Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008322.1 Hibiscus syriacus cultivar Beakdansim tig00111025_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: 456513
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:233174 original size:23 final size:21
Alignment explanation
Indices: 233124--233175 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
233114 CAAACGACCG
* *
233124 AAAAATGTGTCAAAAGGTAGA
1 AAAAACGTGTCAAAAGGCAGA
233145 AAAAACGTGTCATAAAGGCAGA
1 AAAAACGTGTCA-AAAGGCAGA
*
233167 GGAAAACGT
1 -AAAAACGT
233176 TTAATACATG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 11 0.42
22 8 0.31
23 7 0.27
ACGTcount: A:0.50, C:0.10, G:0.25, T:0.15
Consensus pattern (21 bp):
AAAAACGTGTCAAAAGGCAGA
Found at i:237268 original size:22 final size:23
Alignment explanation
Indices: 237235--237278 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
237225 ATGGATGCAC
237235 TGCATGGTGCATCGATGCACTAG
1 TGCATGGTGCATCGATGCACTAG
*
237258 TGCA-GGTGCATGGATGCACTA
1 TGCATGGTGCATCGATGCACTA
237279 CAGGGGTGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.23, C:0.20, G:0.32, T:0.25
Consensus pattern (23 bp):
TGCATGGTGCATCGATGCACTAG
Found at i:237399 original size:29 final size:29
Alignment explanation
Indices: 237367--237429 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 29
237357 GAAACCTTTT
237367 AAAACTTTGAATAAATTCAATT-AAGTCCAA
1 AAAACTTTG--TAAATTCAATTCAAGTCCAA
*
237397 AAATATTTTGTAAATTCAATTCAAGTCCAA
1 AAA-ACTTTGTAAATTCAATTCAAGTCCAA
237427 AAA
1 AAA
237430 CTATTTTGCC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 11 0.37
30 14 0.47
31 5 0.17
ACGTcount: A:0.49, C:0.13, G:0.06, T:0.32
Consensus pattern (29 bp):
AAAACTTTGTAAATTCAATTCAAGTCCAA
Found at i:237425 original size:30 final size:30
Alignment explanation
Indices: 237378--237437 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
237368 AAACTTTGAA
237378 TAAATTCAATTAAGTCCAAAAA-TATTTTG
1 TAAATTCAATTAAGTCCAAAAACTATTTTG
237407 TAAATTCAATTCAAGTCCAAAAACTATTTTG
1 TAAATTCAATT-AAGTCCAAAAACTATTTTG
237438 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACTATTTTG
Found at i:237841 original size:21 final size:21
Alignment explanation
Indices: 237818--237964 Score: 63
Period size: 21 Copynumber: 7.1 Consensus size: 21
237808 GAATCGCGTT
* *
237818 GCGATTCTTGAAAATCGCAAT
1 GCGATTCTTCAAAATCGCAAC
** * * **
237839 GCGATAGTACAAATTCGCATT
1 GCGATTCTTCAAAATCGCAAC
*
237860 GCGATT-TTCCAGAATCGCAAC
1 GCGATTCTT-CAAAATCGCAAC
* * *
237881 GCGAAT-ATGAAAATCGCAAC
1 GCGATTCTTCAAAATCGCAAC
*
237901 GCGA-ACTT-ATAAATCGCAAC
1 GCGATTCTTCA-AAATCGCAAC
**
237921 GCGATTCTT-ACTATCGCAAC
1 GCGATTCTTCAAAATCGCAAC
* * *
237941 GAGTATCCGT-AAAATCGCAAC
1 GCG-ATTCTTCAAAATCGCAAC
237962 GCG
1 GCG
237965 TATCCGTAAA
Statistics
Matches: 94, Mismatches: 27, Indels: 10
0.72 0.21 0.08
Matches are distributed among these distances:
19 1 0.01
20 40 0.43
21 53 0.56
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (21 bp):
GCGATTCTTCAAAATCGCAAC
Found at i:237897 original size:20 final size:20
Alignment explanation
Indices: 237872--237924 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 20
237862 GATTTTCCAG
237872 AATCGCAACGCGAA--TATGAA
1 AATCGCAACGCGAACTTAT--A
237892 AATCGCAACGCGAACTTATA
1 AATCGCAACGCGAACTTATA
237912 AATCGCAACGCGA
1 AATCGCAACGCGA
237925 TTCTTACTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 28 0.90
22 3 0.10
ACGTcount: A:0.42, C:0.25, G:0.19, T:0.15
Consensus pattern (20 bp):
AATCGCAACGCGAACTTATA
Found at i:237964 original size:41 final size:41
Alignment explanation
Indices: 237872--238128 Score: 322
Period size: 41 Copynumber: 6.3 Consensus size: 41
237862 GATTTTCCAG
* ** * * *
237872 AATCGCAACGCGAATATGAAAATCGCAACG-CGA-ACTTATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTA-A
* * * ** *
237912 AATCGCAACGCG-ATTCTTACTATCGCAACGAGTATCCGTAA
1 AATCGCAACGCGTATCCGTA-AATCGCAACGACAATACGTAA
*
237953 AATCGCAACGCGTATCCGTAAATCGCAATGACAATACGTAA
1 AATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTAA
*
237994 AATCACAACGCGTATCCGTAAATCGCAACGACAATACGTAA
1 AATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTAA
* *
238035 AATCGCAACGTGTATCCGTAAATCGTAACGACAATACGTAA
1 AATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTAA
238076 AATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTAA
1 AATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTAA
*
238117 AATCACAACGCG
1 AATCGCAACGCG
238129 ATTTTTAAAG
Statistics
Matches: 189, Mismatches: 24, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
39 3 0.02
40 21 0.11
41 157 0.83
42 8 0.04
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (41 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTAA
Found at i:238694 original size:21 final size:21
Alignment explanation
Indices: 238668--238723 Score: 89
Period size: 19 Copynumber: 2.8 Consensus size: 21
238658 TTTGCAGAAG
238668 AATCGCAACGAGAGAAATGAA
1 AATCGCAACGAGAGAAATGAA
*
238689 AATCGCAAC--GCGAAATGAA
1 AATCGCAACGAGAGAAATGAA
238708 AATCGCAACGAGAGAA
1 AATCGCAACGAGAGAA
238724 TCGCAACGCG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 18 0.58
21 13 0.42
ACGTcount: A:0.50, C:0.18, G:0.23, T:0.09
Consensus pattern (21 bp):
AATCGCAACGAGAGAAATGAA
Found at i:238784 original size:14 final size:14
Alignment explanation
Indices: 238765--238821 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
238755 TGTCATTTCG
238765 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
238779 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
*
238798 CGTTGCGATTCTTT
1 CGTTGCGATTCTCT
238812 CGTTGCGATT
1 CGTTGCGATT
238822 TTCATTTCCA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.23, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:238794 original size:33 final size:33
Alignment explanation
Indices: 238748--238869 Score: 154
Period size: 33 Copynumber: 3.5 Consensus size: 33
238738 CAAAATCGCA
*
238748 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
238781 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
238814 TTGCGATTTTCATTTCCACGTTGCGATAGTCATTCTCTCG
1 TTGCGATTTTCATTT-CGCGTTGC----G--ATTCTCTCG
238854 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
238870 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
33 46 0.59
34 7 0.09
38 1 0.01
39 1 0.01
40 23 0.29
ACGTcount: A:0.11, C:0.23, G:0.20, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:238837 original size:20 final size:19
Alignment explanation
Indices: 238779--238869 Score: 93
Period size: 20 Copynumber: 4.9 Consensus size: 19
238769 GCGATTCTCT
*
238779 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCC
238798 CGTTGCGA--TTC-TTT--
1 CGTTGCGATTTTCATTTCC
238812 CGTTGCGATTTTCATTTCC
1 CGTTGCGATTTTCATTTCC
** *
238831 ACGTTGCGATAGTCATTCTCT
1 -CGTTGCGATTTTCATT-TCC
238852 CGTTGCGATTTTCATTTC
1 CGTTGCGATTTTCATTTC
238870 AACCAAAAGA
Statistics
Matches: 60, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
14 8 0.13
16 6 0.10
17 6 0.10
19 10 0.17
20 28 0.47
21 2 0.03
ACGTcount: A:0.12, C:0.23, G:0.19, T:0.46
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCC
Found at i:240764 original size:93 final size:94
Alignment explanation
Indices: 240551--240774 Score: 353
Period size: 94 Copynumber: 2.4 Consensus size: 94
240541 TAGATTGCTT
* * *
240551 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTCTTTAACACTATGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTATGAAGATAGT
* *
240616 ATTTGTCTTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTCTTCTGTTTTGTCTTTTGGTTAA
*
240645 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAA-ATAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTATGAAGATAGT
240709 ATTTGTC-TCTGTTTTGTCTTTTGGTTAAA
66 ATTTGTCTTCTGTTTTGTCTTTTGGTT-AA
* *
240738 AGTAAATTTGTTCGGTTGCTGCCAATTATGCTAAACT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACT
240775 AATACCCTGA
Statistics
Matches: 121, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
92 18 0.15
93 47 0.39
94 56 0.46
ACGTcount: A:0.24, C:0.14, G:0.17, T:0.45
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTATGAAGATAGT
ATTTGTCTTCTGTTTTGTCTTTTGGTTAA
Found at i:240912 original size:19 final size:19
Alignment explanation
Indices: 240872--240980 Score: 83
Period size: 19 Copynumber: 5.3 Consensus size: 19
240862 TAGTTTACTT
* *
240872 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TCAAAA
*
240892 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATCAAAA
*
240911 TCGCAACGAGAGAATCGCAACGAGAAA
1 TCGCAACGCGA-AAT-----C-A-AAA
*
240938 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATCAAAA
*
240957 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATCAAAA
240976 TCGCA
1 TCGCA
240981 TTGCGATTTT
Statistics
Matches: 75, Mismatches: 6, Indels: 17
0.77 0.06 0.17
Matches are distributed among these distances:
19 42 0.56
20 16 0.21
21 1 0.01
26 3 0.04
27 13 0.17
ACGTcount: A:0.46, C:0.27, G:0.18, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAATCAAAA
Found at i:240941 original size:13 final size:13
Alignment explanation
Indices: 240908--240950 Score: 68
Period size: 13 Copynumber: 3.2 Consensus size: 13
240898 CGCGAAATGA
240908 AAATCGCAACGAG
1 AAATCGCAACGAG
240921 AGAATCGCAACGAG
1 A-AATCGCAACGAG
*
240935 AAATCGCAACGCG
1 AAATCGCAACGAG
240948 AAA
1 AAA
240951 CCAAAATCGC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
13 15 0.54
14 13 0.46
ACGTcount: A:0.47, C:0.23, G:0.23, T:0.07
Consensus pattern (13 bp):
AAATCGCAACGAG
Found at i:240986 original size:19 final size:19
Alignment explanation
Indices: 240935--240980 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
240925 TCGCAACGAG
240935 AAATCGCAACGCGAAACCA
1 AAATCGCAACGCGAAACCA
240954 AAATCGCAACGCGAAACCA
1 AAATCGCAACGCGAAACCA
240973 AAATCGCA
1 AAATCGCA
240981 TTGCGATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.48, C:0.30, G:0.15, T:0.07
Consensus pattern (19 bp):
AAATCGCAACGCGAAACCA
Found at i:240998 original size:19 final size:19
Alignment explanation
Indices: 240976--241107 Score: 116
Period size: 19 Copynumber: 7.8 Consensus size: 19
240966 GAAACCAAAA
240976 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
240995 TCGCATTGCGA--TTC---
1 TCGCATTGCGATTTTCATT
*
241009 TCTCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
241028 TCGCATTGCGA--TTC-TG
1 TCGCATTGCGATTTTCATT
241044 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
241061 TCGCGTTGCGA-TTTC---
1 TCGCATTGCGATTTTCATT
241076 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
241093 TCGCGTTGCGATTTT
1 TCGCATTGCGATTTT
241108 AAGTTTCGTG
Statistics
Matches: 93, Mismatches: 4, Indels: 32
0.72 0.03 0.25
Matches are distributed among these distances:
13 6 0.06
14 20 0.22
15 3 0.03
16 10 0.11
17 13 0.14
18 4 0.04
19 37 0.40
