Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006429.1 Hibiscus syriacus cultivar Beakdansim tig00015519_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: 85186
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Found at i:8799 original size:13 final size:13
Alignment explanation
Indices: 8781--8830 Score: 56
Period size: 14 Copynumber: 4.2 Consensus size: 13
8771 AGGGTCCTTT
8781 TTTCCTATTTTAA
1 TTTCCTATTTTAA
8794 TTTCC--TTTT--
1 TTTCCTATTTTAA
8803 TTT-CTATTTTAA
1 TTTCCTATTTTAA
8815 TTTCCTAATTTTAA
1 TTTCCT-ATTTTAA
8829 TT
1 TT
8831 GGACAAAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
8 1 0.03
9 3 0.10
10 4 0.13
11 4 0.13
12 3 0.10
13 7 0.23
14 9 0.29
ACGTcount: A:0.20, C:0.14, G:0.00, T:0.66
Consensus pattern (13 bp):
TTTCCTATTTTAA
Found at i:8806 original size:22 final size:21
Alignment explanation
Indices: 8775--8820 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
8765 TCTCGTAGGG
*
8775 TCCTTTTTTCCTATTTTAATT
1 TCCTTTTTTTCTATTTTAATT
8796 TCCTTTTTTTCTATTTTAATT
1 TCCTTTTTTTCTATTTTAATT
8817 TCCT
1 TCCT
8821 AATTTTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.13, C:0.20, G:0.00, T:0.67
Consensus pattern (21 bp):
TCCTTTTTTTCTATTTTAATT
Found at i:8826 original size:21 final size:22
Alignment explanation
Indices: 8780--8826 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
8770 TAGGGTCCTT
*
8780 TTTTCCTATTTTAATTTCCT-T
1 TTTTCCTATTTTAATTTCCTAA
*
8801 TTTTTCTATTTTAATTTCCTAA
1 TTTTCCTATTTTAATTTCCTAA
8823 TTTT
1 TTTT
8827 AATTGGACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.17, C:0.15, G:0.00, T:0.68
Consensus pattern (22 bp):
TTTTCCTATTTTAATTTCCTAA
Found at i:10072 original size:20 final size:20
Alignment explanation
Indices: 9978--10346 Score: 451
Period size: 20 Copynumber: 18.4 Consensus size: 20
9968 GATTTTCCAT
* ** *
9978 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
9998 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
10018 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
10038 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
10058 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
10078 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
10098 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
10118 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
10138 AA-CTGCAACGTGTATCCGTA
1 AATC-GCAACGCGTATCCGTA
10158 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
10178 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
10198 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
10218 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
10238 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
10258 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
10278 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
10298 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
10318 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
10338 AATCACAAC
1 AATCGCAAC
10347 ACTTAATTTT
Statistics
Matches: 305, Mismatches: 34, Indels: 20
0.85 0.09 0.06
Matches are distributed among these distances:
19 4 0.01
20 297 0.97
21 4 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:11066 original size:24 final size:24
Alignment explanation
Indices: 11027--11073 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
11017 AAATTTGGTC
11027 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
11051 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
11074 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:11265 original size:12 final size:12
Alignment explanation
Indices: 11248--11272 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
11238 ATATAATCCT
11248 GAAGAAGAAAAA
1 GAAGAAGAAAAA
11260 GAAGAAGAAAAA
1 GAAGAAGAAAAA
11272 G
1 G
11273 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:13568 original size:19 final size:19
Alignment explanation
Indices: 13546--13837 Score: 374
Period size: 19 Copynumber: 16.4 Consensus size: 19
13536 CGGAAAATAC
*
13546 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
13565 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
13579 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
13599 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
13613 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
13632 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
13651 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
13665 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
