAAGAGAAGAAGTTATAGCACCTAAAAAGTGCCGATACTTTATACAAATGTATCGATC
127 A-ATTTAAAAGAGAAGAAG-TATAGCGCCTAAAAAGTGTCGATACTTTAT-CAAATGTATCGATC
* * * *
387385 CTATCAATATAACAGGTAATAATATGACAAAACAGGTCTCGAAATGAT-AAAATCGGTAAAAAGC
189 CTAACAATATAACAGGTAATAATATGACAAAACAGGTATCGAAATGATAAAAACCGATAAAAAGC
* * *
387449 TA-CGGATATATTGAAAGTGTCGATAAATTAATAT-ATTATCGACACTTT-TTATTTAAAAGAGA
254 TACCGGATATATTGAAAGTGTCGATAAA-TAATATAAGTATCAACACTTTGTAATTT-AAAGAGA
*
387511 AGAAGTTATAGCGCCTAAAAAGTG-CGATATTTTATAC
317 AGAAGTTATAGCGCCT-AAAAGTGTCGATACTTTATAC
*
387548 AAATATATCGATATAGCAATATAACAGGTAATAATATGACAAAACAGGTCTCGAATGAT-AAACC
1 AAATATATCGATATAGCAATATAACAGGTAATAATATGACAAAACAAGTCTCGAATGATAAAACC
* *
387612 GGT-AAAAGCTACGGA-ATATTGAAAGTGTCGATAAATTAATATAGTATCGACACTTTCGTAATT
66 GGTAAAAAGCTACGGATATATTGAAAGTGTCGATAAATTAATAAAGTATCGACACTTTTGTAATT
* * *
387675 TAAAAGAGAATACA-TATAGCGCCTAAAAAGTGTCGATACTTTAT-GAATGTA-CGATCATAACA
131 TAAAAGAGAAGA-AGTATAGCGCCTAAAAAGTGTCGATACTTTATCAAATGTATCGATCCTAACA
* *
387737 ATATAATAGGTAA-AATATGACAAAACTGGTATCGAAAT
195 ATATAACAGGTAATAATATGACAAAACAGGTATCGAAAT
387775 AACAAACCGG
Statistics
Matches: 511, Mismatches: 49, Indels: 49
0.84 0.08 0.08
Matches are distributed among these distances:
345 23 0.05
346 21 0.04
347 6 0.01
349 46 0.09
350 95 0.19
351 31 0.06
352 144 0.28
353 67 0.13
354 59 0.12
355 13 0.03
356 6 0.01
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (353 bp):
AAATATATCGATATAGCAATATAACAGGTAATAATATGACAAAACAAGTCTCGAATGATAAAACC
GGTAAAAAGCTACGGATATATTGAAAGTGTCGATAAATTAATAAAGTATCGACACTTTTGTAATT
TAAAAGAGAAGAAGTATAGCGCCTAAAAAGTGTCGATACTTTATCAAATGTATCGATCCTAACAA
TATAACAGGTAATAATATGACAAAACAGGTATCGAAATGATAAAAACCGATAAAAAGCTACCGGA
TATATTGAAAGTGTCGATAAATAATATAAGTATCAACACTTTGTAATTTAAAGAGAAGAAGTTAT
AGCGCCTAAAAGTGTCGATACTTTATAC
Found at i:390453 original size:23 final size:23
Alignment explanation
Indices: 390427--390478 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
390417 TCCGGTTAAA
** *
390427 TACCTATTTTATTATATTAGCGC
1 TACCTATTACATTATATAAGCGC
390450 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAGCGC
*
390473 TGCCTA
1 TACCTA
390479 ATATGTTATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.40
Consensus pattern (23 bp):
TACCTATTACATTATATAAGCGC
Done.