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:241106 original size:13 final size:13
Alignment explanation
Indices: 241058--241087 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
241048 TGCGATTTTC
241058 ATTTCGCGTTGCG
1 ATTTCGCGTTGCG
*
241071 ATTTCTCGTTGCG
1 ATTTCGCGTTGCG
241084 ATTT
1 ATTT
241088 TCATTTCGCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47
Consensus pattern (13 bp):
ATTTCGCGTTGCG
Found at i:241106 original size:32 final size:33
Alignment explanation
Indices: 240981--241105 Score: 207
Period size: 33 Copynumber: 3.8 Consensus size: 33
240971 CAAAATCGCA
*
240981 TTGCGATTTTCATTTCGCATTGCGATTCTCTCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
241014 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
241047 TTGCGATTTTCATTTCGCGTTGCGATT-TCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
241079 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
241106 TTAAGTTTCG
Statistics
Matches: 88, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
32 31 0.35
33 57 0.65
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:241120 original size:20 final size:19
Alignment explanation
Indices: 241045--241123 Score: 71
Period size: 19 Copynumber: 4.4 Consensus size: 19
241035 GCGATTCTGT
*
241045 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTAATTTCG
*
241064 CGTTGCG------ATTTCT
1 CGTTGCGATTTTAATTTCG
*
241077 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTAATTTCG
241096 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTAA-TTTCG
*
241116 TGTTGCGA
1 CGTTGCGA
241124 AAGTAAACTA
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
13 12 0.24
19 25 0.51
20 12 0.24
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
CGTTGCGATTTTAATTTCG
Found at i:241633 original size:21 final size:21
Alignment explanation
Indices: 241577--241639 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
241567 TTCCTTGAGA
*
241577 GTCCCTCCCACCGTTCAAGAG
1 GTCCCTCCCACCATTCAAGAG
** * *
241598 G-CCACTGTCATCATTGAAGAG
1 GTCC-CTCCCACCATTCAAGAG
241619 GTCCCTCCCACCATTCAAGAG
1 GTCCCTCCCACCATTCAAGAG
241640 CCCGATTCAC
Statistics
Matches: 31, Mismatches: 9, Indels: 4
0.70 0.20 0.09
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.24, C:0.37, G:0.19, T:0.21
Consensus pattern (21 bp):
GTCCCTCCCACCATTCAAGAG
Found at i:243007 original size:14 final size:14
Alignment explanation
Indices: 242988--243020 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
242978 ATTGTTTGAT
242988 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
243002 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
243016 TGATT
1 TGATT
243021 CAATAGTAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.21, T:0.42
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:243074 original size:84 final size:84
Alignment explanation
Indices: 242929--243104 Score: 307
Period size: 84 Copynumber: 2.1 Consensus size: 84
242919 TGGCTGCAAT
*** *
242929 AGTTGATTCAATAGTAGATGAGGAAATAATTCTTATTGCTTATTTTTTGATTGTTTGATTGATTT
1 AGTTGATTCAATAGTAGATGAGGAAATAAGAATTATTGCTTATTTTTTGATTGTTTAATTGATTT
242994 GTAAAAGATGATTTGTAAA
66 GTAAAAGATGATTTGTAAA
*
243013 AGTTGATTCAATAGTAGATGGGGAAATAAGAATTATTGCTTATTTTTTGATTGTTTAATTGATTT
1 AGTTGATTCAATAGTAGATGAGGAAATAAGAATTATTGCTTATTTTTTGATTGTTTAATTGATTT
243078 GTAAAAGATGATTTGTAAA
66 GTAAAAGATGATTTGTAAA
243097 AGTTGATT
1 AGTTGATT
243105 TGTTTAATTG
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
84 87 1.00
ACGTcount: A:0.33, C:0.03, G:0.20, T:0.44
Consensus pattern (84 bp):
AGTTGATTCAATAGTAGATGAGGAAATAAGAATTATTGCTTATTTTTTGATTGTTTAATTGATTT
GTAAAAGATGATTTGTAAA
Found at i:243091 original size:14 final size:14
Alignment explanation
Indices: 243072--243107 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
243062 ATTGTTTAAT
243072 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
243086 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
243100 TGATTTGT
1 TGATTTGT
243108 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:243284 original size:52 final size:52
Alignment explanation
Indices: 243214--243324 Score: 213
Period size: 52 Copynumber: 2.1 Consensus size: 52
243204 AAAAATGACT
*
243214 ATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAA
243266 ATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAA
243318 ATCGCAA
1 ATCGCAA
243325 CGAGAGAATC
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 58 1.00
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (52 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAA
Found at i:243299 original size:33 final size:33
Alignment explanation
Indices: 243262--243357 Score: 183
Period size: 33 Copynumber: 2.9 Consensus size: 33
243252 AATGCGAAAT
243262 GAGAATCGCAATGCGAAATGAAAATCGCAACGA
1 GAGAATCGCAATGCGAAATGAAAATCGCAACGA
243295 GAGAATCGCAATGCGAAATGAAAATCGCAACGA
1 GAGAATCGCAATGCGAAATGAAAATCGCAACGA
*
243328 GAGAATCGCAATGTGAAATGAAAATCGCAA
1 GAGAATCGCAATGCGAAATGAAAATCGCAA
243358 TGCGAATTAG
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 62 1.00
ACGTcount: A:0.46, C:0.17, G:0.24, T:0.14
Consensus pattern (33 bp):
GAGAATCGCAATGCGAAATGAAAATCGCAACGA
Found at i:243394 original size:14 final size:14
Alignment explanation
Indices: 243375--243429 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
243365 TAGTTTCGCA
243375 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
243389 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
243406 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
243422 TTGCGATT
1 TTGCGATT
243430 TTCATTTCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 14 0.41
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:243405 original size:33 final size:33
Alignment explanation
Indices: 243368--243498 Score: 181
Period size: 33 Copynumber: 3.8 Consensus size: 33
243358 TGCGAATTAG
243368 TTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
243401 TTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
* *
243434 TTTCGCATTGCGATTTTCATTTCCGCGTTGCAATTTTCA
1 TTTCGCATTGCGA--TTC---T-CTCGTTGCGATTTTCA
*
243473 TTTCGCATTGCGATTCTCTTGTTGCG
1 TTTCGCATTGCGATTCTCTCGTTGCG
243499 GTTGTATTTT
Statistics
Matches: 87, Mismatches: 5, Indels: 12
0.84 0.05 0.12
Matches are distributed among these distances:
33 52 0.60
34 1 0.01
35 3 0.03
37 3 0.03
38 1 0.01
39 27 0.31
ACGTcount: A:0.12, C:0.24, G:0.18, T:0.46
Consensus pattern (33 bp):
TTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
Found at i:243413 original size:19 final size:19
Alignment explanation
Indices: 243389--243487 Score: 127
Period size: 19 Copynumber: 5.4 Consensus size: 19
243379 GATTCTCTCG
243389 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
243408 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
243422 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
243441 TTGCGATTTTCATTTCCGCG
1 TTGCGATTTTCATTT-CGCA
*
243461 TTGCAATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
243480 TTGCGATT
1 TTGCGATT
243488 CTCTTGTTGC
Statistics
Matches: 68, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
14 6 0.09
16 7 0.10
17 7 0.10
19 31 0.46
20 17 0.25
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:243566 original size:20 final size:20
Alignment explanation
Indices: 243506--243566 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 20
243496 GCGGTTGTAT
*
243506 TTTCCGCGTTGCGATAGTCA
1 TTTCCGTGTTGCGATAGTCA
**
243526 -TTAAGATGATTGCGA-ACGTCA
1 TTTCCG-TG-TTGCGATA-GTCA
243547 TTTCCGTGTTGCGATAGTCA
1 TTTCCGTGTTGCGATAGTCA
243567 AATGTATGCC
Statistics
Matches: 31, Mismatches: 5, Indels: 10
0.67 0.11 0.22
Matches are distributed among these distances:
19 3 0.10
20 12 0.39
21 13 0.42
22 3 0.10
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.34
Consensus pattern (20 bp):
TTTCCGTGTTGCGATAGTCA
Found at i:244212 original size:14 final size:14
Alignment explanation
Indices: 244157--244213 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
244147 GCGAAATGAA
*
244157 AATCGCAACGAGAG
1 AATCGCAATGAGAG
*
244171 AATCGCAATACGAACTGAA
1 AATCGCAAT--G-A--GAG
244190 AATCGCAATGAGAG
1 AATCGCAATGAGAG
244204 AATCGCAATG
1 AATCGCAATG
244214 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
16 2 0.06
17 2 0.06
19 11 0.31
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.14
Consensus pattern (14 bp):
AATCGCAATGAGAG
Found at i:244231 original size:33 final size:33
Alignment explanation
Indices: 244139--244232 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
244129 GGAAATGACT
*
244139 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGAGAGA
* *
244172 ATCGCAATACGAACTGAAAATCGCAATGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGAGAGA
244205 ATCGCAATGCGAAATGAAAATCGCAATG
1 ATCGCAATGCGAAATGAAAATCGCAATG
244233 CGGAAATGAA
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAATGAGAGA
Found at i:244266 original size:19 final size:19
Alignment explanation
Indices: 244139--244260 Score: 122
Period size: 19 Copynumber: 6.9 Consensus size: 19
244129 GGAAATGACT
244139 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
244158 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
* *
244172 ATCGCAATACGAACTGAAA
1 ATCGCAATGCGAAATGAAA
*
244191 ATCGCAAT--G--A-GAGA
1 ATCGCAATGCGAAATGAAA
244205 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
244224 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
244244 ATCG-AATGCGAAATGAA
1 ATCGCAATGCGAAATGAA
244261 GCATCGGAAG
Statistics
Matches: 86, Mismatches: 6, Indels: 23
0.75 0.05 0.20
Matches are distributed among these distances:
14 21 0.24
15 1 0.01
16 3 0.03
17 3 0.03
18 9 0.10
19 36 0.42
20 13 0.15
ACGTcount: A:0.46, C:0.16, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:244611 original size:18 final size:18
Alignment explanation
Indices: 244588--244624 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
244578 CGAAATTTAT
244588 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
244606 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
244624 A
1 A
244625 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:244916 original size:33 final size:34
Alignment explanation
Indices: 244834--244909 Score: 111
Period size: 33 Copynumber: 2.3 Consensus size: 34
244824 TTCATTTCCG
*
244834 CGTTGCGATTTTCATATTCGCACTACGATTTTCAT
1 CGTTGCGATTTTCAT-TTCGCACTACGATTCTCAT
*
244869 -GTTGCGATTTTCATTTCGCATTACGATTCTC-T
1 CGTTGCGATTTTCATTTCGCACTACGATTCTCAT
244901 CGTTGCGAT
1 CGTTGCGAT
244910 AGTCATTAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
32 1 0.03
33 23 0.61
34 14 0.37
ACGTcount: A:0.17, C:0.22, G:0.17, T:0.43
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTCGCACTACGATTCTCAT
Found at i:244955 original size:20 final size:20
Alignment explanation
Indices: 244902--244955 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