13684 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
13703 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
13722 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
13741 AATCGCAATGCGAAATGAC
1 AATCGCAATGCGAAATGAA
13760 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
13779 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
13793 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
13811 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
13830 AATCGCAA
1 AATCGCAA
13838 CGAGATAATC
Statistics
Matches: 242, Mismatches: 10, Indels: 42
0.82 0.03 0.14
Matches are distributed among these distances:
14 40 0.17
15 2 0.01
16 11 0.05
17 10 0.04
18 20 0.08
19 146 0.60
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:13661 original size:52 final size:55
Alignment explanation
Indices: 13574--13859 Score: 345
Period size: 52 Copynumber: 5.4 Consensus size: 55
13564 AAATCCCAAC
*
13574 ATGAAAATCGCAATGCGGAAATGAAAATCGCAA-CG-A-GAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAAGCGAATGAAAATCGCAATGCGAA
*
13627 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-CG-A-GAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAAATCGCAATGCGAA
*
13679 ATGAAAATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAAATCGCAATGCGAA
*
13736 ATGAAAATCGCAATGCGAAATGACAATCGCAATGCGAAATGAAAATCGCAA--CGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAAATCGCAATGCGAA
13791 A-G--AATCGCAATGCGAAATG-AAATCGCAATGCGAAATGAAAATCGCAA--CG--
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAAATCGCAATGCGAA
*
13840 A-GATAATCGCAATGCGAAAT
1 ATGAAAATCGCAATGCGAAAT
13860 TATAAACGCA
Statistics
Matches: 221, Mismatches: 5, Indels: 16
0.91 0.02 0.07
Matches are distributed among these distances:
49 2 0.01
51 45 0.20
52 84 0.38
53 16 0.07
54 3 0.01
55 5 0.02
56 1 0.00
57 65 0.29
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (55 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAAATCGCAATGCGAA
Found at i:13975 original size:19 final size:19
Alignment explanation
Indices: 13866--13967 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
13856 AAATTATAAA
13866 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
13885 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
13905 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
13921 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
13938 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
13957 CGCATTGCGAT
1 CGCATTGCGAT
13968 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:14093 original size:14 final size:14
Alignment explanation
Indices: 14074--14110 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
14064 CATCAATTAC
14074 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
14088 ACAAATCATCTTTT
1 ACAAATCAACTTTT
14102 ACAAATCAA
1 ACAAATCAA
14111 TTAAACAATC
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:16084 original size:14 final size:14
Alignment explanation
Indices: 16065--16121 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
16055 GCGAAATGAA
*
16065 AATCGCAACGACAG
1 AATCGCAACGAAAG
16079 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
16096 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
16112 AATCGCAACG
1 AATCGCAACG
16122 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:16092 original size:33 final size:33
Alignment explanation
Indices: 16046--16138 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
16036 GCGAAACCAA
*
16046 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
16079 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
16112 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
16139 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:16103 original size:19 final size:19
Alignment explanation
Indices: 16009--16143 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
15999 TAGTTTACTT
* *
16009 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
16029 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
16048 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
16067 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
16081 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
16100 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
16114 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
16133 TCGCAATGCGA
1 TCGCAACGCGA
16144 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:16161 original size:19 final size:19
Alignment explanation