244892 CGATTCTCTC
*
244902 GTTGCGATAGTCATTAAGAT
1 GTTGCGATAGTCATTAACAT
**
244922 GATTGCGA-ACGTCATTTCCAT
1 G-TTGCGATA-GTCATTAACAT
244943 GTTGCGATAGTCA
1 GTTGCGATAGTCA
244956 AATGCATGCC
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (20 bp):
GTTGCGATAGTCATTAACAT
Found at i:247227 original size:12 final size:12
Alignment explanation
Indices: 247210--247234 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
247200 TCTTCGGGGA
247210 CTTTTTCTTCTT
1 CTTTTTCTTCTT
247222 CTTTTTCTTCTT
1 CTTTTTCTTCTT
247234 C
1 C
247235 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:247434 original size:24 final size:24
Alignment explanation
Indices: 247400--247446 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
247390 CTGAAACATC
247400 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAT
* *
247424 ATCAAAGTCCGGGTATTGACCAA
1 ATCAAAATCCGAGTATTGACCAA
247447 GATGAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.23
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAT
Found at i:248156 original size:20 final size:20
Alignment explanation
Indices: 248131--248251 Score: 197
Period size: 20 Copynumber: 6.0 Consensus size: 20
248121 AAATTTTAGT
* *
248131 GTTGCGATTTATAGATTCTC
1 GTTGCGATTTACAGATTATC
*
248151 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACAGATTATC
248171 GTTGCGATTTACAGATTATC
1 GTTGCGATTTACAGATTATC
*
248191 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACAGATTATC
*
248211 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACAGATTATC
248231 GTTGCGATTTACAGATTATC
1 GTTGCGATTTACAGATTATC
248251 G
1 G
248252 CAACGAGAGA
Statistics
Matches: 93, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 93 1.00
ACGTcount: A:0.21, C:0.16, G:0.22, T:0.40
Consensus pattern (20 bp):
GTTGCGATTTACAGATTATC
Found at i:248224 original size:60 final size:60
Alignment explanation
Indices: 248131--248251 Score: 233
Period size: 60 Copynumber: 2.0 Consensus size: 60
248121 AAATTTTAGT
*
248131 GTTGCGATTTATAGATTCTCGTTGCGATTTACGGATTATCGTTGCGATTTACAGATTATC
1 GTTGCGATTTACAGATTCTCGTTGCGATTTACGGATTATCGTTGCGATTTACAGATTATC
248191 GTTGCGATTTACAGATTCTCGTTGCGATTTACGGATTATCGTTGCGATTTACAGATTATC
1 GTTGCGATTTACAGATTCTCGTTGCGATTTACGGATTATCGTTGCGATTTACAGATTATC
248251 G
1 G
248252 CAACGAGAGA
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.21, C:0.16, G:0.22, T:0.40
Consensus pattern (60 bp):
GTTGCGATTTACAGATTCTCGTTGCGATTTACGGATTATCGTTGCGATTTACAGATTATC
Found at i:248294 original size:14 final size:14
Alignment explanation
Indices: 248275--248302 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
248265 GCAATGCGAA
248275 ATGAAAATCGCAAC
1 ATGAAAATCGCAAC
248289 ATGAAAATCGCAAC
1 ATGAAAATCGCAAC
248303 GCGAACATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.21, G:0.14, T:0.14
Consensus pattern (14 bp):
ATGAAAATCGCAAC
Found at i:248309 original size:20 final size:20
Alignment explanation
Indices: 248289--248402 Score: 169
Period size: 20 Copynumber: 5.8 Consensus size: 20
248279 AAATCGCAAC
248289 ATGAAAATCGCAACGC-GAA
1 ATGAAAATCGCAACGCGGAA
248308 CATGAAAATCGCAACGCGGAA
1 -ATGAAAATCGCAACGCGGAA
* *
248329 ATGAAAATCGGAATGCGGAA
1 ATGAAAATCGCAACGCGGAA
*
248349 ATGAAAATCGCAATGCGGAA
1 ATGAAAATCGCAACGCGGAA
*
248369 ATGAAAATCGCAATGC-GAA
1 ATGAAAATCGCAACGCGGAA
248388 ATGAAAATCGCAACG
1 ATGAAAATCGCAACG
248403 AGAGAATCGC
Statistics
Matches: 89, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
19 17 0.19
20 69 0.78
21 3 0.03
ACGTcount: A:0.46, C:0.18, G:0.24, T:0.13
Consensus pattern (20 bp):
ATGAAAATCGCAACGCGGAA
Found at i:248353 original size:40 final size:39
Alignment explanation
Indices: 248261--248402 Score: 197
Period size: 40 Copynumber: 3.7 Consensus size: 39
248251 GCAACGAGAG
248261 AATCGCAATGCGAAATGAAAATCGCAA--C----ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGCGGAAATGAA
*
248294 AATCGCAACGCGAACATGAAAATCGCAACGCGGAAATGAA
1 AATCGCAATGCGAA-ATGAAAATCGCAACGCGGAAATGAA
* *
248334 AATCGGAATGCGGAAATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAAAATCGCAACGCGGAAATGAA
248374 AATCGCAATGCGAAATGAAAATCGCAACG
1 AATCGCAATGCGAAATGAAAATCGCAACG
248403 AGAGAATCGC
Statistics
Matches: 95, Mismatches: 6, Indels: 10
0.86 0.05 0.09
Matches are distributed among these distances:
33 13 0.14
34 13 0.14
36 1 0.01
39 17 0.18
40 48 0.51
41 3 0.03
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.13
Consensus pattern (39 bp):
AATCGCAATGCGAAATGAAAATCGCAACGCGGAAATGAA
Found at i:248439 original size:25 final size:25
Alignment explanation
Indices: 248407--248489 Score: 76
Period size: 25 Copynumber: 3.3 Consensus size: 25
248397 GCAACGAGAG
*
248407 AATCGCAATGTGAAAATCATCGCAT
1 AATCGCAATGAGAAAATCATCGCAT
*** * * *
248432 AATCGCAATGAGAATCGCAACGAGAG
1 AATCGCAATGAGAAAATCATCG-CAT
*
248458 AATCGCAATGCGAAAATCATCGCAT
1 AATCGCAATGAGAAAATCATCGCAT
*
248483 CATCGCA
1 AATCGCA
248490 TGATTTTCAT
Statistics
Matches: 42, Mismatches: 15, Indels: 2
0.71 0.25 0.03
Matches are distributed among these distances:
25 24 0.57
26 18 0.43
ACGTcount: A:0.40, C:0.23, G:0.19, T:0.18
Consensus pattern (25 bp):
AATCGCAATGAGAAAATCATCGCAT
Found at i:248448 original size:51 final size:51
Alignment explanation
Indices: 248387--248489 Score: 179
Period size: 51 Copynumber: 2.0 Consensus size: 51
248377 CGCAATGCGA
*
248387 AATGAAAATCGCAACGAGAGAATCGCAATGTGAAAATCATCGCATAATCGC
1 AATGAAAATCGCAACGAGAGAATCGCAATGCGAAAATCATCGCATAATCGC
* *
248438 AATGAGAATCGCAACGAGAGAATCGCAATGCGAAAATCATCGCATCATCGC
1 AATGAAAATCGCAACGAGAGAATCGCAATGCGAAAATCATCGCATAATCGC
248489 A
1 A
248490 TGATTTTCAT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.42, C:0.21, G:0.20, T:0.17
Consensus pattern (51 bp):
AATGAAAATCGCAACGAGAGAATCGCAATGCGAAAATCATCGCATAATCGC
Found at i:248568 original size:33 final size:33
Alignment explanation
Indices: 248491--248617 Score: 173
Period size: 33 Copynumber: 3.7 Consensus size: 33
248481 ATCATCGCAT
*
248491 GATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGC
1 GATTTTCATTTCGCATTGCGA--TT-ATCT-CG--TTGC
* *
248530 GATTTTTATTTCGCATTGCGATTCTCTCGTTGC
1 GATTTTCATTTCGCATTGCGATTATCTCGTTGC
248563 GATTTTCATTTCGCATTGCGATTATCTCGTTGC
1 GATTTTCATTTCGCATTGCGATTATCTCGTTGC
248596 GATTTTCATTTCGCATTGCGAT
1 GATTTTCATTTCGCATTGCGAT
248618 AGTCATTTTT
Statistics
Matches: 83, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
33 57 0.69
35 2 0.02
36 2 0.02
37 2 0.02
39 20 0.24
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.46
Consensus pattern (33 bp):
GATTTTCATTTCGCATTGCGATTATCTCGTTGC
Found at i:248625 original size:19 final size:19
Alignment explanation
Indices: 248491--248617 Score: 148
Period size: 19 Copynumber: 7.2 Consensus size: 19
248481 ATCATCGCAT
248491 GATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGC
248510 GATTTTCATTTCCGCATTGC
1 GATTTTCATTT-CGCATTGC
*
248530 GATTTTTATTTCGCATTGC
1 GATTTTCATTTCGCATTGC
*
248549 GA--TTC-TCTCG--TTGC
1 GATTTTCATTTCGCATTGC
248563 GATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGC
*
248582 GA--TT-ATCTCG--TTGC
1 GATTTTCATTTCGCATTGC
248596 GATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGC
248615 GAT
1 GAT
248618 AGTCATTTTT
Statistics
Matches: 91, Mismatches: 6, Indels: 22
0.76 0.05 0.18
Matches are distributed among these distances:
14 12 0.13
16 14 0.15
17 13 0.14
19 34 0.37
20 18 0.20
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.46
Consensus pattern (19 bp):
GATTTTCATTTCGCATTGC
Found at i:248743 original size:14 final size:14
Alignment explanation
Indices: 248724--248760 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
248714 CATCAATTAA
248724 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
248738 ACAAATCATCTTTT
1 ACAAATCAACTTTT
248752 ACAAATCAA
1 ACAAATCAA
248761 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:248830 original size:83 final size:84
Alignment explanation
Indices: 248727--248901 Score: 316
Period size: 84 Copynumber: 2.1 Consensus size: 84
248717 CAATTAAACA
***
248727 AATCAACTTTTACAAATCATCTTTTACAAATCAATTAAACAAT-AAAAAATAAGCAATAATTCTT
1 AATCAACTTTTACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAAGCAATAAGAATT
248791 ATTTCCTCATCTACTATTG
66 ATTTCCTCATCTACTATTG
248810 AATCAACTTTTACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAAGCAATAAGAATT
1 AATCAACTTTTACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAAGCAATAAGAATT
248875 ATTTCCTCATCTACTATTG
66 ATTTCCTCATCTACTATTG
248894 AATCAACT
1 AATCAACT
248902 ATTGCAGCCA
Statistics
Matches: 88, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
83 43 0.49
84 45 0.51
ACGTcount: A:0.45, C:0.18, G:0.03, T:0.34
Consensus pattern (84 bp):
AATCAACTTTTACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAAGCAATAAGAATT
ATTTCCTCATCTACTATTG
Found at i:248833 original size:14 final size:14
Alignment explanation
Indices: 248810--248843 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
248800 TCTACTATTG
248810 AATCAACTTTTACA
1 AATCAACTTTTACA
*
248824 AATCATCTTTTACA
1 AATCAACTTTTACA
248838 AATCAA
1 AATCAA
248844 TTAAACAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.35
Consensus pattern (14 bp):
AATCAACTTTTACA
Found at i:250765 original size:19 final size:19
Alignment explanation
Indices: 250709--250850 Score: 141
Period size: 19 Copynumber: 7.6 Consensus size: 19
250699 TAATTTACTT
* *
250709 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
* **
250729 TCGCAACGTGAAAAATGACTA
1 TCGCAACGCG--AAATGAAAA
250750 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
250769 TCGCAACGAGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
250788 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
250807 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
**
250821 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
250840 TCGCAACGCGA
1 TCGCAACGCGA
250851 TTATAGTTTC
Statistics
Matches: 104, Mismatches: 11, Indels: 15
0.80 0.08 0.12
Matches are distributed among these distances:
14 10 0.10
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 65 0.62
20 8 0.08
21 12 0.12
22 3 0.03
ACGTcount: A:0.46, C:0.24, G:0.18, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:250826 original size:33 final size:35
Alignment explanation
Indices: 250749--250847 Score: 130
Period size: 33 Copynumber: 2.8 Consensus size: 35
250739 AAAAATGACT
*
250749 ATCGCAACGCGAAATGAAAATCGCAACGAGAAATGAAA
1 ATCGCAACGCGAAATGAAAATCGCAAC--G-AATCAAA
250787 ATCGCAACGCGAAATGAAAATCGCAACG-A-CAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGAATCAAA
**
250820 ATCGCAACGCGAAACCAAAATCGCAACG
1 ATCGCAACGCGAAATGAAAATCGCAACG
250848 CGATTATAGT
Statistics
Matches: 58, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
33 29 0.50
34 1 0.02
36 1 0.02
38 27 0.47
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.09
Consensus pattern (35 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAATCAAA
Found at i:250869 original size:19 final size:19
Alignment explanation
Indices: 250857--250959 Score: 117
Period size: 19 Copynumber: 5.7 Consensus size: 19
250847 GCGATTATAG
* **
250857 TTTCACGTTGCGATTTTGG
1 TTTCGCGTTGCGATTTTCA
250876 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
250895 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
*
250914 TTTCTCGTTGCGA--TTC-
1 TTTCGCGTTGCGATTTTCA
* *
250930 --TCTCGTTACGATTTTCA
1 TTTCGCGTTGCGATTTTCA
250947 TTTCGCGTTGCGA
1 TTTCGCGTTGCGA
250960 GAGTCATTTT
Statistics
Matches: 72, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
14 10 0.14
16 3 0.04
17 3 0.04
19 56 0.78
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.47
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:250967 original size:52 final size:53
Alignment explanation
Indices: 250881--250982 Score: 143
Period size: 52 Copynumber: 1.9 Consensus size: 53
250871 TTTGGTTTCG
* ***
250881 CGTTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCTC-GTTGCGATTCTCT
1 CGTTACGATTTTCATTTCGCGTTGCGAGAGTCATTTCTCAGTTGCGATTCTCT
*
250933 CGTTACGATTTTCATTTCGCGTTGCGAGAGTCATTTTTCAGGTTGCGATT
1 CGTTACGATTTTCATTTCGCGTTGCGAGAGTCATTTCTCA-GTTGCGATT
250983 TTAAGTTTCG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
52 34 0.79
54 9 0.21
ACGTcount: A:0.13, C:0.21, G:0.22, T:0.45
Consensus pattern (53 bp):
CGTTACGATTTTCATTTCGCGTTGCGAGAGTCATTTCTCAGTTGCGATTCTCT
Found at i:251220 original size:93 final size:94
Alignment explanation
Indices: 251051--251336 Score: 459
Period size: 93 Copynumber: 3.1 Consensus size: 94
251041 ATGGATTGCA
* * *
251051 TTAC-TTCAACCAAAAGACAAAACAAAGATAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGAAAAATACTAACTTCACAGTGTTAAAGAATACACAGT
251115 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
* *
251144 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACT-ATTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGAAAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
251208 TTAGTAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
* *
251237 TTACTTTCAACCAAAAGACAAAACAAAAGAAAAATACTAACTTCATAGTGTTAAAGAATAAACAG
1 TTACTTTCAACCAAAAGACAAAAC-AAAGAAAAATACTAACTTCACAGTGTTAAAGAATACACAG
* *
251302 TTTAGCAGTATTGGCAGCAACCGAATAAAT
65 TTTAGCAGAATTGGCAGCAACCGAACAAAT
251332 TTACT
1 TTACT
251337 AAGCAATCTA
Statistics
Matches: 178, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
93 80 0.45
94 43 0.24
95 55 0.31
ACGTcount: A:0.47, C:0.17, G:0.13, T:0.23
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGAAAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:252876 original size:26 final size:25
Alignment explanation
Indices: 252825--252878 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
252815 ATACCAAGTT
* *
252825 AGATATACCAAAAACTACACTGTAA
1 AGATATACCAAAAACTAAACTATAA
252850 AGATATACCAAAAACAATAAAC-ATAA
1 AGATATACCAAAAAC--TAAACTATAA
252876 AGA
1 AGA
252879 GTAGTAGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 15 0.60
26 6 0.24
27 4 0.16
ACGTcount: A:0.59, C:0.17, G:0.07, T:0.17
Consensus pattern (25 bp):
AGATATACCAAAAACTAAACTATAA
Found at i:252964 original size:20 final size:20
Alignment explanation
Indices: 252934--253075 Score: 115
Period size: 20 Copynumber: 7.5 Consensus size: 20
252924 TTTTGGTTGA
252934 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
** *
252954 AATGACTATCGCAACGCG-G
1 AATGAAAATCGCAACGAGAG
252973 AAATGAAAATCGCAACGAGAG
1 -AATGAAAATCGCAACGAGAG
** *
252994 AATGACTATCGCAACGCG-G
1 AATGAAAATCGCAACGAGAG
*
253013 AAATGAAAATCGCAA--TGAG
1 -AATGAAAATCGCAACGAGAG
*
253032 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
*
253047 AATGAAAATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
253066 AATGAAAATC
1 AATGAAAATC
253076 ACAATGCGAT
Statistics
Matches: 99, Mismatches: 13, Indels: 21
0.74 0.10 0.16
Matches are distributed among these distances:
14 8 0.08
16 4 0.04
17 2 0.02
18 1 0.01
19 26 0.26
20 57 0.58
21 1 0.01
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.13
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:252976 original size:40 final size:40
Alignment explanation
Indices: 252932--253070 Score: 204
Period size: 40 Copynumber: 3.7 Consensus size: 40
252922 TCTTTTGGTT
252932 GAAATGAAAATCGCAACGAGAGAATGACTATCGCAACGCG
1 GAAATGAAAATCGCAACGAGAGAATGACTATCGCAACGCG
252972 GAAATGAAAATCGCAACGAGAGAATGACTATCGCAACGCG
1 GAAATGAAAATCGCAACGAGAGAATGACTATCGCAACGCG
*
253012 GAAATGAAAATCGCAA--TGAG-A-GA--ATCGCAACGC-
1 GAAATGAAAATCGCAACGAGAGAATGACTATCGCAACGCG
*
253045 GAAATGAAAATCGCAACGCGA-AATGA
1 GAAATGAAAATCGCAACGAGAGAATGA
253071 AAATCACAAT
Statistics
Matches: 93, Mismatches: 2, Indels: 12
0.87 0.02 0.11
Matches are distributed among these distances:
33 16 0.17
34 10 0.11
35 3 0.03
36 4 0.04
37 1 0.01
38 3 0.03
40 56 0.60
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.12
Consensus pattern (40 bp):
GAAATGAAAATCGCAACGAGAGAATGACTATCGCAACGCG
Found at i:253130 original size:21 final size:21
Alignment explanation
Indices: 253104--253195 Score: 92
Period size: 21 Copynumber: 4.8 Consensus size: 21
253094 CGCGTTGCGA
253104 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
**
253125 TTCTCTCGTTGCGATAGTCAT
1 TTCTCTCGTTGCGATTTTCAT
* *
253146 TT-TCGCGTT--GA----GA-
1 TTCTCTCGTTGCGATTTTCAT
253159 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
253180 TTCTCTCGTTGCGATT
1 TTCTCTCGTTGCGATT
253196 CTTCTGCAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 16
0.72 0.08 0.20
Matches are distributed among these distances:
13 2 0.04
14 7 0.12
16 2 0.04
18 2 0.04
20 7 0.12
21 37 0.65
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:253163 original size:55 final size:55
Alignment explanation
Indices: 253091--253194 Score: 199
Period size: 55 Copynumber: 1.9 Consensus size: 55
253081 GCGATTTTGG
*
253091 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGATAGTCAT
1 TTTCGCGTTGAGATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGATAGTCAT
253146 TTTCGCGTTGAGATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGAT
1 TTTCGCGTTGAGATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGAT
253195 TCTTCTGCAA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 48 1.00
ACGTcount: A:0.11, C:0.23, G:0.20, T:0.46
Consensus pattern (55 bp):
TTTCGCGTTGAGATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGATAGTCAT
Found at i:253167 original size:34 final size:35
Alignment explanation
Indices: 253125--253197 Score: 103
Period size: 34 Copynumber: 2.1 Consensus size: 35
253115 CGATTTTCAT
253125 TTCTCTCGTTGCGATAGTCATTT-TCGCGTTGAGA
1 TTCTCTCGTTGCGATAGTCATTTCTCGCGTTGAGA
** * *
253159 TTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGA
1 TTCTCTCGTTGCGATAGTCATTTCTCGCGTTGAGA
253194 TTCT
1 TTCT
253198 TCTGCAAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
34 21 0.62
35 13 0.38
ACGTcount: A:0.11, C:0.23, G:0.19, T:0.47
Consensus pattern (35 bp):
TTCTCTCGTTGCGATAGTCATTTCTCGCGTTGAGA
Found at i:253415 original size:33 final size:31
Alignment explanation
Indices: 253369--253430 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 31
253359 AAATTACCAG
* * *
253369 TAAACTAATCAAAAGTTTCAATATGAAAAACC
1 TAAAATAATCAAAAATTTCAAAAT-AAAAACC
253401 TAAAATAATGCAAAAATTTCAAAATAAAAA
1 TAAAATAAT-CAAAAATTTCAAAATAAAAA
253431 TAATTAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 13 0.50
33 13 0.50
ACGTcount: A:0.60, C:0.11, G:0.05, T:0.24
Consensus pattern (31 bp):
TAAAATAATCAAAAATTTCAAAATAAAAACC
Found at i:253737 original size:20 final size:20
Alignment explanation
Indices: 253712--253886 Score: 133
Period size: 20 Copynumber: 8.7 Consensus size: 20
253702 CTTTAAAAAT
253712 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
253732 CGCGTTACGATTTTTCGTAT-
1 CGCGTTGCGA-TTTACGGATA
* * * *
253752 TGTCGTTGCGATTAACGTATT
1 CG-CGTTGCGATTTACGGATA
* * *
253773 CTCGTTGCGA-TAATCAGA-A
1 CGCGTTGCGATTTA-CGGATA
* *
253792 TCGCGTTGCGATTTACGTATT
1 -CGCGTTGCGATTTACGGATA
*
253813 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
253833 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
253853 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
253874 CGCGTTGCGATTT
1 CGCGTTGCGATTT
253887 TTACGAGTAC
Statistics
Matches: 120, Mismatches: 25, Indels: 20
0.73 0.15 0.12
Matches are distributed among these distances:
19 3 0.03
20 84 0.70
21 33 0.28
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.38
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:253804 original size:40 final size:40
Alignment explanation
Indices: 253755--253947 Score: 180
Period size: 40 Copynumber: 4.8 Consensus size: 40
253745 TTCGTATTGT
*
253755 CGTTGCGATTAACGTATTCTCGTTGCGATAATCA-GAAT-CG
1 CGTTGCGATTTACGTATTCTCGTTGCGAT--TCACGAATACG
* *
253795 CGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGTATTCTCGTTGCGATTCACGAATACG
* * *
253835 CGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACG
1 CGTTGCGA-TTTACGTATTCTCGTTGCGATTCACGAATACG
*
253876 CGTTGCGATTTTTACG-AGTACTCGTTGCGATAGTCA-GAAT-CG
1 CGTTGCGA--TTTACGTA-TTCTCGTTGCGAT--TCACGAATACG
** * *
253918 CGTTGCGATTTATATGTTCGCGTTGCGATT
1 CGTTGCGATTTACGTATTCTCGTTGCGATT
253948 TTCATATTCG
Statistics
Matches: 132, Mismatches: 13, Indels: 18
0.81 0.08 0.11
Matches are distributed among these distances:
38 3 0.02
39 3 0.02
40 53 0.40
41 40 0.30
42 28 0.21
43 3 0.02
44 2 0.02
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (40 bp):
CGTTGCGATTTACGTATTCTCGTTGCGATTCACGAATACG
Found at i:253851 original size:81 final size:81
Alignment explanation
Indices: 253709--253864 Score: 199
Period size: 81 Copynumber: 1.9 Consensus size: 81
253699 GCGCTTTAAA
* * *
253709 AATCGCGTTGCGATTTACGGATACGCGTTACGATTTTTCGTATTGTCGTTGCGATTAACGTATTC
1 AATCGCGTTGCGATTTACGGATACGCGTTACGATTTTACGGATCGTCGTTGCGATTAACGTATTC
253774 TCGTTGCGATAATCAG
66 TCGTTGCGATAATCAG
* * * * *
253790 AATCGCGTTGCGATTTACGTATTCTCGTTGCGA-TTTACGGATACG-CGTTGCGATTTTACGTAT
1 AATCGCGTTGCGATTTACGGATACGCGTTACGATTTTACGGAT-CGTCGTTGCGA-TTAACGTAT
*
253853 TGTCGTTGCGAT
64 TCTCGTTGCGAT
253865 TTACGGATAC
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
80 15 0.23
81 49 0.77
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (81 bp):
AATCGCGTTGCGATTTACGGATACGCGTTACGATTTTACGGATCGTCGTTGCGATTAACGTATTC
TCGTTGCGATAATCAG
Found at i:253887 original size:41 final size:40
Alignment explanation
Indices: 253755--253886 Score: 187
Period size: 40 Copynumber: 3.3 Consensus size: 40
253745 TTCGTATTGT
* * *
253755 CGTTGCGATTAACGTATTCTCGTTGCGA-TAATCAGA-ATCG
1 CGTTGCGATTTACGTATTCTCGTTGCGATTTA-CGGATA-CG
253795 CGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACG
*