Indices: 16139--16267 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
16129 AAAATCGCAA
16139 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
16158 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
16172 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
16191 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
16205 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
16224 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
16243 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
16263 TGCGA
1 TGCGA
16268 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:16181 original size:33 final size:33
Alignment explanation
Indices: 16139--16230 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
16129 AAAATCGCAA
16139 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
16172 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
16205 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
16231 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:16601 original size:93 final size:93
Alignment explanation
Indices: 16311--16781 Score: 903
Period size: 92 Copynumber: 5.1 Consensus size: 93
16301 TTGAATGGAT
16311 AAATTTACTTTCAACCAAAAGAC-AAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
16375 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
16403 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
16467 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
16495 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
16560 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
16588 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATATAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
16652 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
16680 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
16745 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
16773 AAATTTACT
1 AAATTTACT
16782 AAGCAATCTA
Statistics
Matches: 373, Mismatches: 3, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
92 206 0.55
93 167 0.45
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.23
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:16622 original size:185 final size:185
Alignment explanation
Indices: 16311--16781 Score: 917
Period size: 185 Copynumber: 2.6 Consensus size: 185
16301 TTGAATGGAT
16311 AAATTTACTTTCAACCAAAAGAC-AAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
16375 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
16440 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
16495 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
16560 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
*
16625 TATATTTCACAGTGTTAAAGAATATACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
16680 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
16745 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
16782 AAGCAATCTA
Statistics
Matches: 284, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
184 23 0.08
185 261 0.92
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.23
Consensus pattern (185 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:18502 original size:14 final size:14
Alignment explanation
Indices: 18483--18558 Score: 53
Period size: 14 Copynumber: 4.7 Consensus size: 14
18473 TTGAAATGAA
18483 AATCGCAACGAGAG
1 AATCGCAACGAGAG
18497 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
*
18514 ACAATCGCAACGCGAAATGAA
1 --AATCGCAA--CG--A-GAG
18535 AATCGCAACGAGAG
1 AATCGCAACGAGAG
18549 AATCGCAACG
1 AATCGCAACG
18559 CGAAATGAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
14 20 0.38
15 1 0.02
16 5 0.10
17 3 0.06
19 20 0.38
21 1 0.02
22 2 0.04
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:18521 original size:19 final size:19
Alignment explanation
Indices: 18497--18580 Score: 97
Period size: 19 Copynumber: 4.7 Consensus size: 19
18487 GCAACGAGAG
* *
18497 AATCGCAACGCGAGATGAC
1 AATCGCAACGCGAAATGAA
18516 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
18535 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
18549 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
18568 AATCGCAATGCGA
1 AATCGCAACGCGA
18581 TTTTGGTTTC
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 39 0.71
ACGTcount: A:0.43, C:0.23, G:0.24, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:18537 original size:52 final size:52
Alignment explanation
Indices: 18475--18580 Score: 185
Period size: 52 Copynumber: 2.0 Consensus size: 52