253835 CGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACG
1 CGTTGCGA-TTTACGTATTCTCGTTGCGATTTACGGATACG
253876 CGTTGCGATTT
1 CGTTGCGATTT
253887 TTACGAGTAC
Statistics
Matches: 85, Mismatches: 4, Indels: 6
0.89 0.04 0.06
Matches are distributed among these distances:
40 43 0.51
41 42 0.49
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (40 bp):
CGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACG
Found at i:253938 original size:20 final size:20
Alignment explanation
Indices: 253915--253969 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
253905 ATAGTCAGAA
*
253915 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
253935 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
*
253955 TCGCTTTGCGATTTT
1 TCGCGTTGCGATTTT
253970 TGGAAAATCG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 31 0.97
ACGTcount: A:0.13, C:0.18, G:0.22, T:0.47
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:254020 original size:21 final size:20
Alignment explanation
Indices: 253934--254031 Score: 70
Period size: 21 Copynumber: 4.7 Consensus size: 20
253924 GATTTATATG
* *
253934 TTCGCGTTGCGATTTTCATA
1 TTCGCATTGCGATTTTCAAA
* *
253954 TTCGCTTTGCGATTTTTGGAAA
1 TTCGCATTGCGA-TTTT-CAAA
* * * *
253976 ATCGCAATGCGATAGTACAAA
1 TTCGCATTGCGAT-TTTCAAA
*
253997 TTCGCATTGCGATTTTCCAGA
1 TTCGCATTGCGATTTT-CAAA
*
254018 TTCGCGTTGCGATT
1 TTCGCATTGCGATT
254032 CTTGAAACTG
Statistics
Matches: 59, Mismatches: 15, Indels: 7
0.73 0.19 0.09
Matches are distributed among these distances:
20 12 0.20
21 35 0.59
22 12 0.20
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.38
Consensus pattern (20 bp):
TTCGCATTGCGATTTTCAAA
Found at i:256581 original size:50 final size:50
Alignment explanation
Indices: 256527--256627 Score: 159
Period size: 50 Copynumber: 2.0 Consensus size: 50
256517 GATATGTTGC
*
256527 CTCTCTTTATAAC-ATTTTTTGTTGCAAAATGAGTTGCCTCATTCATTTAA
1 CTCTCTTTATAACGA-TTTTTGTCGCAAAATGAGTTGCCTCATTCATTTAA
* *
256577 CTCTCTTTATAACGATTTTTGTCGGAAAATGAGTTGCCTCATTCGTTTAA
1 CTCTCTTTATAACGATTTTTGTCGCAAAATGAGTTGCCTCATTCATTTAA
256627 C
1 C
256628 GATTTCTTGT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
50 46 0.98
51 1 0.02
ACGTcount: A:0.25, C:0.19, G:0.13, T:0.44
Consensus pattern (50 bp):
CTCTCTTTATAACGATTTTTGTCGCAAAATGAGTTGCCTCATTCATTTAA
Found at i:261214 original size:186 final size:186
Alignment explanation
Indices: 260900--261447 Score: 987
Period size: 186 Copynumber: 3.0 Consensus size: 186
260890 GATCTTCCAC
260900 TTCCCGCCACTAACCAGGGGCGTCAGCAGGTTCCATGAGAATAAAATCCGAAGAAGACATGCCAG
1 TTCCCGCCACTAACCAGGGGCGTCAGCAGGTTCCATGAGAATAAAATCCGAAGAAGACATGCCAG
260965 AGCCAAACTTCCCGTCATTAAAGCAATCATACATAAGTCAAAATCGGCCTGCCAAATACAAACAC
66 AGCCAAACTTCCCGTCATTAAAGCAATCATACATAAGTCAAAATCGGCCTGCCAAATACAAACAC
261030 AATTACATCATAAATAAATGGAACATGTCAATAAATAAATAAACCAAATTACTAAA
131 AATTACATCATAAATAAATGGAACATGTCAATAAATAAATAAACCAAATTACTAAA
261086 TTCCCGCCACTAACCAGGGGCGTCAGCAGGTTCCATGAGAATAAAATCCGAAGAAGACATGCCAG
1 TTCCCGCCACTAACCAGGGGCGTCAGCAGGTTCCATGAGAATAAAATCCGAAGAAGACATGCCAG
261151 AGCCAAACTTCCCGTCATTAAAGCAATCATACATAAGTCAAAATCGGCCTGCCAAATACAAACAC
66 AGCCAAACTTCCCGTCATTAAAGCAATCATACATAAGTCAAAATCGGCCTGCCAAATACAAACAC
261216 AATTACATCATAAATAAATGGAACATGTCAATAAATAAATAAACCAAATTACTAAA
131 AATTACATCATAAATAAATGGAACATGTCAATAAATAAATAAACCAAATTACTAAA
*
261272 -T--------T-A--GGGGGCGTCAGCAGGTTCCATGAGAATAAAATCCGAAGAAGACATGCCAG
1 TTCCCGCCACTAACCAGGGGCGTCAGCAGGTTCCATGAGAATAAAATCCGAAGAAGACATGCCAG
261325 AGCCAAACTTCCCGTCATTAAAGCAATCAGTACATAAGTCAAAATCGGCCTGCC-AATACAAACA
66 AGCCAAACTTCCCGTCATTAAAGCAATCA-TACATAAGTCAAAATCGGCCTGCCAAATACAAACA
261389 CAATTACATCATAAATAAATGGAACATGTCAATAAATAAATAAACCAAATTACTAAA
130 CAATTACATCATAAATAAATGGAACATGTCAATAAATAAATAAACCAAATTACTAAA
261446 TT
1 TT
261448 AGTTACACTT
Statistics
Matches: 359, Mismatches: 1, Indels: 15
0.96 0.00 0.04
Matches are distributed among these distances:
174 145 0.40
175 25 0.07
176 1 0.00
177 1 0.00
185 1 0.00
186 186 0.52
ACGTcount: A:0.43, C:0.23, G:0.14, T:0.20
Consensus pattern (186 bp):
TTCCCGCCACTAACCAGGGGCGTCAGCAGGTTCCATGAGAATAAAATCCGAAGAAGACATGCCAG
AGCCAAACTTCCCGTCATTAAAGCAATCATACATAAGTCAAAATCGGCCTGCCAAATACAAACAC
AATTACATCATAAATAAATGGAACATGTCAATAAATAAATAAACCAAATTACTAAA
Found at i:266137 original size:123 final size:121
Alignment explanation
Indices: 265918--266266 Score: 335
Period size: 123 Copynumber: 2.8 Consensus size: 121
265908 GACCGTTAGG
* * * * * *
265918 CTCGGCCTCGATTCAAAATCATTGGTGAATGACTTCTTCTCTCGTTTAAGACCAGCATCGTCGCC
1 CTCGGCCTTGGTTCAAAATCACTGGTGAATGA-TTCTTCTCTCCTTTAAGACCAACATCATCG-C
* *
265983 AG-CATAAAACATTACGCTTGGCCTCGATTCAAAATCACTACCCACATAAGCCT-TTACA
64 AGCCAT-AGACATTACGCTTGGCCTCGGTTCAAAATCACTACCCACATAAG-CTGTTACA
266041 CTCGGCCTTGGTTCAAAATCACTGGTGAATGATGTCTTCTCTCCTTTAAGACCAACATCATCGTC
1 CTCGGCCTTGGTTCAAAATCACTGGTGAATGAT-TCTTCTCTCCTTTAAGACCAACATCATCG-C
* ** **
266106 -GCCATAGACTGTTACGCTTGGCCTCGGTTCAAAATCACTACTGACATAAGCTGTTATG
64 AGCCATAGAC-ATTACGCTTGGCCTCGGTTCAAAATCACTACCCACATAAGCTGTTACA
* * * * * * *
266164 CTTGGCCTTAGCTCAAAAGTACCACTAGTGAATGGTTTCTTATTTCCTTTAAGACCAACATCATC
1 CTCGGCCTTGGTTCAAAA-T--CACTGGTGAAT-GATTCTTCTCTCCTTTAAGACCAACATCATC
** * * * *
266229 GCTTCCATAGGCCCTTACGCTTGGCCTTGGCTCAAAAT
62 GCAGCCATA-GACATTACGCTTGGCCTCGGTTCAAAAT
266267 ATTTGGTGAA
Statistics
Matches: 190, Mismatches: 26, Indels: 17
0.82 0.11 0.07
Matches are distributed among these distances:
122 7 0.04
123 113 0.59
124 1 0.01
125 1 0.01
126 64 0.34
127 4 0.02
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.30
Consensus pattern (121 bp):
CTCGGCCTTGGTTCAAAATCACTGGTGAATGATTCTTCTCTCCTTTAAGACCAACATCATCGCAG
CCATAGACATTACGCTTGGCCTCGGTTCAAAATCACTACCCACATAAGCTGTTACA
Found at i:266333 original size:81 final size:81
Alignment explanation
Indices: 266191--266347 Score: 179
Period size: 81 Copynumber: 1.9 Consensus size: 81
266181 AGTACCACTA
* * * ** * *
266191 GTGAATGGTTTCTTATTTCCTTTAAGACCAACATCATCGCTTCCATAGGCCCTTACGCTTGGCCT
1 GTGAATGGCTTCTTATCTCATTTAAGACCAACATCATCGCCACCATAAGCCCTTACCCTTGGCCT
*
266256 TGGCTCAAAATATTTG
66 CGGCTCAAAATATTTG
* * *** *
266272 GTGAATGGCTTCTTCTCTCATTTAAGACCAACATCATTGCCACCATAAGTTGTTACCCTTGGTCT
1 GTGAATGGCTTCTTATCTCATTTAAGACCAACATCATCGCCACCATAAGCCCTTACCCTTGGCCT
*
266337 CGGTTCAAAAT
66 CGGCTCAAAAT
266348 CACTACTGAC
Statistics
Matches: 61, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
81 61 1.00
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.35
Consensus pattern (81 bp):
GTGAATGGCTTCTTATCTCATTTAAGACCAACATCATCGCCACCATAAGCCCTTACCCTTGGCCT
CGGCTCAAAATATTTG
Found at i:266376 original size:42 final size:42
Alignment explanation
Indices: 266315--266394 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
266305 TCATTGCCAC
*
266315 CATAAGTTGTTACCCTTGGTCTCGGTTCAAAATCACTACTGA
1 CATAAGTTGTTACCCTTGGTCTCAGTTCAAAATCACTACTGA
*** * *
266357 CATAAGTTGTTATGTTTGGTCTTAGTTGAAAATCACTA
1 CATAAGTTGTTACCCTTGGTCTCAGTTCAAAATCACTA
266395 GTGAATGATT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (42 bp):
CATAAGTTGTTACCCTTGGTCTCAGTTCAAAATCACTACTGA
Found at i:266577 original size:80 final size:79
Alignment explanation
Indices: 266424--266641 Score: 210
Period size: 80 Copynumber: 2.7 Consensus size: 79
266414 TTTTTGTCCT
* * * * * *
266424 TTAAGACCAGAATCATAGCCTCCATAGGCGGTTACGCTTAGCCAGTGTTCAAAATCATTGGTGAA
1 TTAAGACCAGCATCATTGCCTCCATAGGCCGTTACGCTTGGCTAG-GTTCAAAATCATTAGTGAA
* *
266489 TGGCTTTTT-T-TTCG
65 AGACTTTTTCTCTT-G
* * *
266503 TGTAAGACCAGCATCATTGCCACCATAAGCCGTTACGCTTGGTCTTGGTTCAAAATCATTAGTGA
1 T-TAAGACCAGCATCATTGCCTCCATAGGCCGTTACGCTTGG-CTAGGTTCAAAATCATTAGTGA
*
266568 AAGATTTTTTCTCTTG
64 AAGACTTTTTCTCTTG
* *
266584 TTGAAGACC-GCCATCATTGCCTCCATAGGACATTACGCTTGGCCTCA-GTTCAAAATCA
1 TT-AAGACCAG-CATCATTGCCTCCATAGGCCGTTACGCTTGG-CT-AGGTTCAAAATCA
266642 CCGGTGAATG
Statistics
Matches: 114, Mismatches: 18, Indels: 12
0.79 0.12 0.08
Matches are distributed among these distances:
79 1 0.01
80 60 0.53
81 51 0.45
82 2 0.02
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (79 bp):
TTAAGACCAGCATCATTGCCTCCATAGGCCGTTACGCTTGGCTAGGTTCAAAATCATTAGTGAAA
GACTTTTTCTCTTG
Found at i:266672 original size:81 final size:79
Alignment explanation
Indices: 266420--266677 Score: 234
Period size: 81 Copynumber: 3.2 Consensus size: 79
266410 ACTCTTTTTG
* * * ***
266420 TCCTTTAAGACCAGAATCATAGCCTCCATAGGCGGTTACGCTTAGCCAGTGTTCAAAATCATTGG
1 TCCTTTAAGACCAGCATCATTGCCTCCATAGGC-GTTACGCTTGGCCTCAGTTCAAAATCATTGG
*
266485 TGAATGGCTTTTT-TT
65 TGAAT-GTTTTTTCTT
* * * * * ** *
266500 TCGTGTAAGACCAGCATCATTGCCACCATAAGCCGTTACGCTTGGTCTTGGTTCAAAATCATTAG
1 TCCTTTAAGACCAGCATCATTGCCTCCAT-AGGCGTTACGCTTGGCCTCAGTTCAAAATCATTGG
*
266565 TGAAAGATTTTTTCTCT
65 TGAATG-TTTTTTCT-T
* * * **
266582 T-GTTGAAGACC-GCCATCATTGCCTCCATAGGACATTACGCTTGGCCTCAGTTCAAAATCACCG
1 TCCTTTAAGACCAG-CATCATTGCCTCCATAGG-CGTTACGCTTGGCCTCAGTTCAAAATCATTG
266645 GTGAATGTTTTCTTCTT
64 GTGAATGTTTT-TTCTT
266662 TCCTTTAAGACCAGCA
1 TCCTTTAAGACCAGCA
266678 ACATCCCCGC
Statistics
Matches: 141, Mismatches: 28, Indels: 17
0.76 0.15 0.09
Matches are distributed among these distances:
79 1 0.01
80 67 0.48
81 70 0.50
82 3 0.02
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.33
Consensus pattern (79 bp):
TCCTTTAAGACCAGCATCATTGCCTCCATAGGCGTTACGCTTGGCCTCAGTTCAAAATCATTGGT
GAATGTTTTTTCTT
Found at i:267949 original size:3 final size:3
Alignment explanation
Indices: 267941--268008 Score: 82
Period size: 3 Copynumber: 22.0 Consensus size: 3
267931 TCATTTAAGC
** **
267941 TTA TTA TTA TTA TTA AAA TTA AAA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
267989 TTA TTA TATA TTA TTTA TTA
1 TTA TTA T-TA TTA -TTA TTA
268009 AAAATTACAA
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
3 49 0.89
4 6 0.11
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:269127 original size:22 final size:22
Alignment explanation
Indices: 269086--269153 Score: 118
Period size: 22 Copynumber: 3.0 Consensus size: 22
269076 CTCGTATAAA
*
269086 TGCACCAAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
269109 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
269131 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
269153 T
1 T
269154 ATGTCCATAA
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 33 0.75
23 11 0.25
ACGTcount: A:0.28, C:0.28, G:0.25, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:269412 original size:30 final size:30
Alignment explanation
Indices: 269367--269425 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
269357 ATCGCGTAGT
* *
269367 CATATTATTTCCATACCTTTATCACATAGA
1 CATATCATTTACATACCTTTATCACATAGA
269397 CATATCATTTACATACCTTTATCACATAG
1 CATATCATTTACATACCTTTATCACATAG
269426 CTCATATAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.34, C:0.24, G:0.03, T:0.39
Consensus pattern (30 bp):
CATATCATTTACATACCTTTATCACATAGA
Found at i:269935 original size:66 final size:67
Alignment explanation
Indices: 269788--269938 Score: 223
Period size: 67 Copynumber: 2.3 Consensus size: 67
269778 TTTTTCTCAT
* * *
269788 GGGGGAATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGA
1 GGGGGTATCGGTT-CCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGA
269853 TGA
65 TGA
* * * *
269856 GGGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATTCAT-TTCGTT
1 GGGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGAT
269920 GA
66 GA
269922 GGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
269939 TCGAATGAGT
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
66 23 0.30
67 41 0.54
68 12 0.16
ACGTcount: A:0.17, C:0.27, G:0.28, T:0.27
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGAT
GA
Found at i:269951 original size:67 final size:67
Alignment explanation
Indices: 269788--269960 Score: 206
Period size: 67 Copynumber: 2.6 Consensus size: 67
269778 TTTTTCTCAT
* * * *
269788 GGGGGAATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGA
1 GGGGGTATCGGTT-CCCCCCTGGGAGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGA
269853 TGA
65 TGA
* * * * *
269856 GGGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATTCAT-TTCGTT
1 GGGGGTATCGGTTCCCCCCTGGGAGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGAT
269920 GA
66 GA
* *
269922 GGGGGTATCGGTTCCCCTC-GAATGAGTACCGATTCCCCT
1 GGGGGTATCGGTTCCCCCCTG--GGAGTACCGATTCCCCT
269961 AACCCAGAAA
Statistics
Matches: 93, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
65 1 0.01
66 24 0.26
67 56 0.60
68 12 0.13
ACGTcount: A:0.18, C:0.28, G:0.27, T:0.27
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCCCTGGGAGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGAT
GA
Found at i:281151 original size:14 final size:15
Alignment explanation
Indices: 281132--281161 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
281122 CAACAAAGAA
281132 AGAAGAA-AAAAAAG
1 AGAAGAAGAAAAAAG
281146 AGAAGAAGAAAAAAG
1 AGAAGAAGAAAAAAG
281161 A
1 A
281162 AAATTGAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (15 bp):
AGAAGAAGAAAAAAG
Found at i:281153 original size:17 final size:16
Alignment explanation
Indices: 281126--281159 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
281116 CTTATCCAAC
281126 AAAGAAAGAAGAAAAA
1 AAAGAAAGAAGAAAAA
281142 AAAGAGAAGAAGAAAAA
1 AAAGA-AAGAAGAAAAA
281159 A
1 A
281160 GAAAATTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (16 bp):
AAAGAAAGAAGAAAAA
Found at i:283519 original size:83 final size:83
Alignment explanation
Indices: 283380--283746 Score: 603
Period size: 83 Copynumber: 4.4 Consensus size: 83
283370 TGTGATATCC
283380 CAGAACCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAG
1 CAGAACCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAG
283445 TTATCTGATCTGG-TTGAA
66 TTATCTGATCTGGTTTG-A
* * *
283463 CAGAACCAATCATTGAATTCAGAAGATAAATTTGCCAATATCATCTTCTGGAAGTGTTCTTTGAG
1 CAGAACCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAG
283528 TTATCTGATCTGG-TTGAA
66 TTATCTGATCTGGTTTG-A
* * * *
283546 CAGAACCAATCATTGAATTCAGAAGATAAATTTGCCAATATCATCTTCTGGAAGTGTTCTTTGAA
1 CAGAACCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAG
*
283611 TTATCTGATCTGGTTTGG
66 TTATCTGATCTGGTTTGA
283629 CAGAACCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAG
1 CAGAACCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAG
283694 TTATCTGATCTGGTTTGA
66 TTATCTGATCTGGTTTGA
* * *
283712 CAAAACCAATCATTAAATTTGGAAGATGAATTTGC
1 CAGAACCAATCATTGAATTTAGAAGATGAATTTGC
283747 TCATAGTAGA
Statistics
Matches: 270, Mismatches: 13, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
83 267 0.99
84 3 0.01
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (83 bp):
CAGAACCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAG
TTATCTGATCTGGTTTGA
Found at i:286452 original size:22 final size:22
Alignment explanation
Indices: 286423--286477 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
286413 ATCTACACTC
286423 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
286445 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
286467 TTCAAAGATGA
1 TTCAAAGATGA
286478 AAGCTTTATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:287401 original size:76 final size:76
Alignment explanation
Indices: 287152--288254 Score: 2047
Period size: 76 Copynumber: 14.6 Consensus size: 76
287142 CTATTTCTCA
* * *
287152 CATCTGTAAGTCCTTCAGTGCATAATGTTTCTAAAAAGCCTTCGGGAGC-TTTTGAGGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
287216 ATCCTTC-GGT
66 AACCTTCGGGT
287226 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
287290 ATCCTTCGGGT
66 AACCTTCGGGT
287301 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
287366 AACCTTCGGGT
66 AACCTTCGGGT
287377 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
287442 AACCTTCGGGT
66 AACCTTCGGGT
287453 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
287518 AACCTTCGGGT
66 AACCTTCGGGT
287529 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
287594 AACCTTCGGGT
66 AACCTTCGGGT
287605 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
287670 AACCTTCGGGT
66 AACCTTCGGGT
*
287681 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGACGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
287746 AACCTTCGGGT
66 AACCTTCGGGT
287757 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
287822 AACCTTCGGGT
66 AACCTTCGGGT
287833 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
287898 AACCTTCGGGT
66 AACCTTCGGGT
287909 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
287974 AACCTTCGGGT
66 AACCTTCGGGT
287985 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
288049 AACCTTCGGGT
66 AACCTTCGGGT
* *
288060 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTGTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
288125 AGCCTTCGGGT
66 AACCTTCGGGT
*
288136 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGTAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
288201 AGCCTTAGGGT
66 AACCTTCGGGT
*
288212 CATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAA-CCTTCGG
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGG
288255 TCATCTGTAA
Statistics
Matches: 1012, Mismatches: 14, Indels: 6
0.98 0.01 0.01
Matches are distributed among these distances:
74 75 0.07
75 130 0.13
76 807 0.80
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AACCTTCGGGT
Found at i:288265 original size:44 final size:44
Alignment explanation
Indices: 288189--288334 Score: 247
Period size: 44 Copynumber: 3.3 Consensus size: 44
288179 GGTAGCTTTT
* *
288189 TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAACCTT-CGGTCATCTGTAAGTCCTTCAGTGCA
288234 TGATGTTTTCAAAACCTTCGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGTCATCTGTAAGTCCTTCAGTGCA
* *
288278 TGATGTTTTCAAAACCTTCGGTTATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGTCATCTGTAAGTCCTTCAGTGCA
288322 TGATGTTTTCAAA
1 TGATGTTTTCAAA
288335 CATTTCCATC
Statistics
Matches: 97, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
44 80 0.82
45 17 0.18
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.37
Consensus pattern (44 bp):
TGATGTTTTCAAAACCTTCGGTCATCTGTAAGTCCTTCAGTGCA
Found at i:288295 original size:25 final size:25
Alignment explanation
Indices: 288223--288296 Score: 70
Period size: 25 Copynumber: 3.2 Consensus size: 25
288213 ATCTGTAAGT
288223 CCTTCAGTGCATGATGTTTTCAAAA
1 CCTTCAGTGCATGATGTTTTCAAAA
* * **
288248 CCTTCGGT-CAT-CTG---T-AAGT
1 CCTTCAGTGCATGATGTTTTCAAAA
288267 CCTTCAGTGCATGATGTTTTCAAAA
1 CCTTCAGTGCATGATGTTTTCAAAA
288292 CCTTC
1 CCTTC
288297 GGTTATCTGT
Statistics
Matches: 35, Mismatches: 8, Indels: 12
0.64 0.15 0.22
Matches are distributed among these distances:
19 9 0.26
20 4 0.11
21 2 0.06
23 2 0.06
24 4 0.11
25 14 0.40
ACGTcount: A:0.23, C:0.24, G:0.16, T:0.36
Consensus pattern (25 bp):
CCTTCAGTGCATGATGTTTTCAAAA
Found at i:288469 original size:3 final size:3
Alignment explanation
Indices: 288461--288528 Score: 82
Period size: 3 Copynumber: 22.0 Consensus size: 3
288451 TCATTTAAGC
** **
288461 TTA TTA TTA TTA TTA AAA TTA AAA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
288509 TTA TTA TATA TTA TTTA TTA
1 TTA TTA T-TA TTA -TTA TTA
288529 AAAATTACAA
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
3 49 0.89
4 6 0.11
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:297943 original size:26 final size:27
Alignment explanation
Indices: 297907--297962 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
297897 ATGGTTTTCG
* *
297907 TAAATCCGACATTAAATATTAAT-AAT
1 TAAATCCGACATCAAACATTAATAAAT
*
297933 TAAATCCGACATCAAGCATTAATAAAT
1 TAAATCCGACATCAAACATTAATAAAT
297960 TAA
1 TAA
297963 TAAATTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 20 0.77
27 6 0.23
ACGTcount: A:0.50, C:0.14, G:0.05, T:0.30
Consensus pattern (27 bp):
TAAATCCGACATCAAACATTAATAAAT
Found at i:299750 original size:15 final size:14
Alignment explanation
Indices: 299732--299761 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
299722 TGAACAATAT
299732 ATATGTATTTATAAA
1 ATATGTATTTA-AAA
299747 ATATGTATTTAAAA
1 ATATGTATTTAAAA
299761 A
1 A
299762 GCTATCCGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (14 bp):
ATATGTATTTAAAA
Found at i:299921 original size:36 final size:35
Alignment explanation
Indices: 299867--300195 Score: 169
Period size: 35 Copynumber: 9.5 Consensus size: 35
299857 TTTAAATATA
299867 ATTTTTG-AAA-ATAT-ATATATGTTTTGAAAACG
1 ATTTTTGAAAACATATAATATATGTTTTGAAAACG
299899 TATTTTTGAAAACATATAATATATAGTTTTTGAAAAC-
1 -ATTTTTGAAAACATATAATATAT-G-TTTTGAAAACG
299936 A----T------ATATAATATAGT-TTTTGAAAACG
1 ATTTTTGAAAACATATAATATA-TGTTTTGAAAACG
* *
299961 TATTTTTGAAAACATATAATATATAGTTTTTTAAAATG
1 -ATTTTTGAAAACATATAATATAT-G-TTTTGAAAACG
* *
299999 A-TTTTGAAAACGTATAATATATAGTTTTTAAAACG
1 ATTTTTGAAAACATATAATATAT-GTTTTGAAAACG
* * * * *
300034 -GTTTTGTAAACGTATAATATATTTTTTTAAAACCG
1 ATTTTTGAAAACATATAATATATGTTTTGAAAA-CG
* * * *
300069 -GTTTTGAAAACGTATAATATATGATTTTTTAAAAATG
1 ATTTTTGAAAACATATAATATATG---TTTTGAAAACG
* *
300106 GTTTTTGGAACACATTTATAATATA-GTTTT-AAAACG
1 ATTTTT-GAAAACA--TATAATATATGTTTTGAAAACG
* * * *
300142 TATTTTTAAAAACATATATATATAGTTTTTTAAAAATG
1 -ATTTTTGAAAACATATA-ATATA-TGTTTTGAAAACG
*
300180 -TTTTTGAAAACGTATA
1 ATTTTTGAAAACATATA
300196 TAATTTATAT
Statistics
Matches: 240, Mismatches: 21, Indels: 67
0.73 0.06 0.20
Matches are distributed among these distances:
24 10 0.04
26 11 0.05
27 1 0.00
30 1 0.00
32 1 0.00
33 7 0.03
34 16 0.07
35 63 0.26
36 63 0.26
37 16 0.07
38 36 0.15
39 5 0.02
40 1 0.00
41 9 0.04
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.44
Consensus pattern (35 bp):
ATTTTTGAAAACATATAATATATGTTTTGAAAACG