18465 TCTTTTGGTT
* *
18475 GAAATGAAAATCGCAACGAGAGAATCGCAACGCGAGATGACAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAACGC
*
18527 GAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAACGC
18579 GA
1 GA
18581 TTTTGGTTTC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.44, C:0.21, G:0.25, T:0.10
Consensus pattern (52 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAACGC
Found at i:18611 original size:14 final size:14
Alignment explanation
Indices: 18592--18646 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
18582 TTTGGTTTCG
18592 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
18606 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
18625 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
18639 CGTTGCGA
1 CGTTGCGA
18647 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:18624 original size:33 final size:33
Alignment explanation
Indices: 18576--18646 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
18566 AAAATCGCAA
**
18576 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
18609 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
18642 TGCGA
1 TGCGA
18647 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:18654 original size:33 final size:33
Alignment explanation
Indices: 18587--18668 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
18577 GCGATTTTGG
***
18587 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
18620 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
18653 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
18669 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:18673 original size:20 final size:20
Alignment explanation
Indices: 18599--18687 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
18589 TCGCGTTGCG
18599 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
18619 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
18632 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
18652 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
18672 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
18688 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:18809 original size:33 final size:33
Alignment explanation
Indices: 18767--18837 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
18757 AATACTAACT
*
18767 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
18800 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
18833 TGAAA
1 TGAAA
18838 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:19071 original size:22 final size:22
Alignment explanation
Indices: 19019--19073 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
19009 TGGTTGTGAG
**
19019 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
19041 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
19063 GGATTTCTTCG
1 GGATTTCTTCG
19074 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:19244 original size:20 final size:20
Alignment explanation
Indices: 19219--19411 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
19209 CTTTAAATAT
19219 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
19239 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
19261 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
19280 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
19300 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
19320 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
19340 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
19360 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
19380 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
19400 CGCGTTGCGATT
1 CGCGTTGCGATT
19412 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:19406 original size:60 final size:60
Alignment explanation
Indices: 19219--19411 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
19209 CTTTAAATAT
**
19219 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
19280 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
19340 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
19400 CGCGTTGCGATT
1 CGCGTTGCGATT
19412 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:19492 original size:20 final size:20
Alignment explanation
Indices: 19467--19518 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
19457 AAGAATCGCG
*
19467 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
19487 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
19507 TTGCGATTCTGG
1 TTGCGATTCTGG