Found at i:299933 original size:24 final size:24
Alignment explanation
Indices: 299901--299959 Score: 102
Period size: 24 Copynumber: 2.5 Consensus size: 24
299891 TGAAAACGTA
299901 TTTTTGAAAACATATA-ATATATAG
1 TTTTTGAAAACATATATA-ATATAG
299925 TTTTTGAAAACATATATAATATAG
1 TTTTTGAAAACATATATAATATAG
299949 TTTTTGAAAAC
1 TTTTTGAAAAC
299960 GTATTTTTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 33 0.97
25 1 0.03
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.42
Consensus pattern (24 bp):
TTTTTGAAAACATATATAATATAG
Found at i:299959 original size:62 final size:58
Alignment explanation
Indices: 299862--299996 Score: 209
Period size: 62 Copynumber: 2.3 Consensus size: 58
299852 ATAATTTTAA
*
299862 ATATAATTTTTG-AAAATATATATATGTTTTGAAAACGTATTTTTGAAAACATATAAT
1 ATATAGTTTTTGAAAAATATATATATGTTTTGAAAACGTATTTTTGAAAACATATAAT
299919 ATATAGTTTTTGAAAACATATATAATATAGTTTTTGAAAACGTATTTTTGAAAACATATAAT
1 ATATAGTTTTTGAAAA-ATATAT-ATAT-G-TTTTGAAAACGTATTTTTGAAAACATATAAT
*
299981 ATATAGTTTTTTAAAA
1 ATATAGTTTTTGAAAA
299997 TGATTTTGAA
Statistics
Matches: 71, Mismatches: 2, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
57 11 0.15
58 3 0.04
59 6 0.08
60 4 0.06
61 1 0.01
62 46 0.65
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.44
Consensus pattern (58 bp):
ATATAGTTTTTGAAAAATATATATATGTTTTGAAAACGTATTTTTGAAAACATATAAT
Found at i:299967 original size:38 final size:37
Alignment explanation
Indices: 299925--300199 Score: 209
Period size: 36 Copynumber: 7.5 Consensus size: 37
299915 TAATATATAG
*
299925 TTTTTGAAAACATATATAATATAGTTTTTGAAAACGT
1 TTTTTGAAAACATATATAATATAGTTTTTTAAAACGT
*
299962 ATTTTTGAAAACATATA-ATATATAGTTTTTTAAAATG-
1 -TTTTTGAAAACATATATA-ATATAGTTTTTTAAAACGT
* *
299999 ATTTTGAAAACGTATA-ATATATAG-TTTTTAAAACG-
1 TTTTTGAAAACATATATA-ATATAGTTTTTTAAAACGT
* * * *
300034 GTTTTGTAAAC--GTATAATATATTTTTTTAAAACCG-
1 TTTTTGAAAACATATATAATATAGTTTTTTAAAA-CGT
* * *
300069 GTTTTGAAAAC--GTATAATATATGATTTTTTAAAAATGGT
1 TTTTTGAAAACATATATAATATA-G-TTTTTT-AAAA-CGT
* * *
300108 TTTTGGAACACATTTATAATATAG--TTTTAAAACGT
1 TTTTTGAAAACATATATAATATAGTTTTTTAAAACGT
* *
300143 ATTTTTAAAAACATATAT-ATATAGTTTTTTAAAA-AT
1 -TTTTTGAAAACATATATAATATAGTTTTTTAAAACGT
*
300179 GTTTTTGAAAACGTATATAAT
1 -TTTTTGAAAACATATATAAT
300200 TTATATAGTT
Statistics
Matches: 197, Mismatches: 26, Indels: 29
0.78 0.10 0.12
Matches are distributed among these distances:
33 7 0.04
34 10 0.05
35 49 0.25
36 55 0.28
37 21 0.11
38 37 0.19
39 8 0.04
40 1 0.01
41 9 0.05
ACGTcount: A:0.40, C:0.05, G:0.11, T:0.44
Consensus pattern (37 bp):
TTTTTGAAAACATATATAATATAGTTTTTTAAAACGT
Found at i:300196 original size:36 final size:36
Alignment explanation
Indices: 299924--300197 Score: 229
Period size: 35 Copynumber: 7.5 Consensus size: 36
299914 ATAATATATA
* *
299924 GTTTTTGAAAACATATATAATATAGTTTTTGAAAACGT
1 GTTTTTGAAAACATATAT-ATATAGTTTTTTAAAA-AT
*
299962 ATTTTTGAAAACATATAATATATAGTTTTTT-AAAAT
1 GTTTTTGAAAACATAT-ATATATAGTTTTTTAAAAAT
* * *
299998 GATTTTGAAAACGTATAATATATAG-TTTTT-AAAAC
1 GTTTTTGAAAACATAT-ATATATAGTTTTTTAAAAAT
* * * * **
300033 GGTTTTGTAAACGTATA-ATATATTTTTTTAAAACC
1 GTTTTTGAAAACATATATATATAGTTTTTTAAAAAT
* *
300068 GGTTTTGAAAACGTATA-ATATATGATTTTTTAAAAAT
1 GTTTTTGAAAACATATATATATA-G-TTTTTTAAAAAT
* * *
300105 GGTTTTTGGAACACATTTATAATATAG--TTTTAAAACGT
1 -GTTTTT-GAAAACATATAT-ATATAGTTTTTTAAAA-AT
* *
300143 ATTTTTAAAAACATATATATATAGTTTTTTAAAAAT
1 GTTTTTGAAAACATATATATATAGTTTTTTAAAAAT
*
300179 GTTTTTGAAAACGTATATA
1 GTTTTTGAAAACATATATA
300198 ATTTATATAG
Statistics
Matches: 196, Mismatches: 28, Indels: 26
0.78 0.11 0.10
Matches are distributed among these distances:
33 5 0.03
34 6 0.03
35 54 0.28
36 49 0.25
37 34 0.17
38 32 0.16
39 10 0.05
40 1 0.01
41 5 0.03
ACGTcount: A:0.40, C:0.05, G:0.11, T:0.44
Consensus pattern (36 bp):
GTTTTTGAAAACATATATATATAGTTTTTTAAAAAT
Found at i:300296 original size:21 final size:21
Alignment explanation
Indices: 300248--300296 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
300238 ATACATATTA
*
300248 TTATTAGTATTTTATTTTTCGT
1 TTATTAATATTTTATTTTTC-T
300270 TT-TTAATATTTTATTTGTT-T
1 TTATTAATATTTTATTT-TTCT
300290 TTATTAA
1 TTATTAA
300297 CTTATCATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 3 0.12
21 17 0.71
22 4 0.17
ACGTcount: A:0.22, C:0.02, G:0.06, T:0.69
Consensus pattern (21 bp):
TTATTAATATTTTATTTTTCT
Found at i:303738 original size:25 final size:25
Alignment explanation
Indices: 303690--303739 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
303680 AGGGTAACTC
* *
303690 TTTTATGGGATTTACTGCAGTATGA
1 TTTTATGAGATTTACTGCACTATGA
*
303715 TTTTATGAGATTTACTGGACTATGA
1 TTTTATGAGATTTACTGCACTATGA
303740 CTTGTTTAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.44
Consensus pattern (25 bp):
TTTTATGAGATTTACTGCACTATGA
Found at i:309966 original size:29 final size:29
Alignment explanation
Indices: 309924--309989 Score: 123
Period size: 29 Copynumber: 2.3 Consensus size: 29
309914 CCGCTGCTAT
309924 TTTCGTAAATATTTTTAAAAGGGTGTTAG
1 TTTCGTAAATATTTTTAAAAGGGTGTTAG
*
309953 TTTCGTAAATATTTTTAAAAGGGTGTTAT
1 TTTCGTAAATATTTTTAAAAGGGTGTTAG
309982 TTTCGTAA
1 TTTCGTAA
309990 TTAATTTCTG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.30, C:0.05, G:0.18, T:0.47
Consensus pattern (29 bp):
TTTCGTAAATATTTTTAAAAGGGTGTTAG
Found at i:312865 original size:2 final size:2
Alignment explanation
Indices: 312858--312882 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
312848 ACATTTGATT
312858 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 T
312883 TGAGTCTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:316291 original size:9 final size:9
Alignment explanation
Indices: 316277--316337 Score: 59
Period size: 10 Copynumber: 6.3 Consensus size: 9
316267 AGGGCTGGAA
316277 ACCGGTTTG
1 ACCGGTTTG
*
316286 ACCGGTTTTCA
1 ACCGG-TTT-G
316297 ACCGGTTCTG
1 ACCGGTT-TG
*
316307 ACCGGTTCG
1 ACCGGTTTG
316316 AACCGGTTTG
1 -ACCGGTTTG
*
316326 ACCGGTCTG
1 ACCGGTTTG
316335 ACC
1 ACC
316338 CGATCCGACC
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
9 17 0.40
10 20 0.47
11 6 0.14
ACGTcount: A:0.15, C:0.30, G:0.28, T:0.28
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:316301 original size:20 final size:20
Alignment explanation
Indices: 316276--316331 Score: 80
Period size: 20 Copynumber: 2.8 Consensus size: 20
316266 GAGGGCTGGA
316276 AACCGGTTTGACCGGTTTTC-
1 AACCGGTTTGACCGG-TTTCG
316296 AACCGGTTCTGACCGG-TTCG
1 AACCGGTT-TGACCGGTTTCG
316316 AACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
316332 CTGACCCGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.30
20 16 0.48
21 7 0.21
ACGTcount: A:0.16, C:0.27, G:0.29, T:0.29
Consensus pattern (20 bp):
AACCGGTTTGACCGGTTTCG
Found at i:316312 original size:10 final size:10
Alignment explanation
Indices: 316277--316337 Score: 58
Period size: 9 Copynumber: 6.3 Consensus size: 10
316267 AGGGCTGGAA
316277 ACCGGTT-TG
1 ACCGGTTCTG
* *
316286 ACCGGTTTTCA
1 ACCGGTTCT-G
316297 ACCGGTTCTG
1 ACCGGTTCTG
316307 ACCGGTTC-G
1 ACCGGTTCTG
316316 AACCGGTT-TG
1 -ACCGGTTCTG
316326 ACCGG-TCTG
1 ACCGGTTCTG
316335 ACC
1 ACC
316338 CGATCCGACC
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
8 1 0.02
9 18 0.41
10 17 0.39
11 8 0.18
ACGTcount: A:0.15, C:0.30, G:0.28, T:0.28
Consensus pattern (10 bp):
ACCGGTTCTG
Found at i:323598 original size:17 final size:17
Alignment explanation
Indices: 323576--323610 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
323566 CCCGACCCGA
323576 CCGACCCGACCGTTGAC
1 CCGACCCGACCGTTGAC
323593 CCGACCCGACCGTTGAC
1 CCGACCCGACCGTTGAC
323610 C
1 C
323611 GTTGACCGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.49, G:0.23, T:0.11
Consensus pattern (17 bp):
CCGACCCGACCGTTGAC
Found at i:328056 original size:21 final size:21
Alignment explanation
Indices: 328030--328078 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
328020 ACACCACGAA
* *
328030 CGACATTGTCTTCAAAGACTT
1 CGACATCGTCTTCAAAAACTT
328051 CGACATCGTCTTCAAAAACTT
1 CGACATCGTCTTCAAAAACTT
328072 CGACATC
1 CGACATC
328079 TTCCTCATCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.31, C:0.29, G:0.12, T:0.29
Consensus pattern (21 bp):
CGACATCGTCTTCAAAAACTT
Found at i:328694 original size:18 final size:16
Alignment explanation
Indices: 328670--328714 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 16
328660 AATTAAATAA
328670 AATAATTAATAATTTTT
1 AATAATTAAT-ATTTTT
328687 ATATAATTAAT-TTTTT
1 A-ATAATTAATATTTTT
*
328703 AAAAATTAATAT
1 AATAATTAATAT
328715 ATAATATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 8 0.32
16 7 0.28
17 1 0.04
18 9 0.36
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
AATAATTAATATTTTT
Found at i:328748 original size:29 final size:27
Alignment explanation
Indices: 328707--328783 Score: 68
Period size: 29 Copynumber: 2.8 Consensus size: 27
328697 TTTTTTAAAA
*
328707 ATTAATA-TATAATATTTAAATG-TATTT
1 ATTAATATTTTAATATTTAAA-GATA-TT
*
328734 ATTAATATTTTTAATAATATAAAGATATT
1 ATTAATA-TTTTAAT-ATTTAAAGATATT
* *
328763 ATTATTATTTTAATAATTAAA
1 ATTAATATTTTAATATTTAAA
328784 AAACAGAACT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
27 12 0.29
28 7 0.17
29 14 0.34
30 8 0.20
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.51
Consensus pattern (27 bp):
ATTAATATTTTAATATTTAAAGATATT
Found at i:329761 original size:28 final size:28
Alignment explanation
Indices: 329729--329782 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
329719 TCTCATAAAA
329729 TGTAATATTATCTAAGAAAATAAGAGGT
1 TGTAATATTATCTAAGAAAATAAGAGGT
329757 TGTAATATTATCTAAGAAAATAAGAG
1 TGTAATATTATCTAAGAAAATAAGAG
329783 TTAATGAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.48, C:0.04, G:0.17, T:0.31
Consensus pattern (28 bp):
TGTAATATTATCTAAGAAAATAAGAGGT
Found at i:335984 original size:29 final size:28
Alignment explanation
Indices: 335911--336000 Score: 99
Period size: 29 Copynumber: 3.1 Consensus size: 28
335901 CTAAAGTATT
* *
335911 TTTTTGGTCAAAGTAAGTACTTAAACTTA
1 TTTTTGGTCAAAATAAGTACTTAAA-ATA
*
335940 TCCTTTTGGTCAAAATAAGTACATAAAATA
1 T--TTTTGGTCAAAATAAGTACTTAAAATA
* *
335970 TTTGTTGGTCAAAATAGGTACTTAAAGTA
1 TTT-TTGGTCAAAATAAGTACTTAAAATA
335999 TT
1 TT
336001 CAATCTTTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
28 2 0.04
29 25 0.48
30 3 0.06
31 22 0.42
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.39
Consensus pattern (28 bp):
TTTTTGGTCAAAATAAGTACTTAAAATA
Found at i:338508 original size:19 final size:18
Alignment explanation
Indices: 338486--338527 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
338476 AGTATGATCC
338486 ATTTA-TTAAAATTTAATT
1 ATTTACTTAAAA-TTAATT
*
338504 AATTTACTTCAAATTAATT
1 -ATTTACTTAAAATTAATT
338523 ATTTA
1 ATTTA
338528 AAGAAAATCC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 5 0.24
19 11 0.52