19519 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:19743 original size:24 final size:26
Alignment explanation
Indices: 19701--19754 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 26
19691 ACCCCGTTAC
19701 ATAATATGTTATTTATATTATATAAT
1 ATAATATGTTATTTATATTATATAAT
* *
19727 ATAA-ATG-TATTTTTATTATATAGT
1 ATAATATGTTATTTATATTATATAAT
19751 ATAA
1 ATAA
19755 CATGCATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 19 0.73
25 3 0.12
26 4 0.15
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.52
Consensus pattern (26 bp):
ATAATATGTTATTTATATTATATAAT
Found at i:20388 original size:32 final size:33
Alignment explanation
Indices: 20342--20420 Score: 90
Period size: 32 Copynumber: 2.4 Consensus size: 33
20332 ACCATTTGTT
* *
20342 TTATTTTTCTTTTAATTTA-GTATTTTCTTTTA
1 TTATTTTTCTTTTAATTCACGTATTTTATTTTA
*
20374 TTATTTTT-TATTTAATTCACGTTTTTTATTTTA
1 TTATTTTTCT-TTTAATTCACGTATTTTATTTTA
*
20407 TTTTATTTTCTTTT
1 TTAT-TTTTCTTTT
20421 CTTAATCCGA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
31 1 0.03
32 16 0.41
33 14 0.36
34 7 0.18
35 1 0.03
ACGTcount: A:0.18, C:0.06, G:0.03, T:0.73
Consensus pattern (33 bp):
TTATTTTTCTTTTAATTCACGTATTTTATTTTA
Found at i:20537 original size:19 final size:19
Alignment explanation
Indices: 20515--20556 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
20505 TTTTTACTTG
20515 TTTTCATTTATTATTATTT
1 TTTTCATTTATTATTATTT
* *
20534 TTTTCATTTATTTTTCTTT
1 TTTTCATTTATTATTATTT
20553 TTTT
1 TTTT
20557 AATACTAGCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTTCATTTATTATTATTT
Found at i:23097 original size:23 final size:22
Alignment explanation
Indices: 23037--23097 Score: 54
Period size: 23 Copynumber: 2.7 Consensus size: 22
23027 ATCAGAAAAT
*
23037 AAAATAATTAATAATAATTTTTGA
1 AAAAT-ATAAATAA-AATTTTTGA
23061 AAAATATAAA-AAAATTTGTCTGA
1 AAAATATAAATAAAATTT-T-TGA
*
23084 AAATTA-AAATAAAA
1 AAAATATAAATAAAA
23098 GATTATAGTC
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
21 5 0.16
22 6 0.19
23 16 0.50
24 5 0.16
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.33
Consensus pattern (22 bp):
AAAATATAAATAAAATTTTTGA
Found at i:30477 original size:96 final size:96
Alignment explanation
Indices: 30313--30506 Score: 309
Period size: 96 Copynumber: 2.0 Consensus size: 96
30303 TAGTAATTAA
*
30313 TAGATTCCATGATCCATTAATCAAGAACAATTATATTTTCCAGTGAAAACAAGAAACCAGATAAC
1 TAGATTCCATGATCCATAAATCAAGAACAATTATATTTTCCAGTGAAAACAAGAAACCAGATAAC
*
30378 ACATTTTAGGTAACCATAGTTCATAAACCAG
66 ACATTTCAGGTAACCATAGTTCATAAACCAG
* * * *
30409 TAGATTCTATGATCCATAAATCGAGAA-ATATTATATTTTCCAGTGAAAACAGGAAACCATATAA
1 TAGATTCCATGATCCATAAATCAAGAACA-ATTATATTTTCCAGTGAAAACAAGAAACCAGATAA
*
30473 CACATTTCAGGTAACCATAGTTTATAAACCAG
65 CACATTTCAGGTAACCATAGTTCATAAACCAG
30505 TA
1 TA
30507 AATTAAGAAA
Statistics
Matches: 90, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
95 1 0.01
96 89 0.99
ACGTcount: A:0.42, C:0.18, G:0.12, T:0.28
Consensus pattern (96 bp):
TAGATTCCATGATCCATAAATCAAGAACAATTATATTTTCCAGTGAAAACAAGAAACCAGATAAC
ACATTTCAGGTAACCATAGTTCATAAACCAG
Found at i:36265 original size:22 final size:22
Alignment explanation
Indices: 36224--36291 Score: 127
Period size: 22 Copynumber: 3.0 Consensus size: 22
36214 CTCGTATAAA
36224 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
36247 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
36269 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
36291 T
1 T
36292 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 33 0.73
23 12 0.27
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:37079 original size:66 final size:67
Alignment explanation
Indices: 36946--37104 Score: 196
Period size: 67 Copynumber: 2.4 Consensus size: 67
36936 ATCGGTTCCC
* * *
36946 CCCCCCCGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGATGAGGAGGTATCGG
1 CCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGATGAGGAGGTATCGG
37011 TT
66 TT
* * * * *
37013 CCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATTCAT-TTCGTTGAGGGGGTATCGG
1 CCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGATGAGGAGGTATCGG
37077 TT
66 TT
* *
37079 -CCCCTTGAATGGGTACCGATTCCCCT
1 CCCCCCTG--GGGGTACCGATTCCCCT
37105 AACCCAGAAA
Statistics
Matches: 80, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
65 6 0.08
66 18 0.22
67 56 0.70
ACGTcount: A:0.18, C:0.29, G:0.25, T:0.28
Consensus pattern (67 bp):
CCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGATGAGGAGGTATCGG
TT
Found at i:43177 original size:22 final size:22