20 5 0.24
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (18 bp):
ATTTACTTAAAATTAATT
Found at i:339148 original size:2 final size:2
Alignment explanation
Indices: 339098--339134 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
339088 TAAAACATTA
339098 AT AT 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 AT AT A
339135 AGTCATGTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:340926 original size:43 final size:43
Alignment explanation
Indices: 340865--341064 Score: 138
Period size: 43 Copynumber: 4.5 Consensus size: 43
340855 GTTAGAGATA
340865 ACACGGTTCCTACGTGATGAGGAAGTCTAGCTATCTAAGGGTG
1 ACACGGTTCCTACGTGATGAGGAAGTCTAGCTATCTAAGGGTG
* * * *** *
340908 ACACGGCTCCTACGTGATGA-GAAG-ATA--TGGTCGGTGGATG
1 ACACGGTTCCTACGTGATGAGGAAGTCTAGCT-ATCTAAGGGTG
* * * * *
340948 ACATGGTTCCTACGTGATTAGGAAGTCTGGCCATCTTTAGGGAAGATG
1 ACACGGTTCCTACGTGATGAGGAAGTCTAGCTATC--TAAGG--G-TG
* * *
340996 ATAACATGGTTCCTACATGATGAGGAAGTCTGGCTATCTAAGGGTG
1 ---ACACGGTTCCTACGTGATGAGGAAGTCTAGCTATCTAAGGGTG
**
341042 ACACGACTCCTACGTGATGAGGA
1 ACACGGTTCCTACGTGATGAGGA
341065 GATTTAGTCA
Statistics
Matches: 118, Mismatches: 26, Indels: 26
0.69 0.15 0.15
Matches are distributed among these distances:
39 1 0.01
40 23 0.19
41 6 0.05
42 5 0.04
43 40 0.34
45 2 0.02
46 2 0.02
47 1 0.01
48 2 0.02
49 4 0.03
51 32 0.27
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.26
Consensus pattern (43 bp):
ACACGGTTCCTACGTGATGAGGAAGTCTAGCTATCTAAGGGTG
Found at i:341052 original size:134 final size:134
Alignment explanation
Indices: 340861--341388 Score: 645
Period size: 134 Copynumber: 4.0 Consensus size: 134
340851 TAAAGTTAGA
* *
340861 GATAACACGGTTCCTACGTGATGAGGAAGTCTAGCTATCTAAGGGTGACACGGCTCCTACGTGAT
1 GATAACACGGTTCCTACGTGATGAGGAAGTCTGGCTATCTAAGGGTGACACGACTCCTACGTGAT
* * * *
340926 GAGAAGATATGGTCGGTGGATGACATGGTTCCTACGTGATTAGGAAGTCTGGCCATCTTTAGGGA
66 GAGGAGATCTGGTCGGTGGATGACACGGTTCCTACGTGATAAGGAAGTCTGGCCATCTTTAGGGA
340991 AGAT
131 AGAT
* *
340995 GATAACATGGTTCCTACATGATGAGGAAGTCTGGCTATCTAAGGGTGACACGACTCCTACGTGAT
1 GATAACACGGTTCCTACGTGATGAGGAAGTCTGGCTATCTAAGGGTGACACGACTCCTACGTGAT
* * * * * * *
341060 GAGGAGATTTAGTCAGTGGATGATATGGTTCCTACGCGATAAGGAAGTCTGGTCATCTTTAGGGA
66 GAGGAGATCTGGTCGGTGGATGACACGGTTCCTACGTGATAAGGAAGTCTGGCCATCTTTAGGGA
341125 AGAT
131 AGAT
* * * *
341129 GATAACACGGTTCCTAC--GATGAGAAAGTCTGACTATTTAAGTGTGACACGGA-TCCTACGTGA
1 GATAACACGGTTCCTACGTGATGAGGAAGTCTGGCTATCTAAGGGTGACAC-GACTCCTACGTGA
* * * **
341191 TGAGGAGATCTGGTTGGTGGATGACACGGTTCCTACGTGATGAGGAATTCTAACCATCTTTAGGG
65 TGAGGAGATCTGGTCGGTGGATGACACGGTTCCTACGTGATAAGGAAGTCTGGCCATCTTTAGGG
341256 AAGAT
130 AAGAT
* * * * * * * * * * * *
341261 TATAACATGGTTCTTATGTGATGAGGATGGCTGGTTATTTAAGGTTGACATGGCTCCTACGTGTT
1 GATAACACGGTTCCTACGTGATGAGGAAGTCTGGCTATCTAAGGGTGACACGACTCCTACGTGAT
* * *
341326 GAGGAGATCT-GT-GGTAGATGACACGGTTCCTACGTGATAAGGACGGT-TGGCCATTTTTAGGG
66 GAGGAGATCTGGTCGGTGGATGACACGGTTCCTACGTGATAAGGA-AGTCTGGCCATCTTTAGGG
341388 A
130 A
341389 TAATGGTTTC
Statistics
Matches: 339, Mismatches: 50, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
132 151 0.45
133 6 0.02
134 182 0.54
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.28
Consensus pattern (134 bp):
GATAACACGGTTCCTACGTGATGAGGAAGTCTGGCTATCTAAGGGTGACACGACTCCTACGTGAT
GAGGAGATCTGGTCGGTGGATGACACGGTTCCTACGTGATAAGGAAGTCTGGCCATCTTTAGGGA
AGAT
Found at i:341522 original size:36 final size:35
Alignment explanation
Indices: 341457--341527 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 35
341447 CTCATAGATT
* *
341457 TTTGTTTCAAAAGAAATTTCTCAAGAGAGACAAAA
1 TTTGTTTCAAAAGAAATGTCTCAAAAGAGACAAAA
**
341492 TTTGTTTCAAGGGAAACTGTCTCAAAAGAGACAAAA
1 TTTGTTTCAAAAGAAA-TGTCTCAAAAGAGACAAAA
341528 CTTCAAGAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 14 0.45
36 17 0.55
ACGTcount: A:0.44, C:0.13, G:0.17, T:0.27
Consensus pattern (35 bp):
TTTGTTTCAAAAGAAATGTCTCAAAAGAGACAAAA
Found at i:341538 original size:17 final size:17
Alignment explanation
Indices: 341513--341547 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
341503 GGAAACTGTC
341513 TCAAAAGAGACAAAACT
1 TCAAAAGAGACAAAACT
*
341530 TCAAGAGAGACAAAACT
1 TCAAAAGAGACAAAACT
341547 T
1 T
341548 TGTTTCAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.54, C:0.17, G:0.14, T:0.14
Consensus pattern (17 bp):
TCAAAAGAGACAAAACT
Found at i:341616 original size:122 final size:118
Alignment explanation
Indices: 341412--341630 Score: 296
Period size: 122 Copynumber: 1.8 Consensus size: 118
341402 AGAAACCATC
*
341412 TCAAGGGAGACAAAATTTGTTTCAAGGGAAAAAGACTCATAGATTTTTGTTTCAAAAGAAATTTC
1 TCAAGAGAGACAAAATTTGTTTCAAGGGAAAAAGACTCATAGATTTTTGTTTCAAAAGAAATTTC
341477 TCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAAAGAGACAAAACT
66 TCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAAAGAGACAAAACT
* * * * * * *
341530 TCAAGAGAGACAAAACTTTGTTTCAATGGAAATAA-TCTCAATGGTTTTTATGTTTCTAGAGAGA
1 TCAAGAGAGACAAAA-TTTGTTTCAAGGGAAA-AAGACTC-ATAGATTTT-TGTTTCAAAAGAAA
**
341594 TTGTCTCAAGAGAGACAAAATTTGTTTTGAGGGAAAC
62 TT-TCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAC
341631 AATCTAAAAG
Statistics
Matches: 86, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
118 14 0.16
119 18 0.21
120 9 0.10
121 13 0.15
122 32 0.37
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (118 bp):
TCAAGAGAGACAAAATTTGTTTCAAGGGAAAAAGACTCATAGATTTTTGTTTCAAAAGAAATTTC
TCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAAAGAGACAAAACT
Found at i:341736 original size:38 final size:37
Alignment explanation
Indices: 341688--341765 Score: 102
Period size: 38 Copynumber: 2.1 Consensus size: 37
341678 GTTTTGAGGG
* *
341688 AAAACTGTCTCAAGGGAGACGAAATTTACTTTAAGAGA
1 AAAACTGTCTCAAGCGAGACAAAATTTACTTTAAGA-A
* **
341726 AAAATTGTCTCAAGCGAGACAAAATTTGTTTTAAGAA
1 AAAACTGTCTCAAGCGAGACAAAATTTACTTTAAGAA
341763 AAA
1 AAA
341766 TTTTCTCTAG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
37 4 0.11
38 31 0.89
ACGTcount: A:0.45, C:0.12, G:0.18, T:0.26
Consensus pattern (37 bp):
AAAACTGTCTCAAGCGAGACAAAATTTACTTTAAGAA
Found at i:349539 original size:23 final size:22
Alignment explanation
Indices: 349503--349584 Score: 87
Period size: 23 Copynumber: 3.7 Consensus size: 22
349493 AAACCCGACT
*
349503 GGTGTATCGATGCACATTCAAG
1 GGTGCATCGATGCACATTCAAG
* *
349525 GCGTGCATCGGTGCACCTTCATA-
1 G-GTGCATCGATGCACATTCA-AG
*
349548 -GTGAATCGATGCACATTCAAG
1 GGTGCATCGATGCACATTCAAG
349569 GGATGCATCGATGCAC
1 GG-TGCATCGATGCAC
349585 TAACTAGTGT
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
20 1 0.02
21 16 0.33
22 2 0.04
23 28 0.58
24 1 0.02
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (22 bp):
GGTGCATCGATGCACATTCAAG
Found at i:360026 original size:193 final size:194
Alignment explanation
Indices: 359411--360120 Score: 964
Period size: 194 Copynumber: 3.7 Consensus size: 194
359401 TAAAAGTGTT
* ** *
359411 GATAATATGATACATATATTTATTAAAGTATCGATACCTTCAACATATCTTGTAGCACTTTACCG
1 GATAATATGATACATATACTTATTAAAGTATCGATACCTTCAACATATCCGGTAGCTCTTTACCG
**
359476 GTTTTGTCATACTGAAACCGACTTTGTCATATTTTAACTTGTTATATTGTCATGTATCGATACAT
66 GTTTTGTCATACTGAAACCGGTTTTGTCATATTTTAACTTGTTATATTGTCATGTATCGATACAT
* *
359541 GTTTATAAAGTATCAATACTTTATAGGCGACATTATTGCAATTCTTTTAAATTCCTAAAGTATC
131 GTTTATAAAGTATCGATACTTTATAGGCGTCATTATTGCAATTCTTTTAAATTCCTAAAGTATC
* * * *
359605 GATAATATGATACATATACTTATTAAAGTATTGATACTTTCAACATATCCGGTAGCGCTTTACCA
1 GATAATATGATACATATACTTATTAAAGTATCGATACCTTCAACATATCCGGTAGCTCTTTACCG
359670 GTTTTGTCATACTGAAACCGGTTTTGTCATATTTTAACTTGTTATATTGTCATGTATCGATACAT
66 GTTTTGTCATACTGAAACCGGTTTTGTCATATTTTAACTTGTTATATTGTCATGTATCGATACAT
*
359735 GTTTATAAAGTATTGATACTTTATAGGCGTCATTATTGCAATTCTTTTAAATTCCTAAAGTATC
131 GTTTATAAAGTATCGATACTTTATAGGCGTCATTATTGCAATTCTTTTAAATTCCTAAAGTATC
*
359799 GATAATATGATACATATACTTATTAAAGTATCGATACCTTCAACATATCCGGTAGCTCTTTATCG
1 GATAATATGATACATATACTTATTAAAGTATCGATACCTTCAACATATCCGGTAGCTCTTTACCG
* * *
359864 GTTTTGTCATATTGAAACCGGTTTTGTCATATTTTTAC-TGTTATATTGTCATGTATCGATAAAT
66 GTTTTGTCATACTGAAACCGGTTTTGTCATATTTTAACTTGTTATATTGTCATGTATCGATACAT
* * * * * *
359928 GTTTATAAAGTATCGATACTTTATAGGCGTTATTACTGTAATTTTTTTAAATTCATAAAGTATT
131 GTTTATAAAGTATCGATACTTTATAGGCGTCATTATTGCAATTCTTTTAAATTCCTAAAGTATC
* * ** ** * * * *
359992 GATAATTTGGTGTATATACTTAGAAAAATATCGATACAAATTTCAATA-ATTCAGGTA--T-TTC
1 GATAATATGATACATATACTTATTAAAGTATCGATAC---CTTCAACATA-TCCGGTAGCTCTT-
* * * * * * *
360053 TATCGATTTTGTCAAATTGAAACCGGTTTTGTCAAATTTCAACCTT-TTATATTGTTATGTATCG
61 TACCGGTTTTGTCATACTGAAACCGGTTTTGTCATATTTTAA-CTTGTTATATTGTCATGTATCG
360117 ATAC
125 ATAC
360121 TTATTTGAAA
Statistics
Matches: 465, Mismatches: 44, Indels: 13
0.89 0.08 0.02
Matches are distributed among these distances:
193 114 0.25
194 316 0.68
195 22 0.05
196 13 0.03
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (194 bp):
GATAATATGATACATATACTTATTAAAGTATCGATACCTTCAACATATCCGGTAGCTCTTTACCG
GTTTTGTCATACTGAAACCGGTTTTGTCATATTTTAACTTGTTATATTGTCATGTATCGATACAT
GTTTATAAAGTATCGATACTTTATAGGCGTCATTATTGCAATTCTTTTAAATTCCTAAAGTATC
Found at i:360868 original size:35 final size:35
Alignment explanation
Indices: 360822--360897 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
360812 AAAACAGTAC
* *
360822 TCAATTTCATTCTAAACACTAAATTCTAAAATAAT
1 TCAATTACATTCTAAACACAAAATTCTAAAATAAT
* *
360857 TCAATTACATTCTGAACCCAAAATTCTAAAATAAT
1 TCAATTACATTCTAAACACAAAATTCTAAAATAAT
360892 TCAATT
1 TCAATT
360898 TCCATCTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.45, C:0.18, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTACATTCTAAACACAAAATTCTAAAATAAT
Found at i:361997 original size:35 final size:34
Alignment explanation
Indices: 361948--362061 Score: 156
Period size: 35 Copynumber: 3.3 Consensus size: 34
361938 TATTCATCCT
*
361948 TAAATTGAAGTATTTTAGAATTTGGGGTTTAGAA
1 TAAATTGAACTATTTTAGAATTTGGGGTTTAGAA
* * *
361982 TATAATTGAATTATTTTGGAATTTAGGGTTTAGAA
1 TA-AATTGAACTATTTTAGAATTTGGGGTTTAGAA
*
362017 TGAAATTGAACTACTTTAGAATTTGGGGTTTAGAA
1 T-AAATTGAACTATTTTAGAATTTGGGGTTTAGAA
362052 TAAAATTGAA
1 T-AAATTGAA
362062 GACTGTTTTG
Statistics
Matches: 70, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
34 2 0.03
35 67 0.96
36 1 0.01
ACGTcount: A:0.37, C:0.02, G:0.21, T:0.40
Consensus pattern (34 bp):
TAAATTGAACTATTTTAGAATTTGGGGTTTAGAA
Found at i:363834 original size:3 final size:3
Alignment explanation
Indices: 363819--363870 Score: 63
Period size: 3 Copynumber: 17.7 Consensus size: 3
363809 GGGTTAAAAA
* *
363819 TAT TAT TA- AAT TAT TAT TAT TAT TAT TAT TAT TAT TAAT T-T TAG
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT
363863 TAT TAT TA
1 TAT TAT TA
363871 AGTGTGTTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
2 3 0.07
3 36 0.86
4 3 0.07
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
TAT
Done.