Alignment explanation
Indices: 43136--43203 Score: 127
Period size: 22 Copynumber: 3.0 Consensus size: 22
43126 CTCGTATAAA
43136 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
43159 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
43181 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
43203 T
1 T
43204 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 33 0.73
23 12 0.27
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:43987 original size:66 final size:67
Alignment explanation
Indices: 43841--44012 Score: 204
Period size: 67 Copynumber: 2.6 Consensus size: 67
43831 CTTTTCTCAT
* * * *
43841 GGGGAATCGGTTCCCCCCCCGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGAT
1 GGGGTATCGGTT-CCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGAT
43906 GAG
65 GAG
* * * * *
43909 GAGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATTCAT-TTCGTTG
1 GGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGATG
43973 AG
66 AG
* *
43975 GGGGTATCGGTT-CCCCTTGAATGGGTACCGATTCCCCT
1 GGGGTATCGGTTCCCCCCTG--GGGGTACCGATTCCCCT
44013 AACCCAGAAA
Statistics
Matches: 90, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
65 6 0.07
66 18 0.20
67 56 0.62
68 10 0.11
ACGTcount: A:0.18, C:0.28, G:0.27, T:0.27
Consensus pattern (67 bp):
GGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGATG
AG
Found at i:52715 original size:24 final size:24
Alignment explanation
Indices: 52683--52759 Score: 154
Period size: 24 Copynumber: 3.2 Consensus size: 24
52673 CCAAATGAAA
52683 CACTTGTGAGGAAGTTGGTTTACT
1 CACTTGTGAGGAAGTTGGTTTACT
52707 CACTTGTGAGGAAGTTGGTTTACT
1 CACTTGTGAGGAAGTTGGTTTACT
52731 CACTTGTGAGGAAGTTGGTTTACT
1 CACTTGTGAGGAAGTTGGTTTACT
52755 CACTT
1 CACTT
52760 TCAAAATCGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 53 1.00
ACGTcount: A:0.21, C:0.14, G:0.27, T:0.38
Consensus pattern (24 bp):
CACTTGTGAGGAAGTTGGTTTACT
Found at i:52805 original size:28 final size:28
Alignment explanation
Indices: 52773--52827 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
52763 AAATCGTGGC
52773 AATCAAAGAAGAC-GACTATCATCGAGGT
1 AATCAAAGAAGACAG-CTATCATCGAGGT
52801 AATCAAAGAAGACAGCTATCATCGAGG
1 AATCAAAGAAGACAGCTATCATCGAGG
52828 CTAAGAACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 25 0.96
29 1 0.04
ACGTcount: A:0.44, C:0.18, G:0.22, T:0.16
Consensus pattern (28 bp):
AATCAAAGAAGACAGCTATCATCGAGGT
Found at i:57174 original size:21 final size:21
Alignment explanation
Indices: 57104--57180 Score: 77
Period size: 21 Copynumber: 3.5 Consensus size: 21
57094 TTTTGTGCAT
57104 AATGCATCGATACA-CTATGA
1 AATGCATCGATACATCTATGA
*
57124 AAGTGCATCGATACATCCTTTTGA
1 AA-TGCATCGATACAT-C-TATGA
57148 ATATGCATCGATACATC-ATGA
1 A-ATGCATCGATACATCTATGA
*
57169 AGATGCACCGAT
1 A-ATGCATCGAT
57181 GCACTACTTG
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
20 2 0.04
21 25 0.52
23 2 0.04
24 18 0.38
25 1 0.02
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (21 bp):
AATGCATCGATACATCTATGA
Found at i:58808 original size:12 final size:13
Alignment explanation
Indices: 58785--58814 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
58775 TTATTTTGGA
58785 TGATTATATGTTT
1 TGATTATATGTTT
58798 TGATT-TATGTTT
1 TGATTATATGTTT
58810 TGATT
1 TGATT
58815 GCTTGGATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.20, C:0.00, G:0.17, T:0.63
Consensus pattern (13 bp):
TGATTATATGTTT
Found at i:59099 original size:16 final size:17
Alignment explanation
Indices: 59071--59107 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
59061 GATTTAACAA
59071 AAAGGGGGAGAAGTGTT
1 AAAGGGGGAGAAGTGTT
59088 AAAGGGGG-GAAGTGTT
1 AAAGGGGGAGAAGTGTT
59104 AAAG
1 AAAG
59108 TAAGGGGGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.38, C:0.00, G:0.46, T:0.16
Consensus pattern (17 bp):
AAAGGGGGAGAAGTGTT
Found at i:61219 original size:19 final size:19
Alignment explanation
Indices: 61195--61252 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 19
61185 CAAAAATCGA
61195 TTTTTTCGGTTCGGTTCGG
1 TTTTTTCGGTTCGGTTCGG
*
61214 TTTTTT---TAACGGTTCGG
1 TTTTTTCGGT-TCGGTTCGG
*
61231 ATTTTTCGGTTCGGTTCGG
1 TTTTTTCGGTTCGGTTCGG
61250 TTT
1 TTT
61253 ATCGGTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
16 1 0.03
17 13 0.42
19 16 0.52
20 1 0.03
ACGTcount: A:0.05, C:0.14, G:0.28, T:0.53
Consensus pattern (19 bp):
TTTTTTCGGTTCGGTTCGG
Found at i:61259 original size:18 final size:19
Alignment explanation
Indices: 61223--61259 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
61213 GTTTTTTTAA
*
61223 CGGTTCGGATTTTTCGGTT
1 CGGTTCGGATTTATCGGTT
61242 CGGTTCGG-TTTATCGGTT
1 CGGTTCGGATTTATCGGTT
61260 TTTCAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.05, C:0.16, G:0.32, T:0.46
Consensus pattern (19 bp):
CGGTTCGGATTTATCGGTT
Found at i:61394 original size:5 final size:5
Alignment explanation
Indices: 61384--61408 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
61374 AAAGCCTTTA
61384 AACCG AACCG AACCG AACCG AACCG
1 AACCG AACCG AACCG AACCG AACCG
61409 TTTTACTCGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.40, G:0.20, T:0.00
Consensus pattern (5 bp):
AACCG
Found at i:66065 original size:24 final size:24
Alignment explanation
Indices: 66038--66146 Score: 105
Period size: 24 Copynumber: 4.5 Consensus size: 24
66028 AAACGGAGAT
* * *
66038 ATCAAAAATCAAAACAAAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* *
66062 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAG
66086 ATCAGAAATCAGAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* * *
66110 GTAATG-TATCAGAACAGAATTCA-
1 ATCA-GAAATCAGAACAGAATTCAG
*
66133 AGTCGGAAATCAGA
1 A-TCAGAAATCAGA
66147 TAAAATATTT
Statistics
Matches: 68, Mismatches: 14, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
23 1 0.01
24 66 0.97
25 1 0.01
ACGTcount: A:0.50, C:0.17, G:0.16, T:0.18
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAG
Found at i:66109 original size:12 final size:12
Alignment explanation
Indices: 66050--66109 Score: 59
Period size: 12 Copynumber: 5.0 Consensus size: 12
66040 CAAAAATCAA
*
66050 AACAAAATTCAG
1 AACAGAATTCAG
*
66062 ATCAG-ATATCAG
1 AACAGAAT-TCAG
*
66074 AACAGAATCCAG
1 AACAGAATTCAG
* *
66086 ATCAGAAATCAG
1 AACAGAATTCAG
66098 AACAGAATTCAG
1 AACAGAATTCAG
66110 GTAATGTATC
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
11 2 0.05
12 33 0.89
13 2 0.05
ACGTcount: A:0.50, C:0.18, G:0.15, T:0.17
Consensus pattern (12 bp):
AACAGAATTCAG
Found at i:68608 original size:15 final size:16
Alignment explanation
Indices: 68577--68617 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
68567 GTCAAAGTTT
68577 TGGTCAACGTCAGTCAA
1 TGGTCAACG-CAGTCAA
68594 TGGTCAACG-AGTCAA
1 TGGTCAACGCAGTCAA
*
68609 CGGTCAACG
1 TGGTCAACG
68618 GGTCGAGTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.61
17 9 0.39
ACGTcount: A:0.29, C:0.24, G:0.27, T:0.20
Consensus pattern (16 bp):
TGGTCAACGCAGTCAA
Found at i:70726 original size:24 final size:24
Alignment explanation
Indices: 70699--70753 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
70689 AAACGGAGAT
*
70699 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAAAACAGAATCCAG
* * *
70723 ATCAGATATCATAACAGAATCCAT
1 ATCAGAAATCAAAACAGAATCCAG
70747 ATCAGAA
1 ATCAGAA
70754 TTCAGGTAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.51, C:0.18, G:0.11, T:0.20
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATCCAG
Found at i:75630 original size:20 final size:21
Alignment explanation
Indices: 75588--75629 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
75578 AACTGAGTGG
75588 AATTTAACTACAAACAATAAA
1 AATTTAACTACAAACAATAAA
75609 AATTTAACTAC-AAC-ATAAA
1 AATTTAACTACAAACAATAAA
75628 AA
1 AA
75630 AAATACAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 7 0.33
20 3 0.14
21 11 0.52
ACGTcount: A:0.62, C:0.14, G:0.00, T:0.24
Consensus pattern (21 bp):
AATTTAACTACAAACAATAAA
Found at i:75949 original size:22 final size:23
Alignment explanation
Indices: 75907--75949 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
75897 TTTATAGTAT
*
75907 TAAATTAATTTTTAAAAATATAG
1 TAAATTAATTATTAAAAATATAG
*
75930 TAAATT-ATTATTAAATATAT
1 TAAATTAATTATTAAAAATAT
75950 TATTTTTAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
TAAATTAATTATTAAAAATATAG
Found at i:76892 original size:24 final size:23
Alignment explanation
Indices: 76865--76932 Score: 75
Period size: 24 Copynumber: 2.9 Consensus size: 23
76855 TTTAATATCG
*
76865 ATATAAAAATATTTAAAAAATCAA
1 ATATAAAAATATTAAAAAAAT-AA
* *
76889 ATATACAAATACTAAAAAAATAA
1 ATATAAAAATATTAAAAAAATAA
76912 ATTACTAAAAA-ATTAAAAAAA
1 A-TA-TAAAAATATTAAAAAAA
76933 CTAAGAACAC
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
23 3 0.08
24 29 0.78
25 5 0.14
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (23 bp):
ATATAAAAATATTAAAAAAATAA
Found at i:76919 original size:16 final size:16
Alignment explanation
Indices: 76898--76928 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
76888 AATATACAAA
76898 TACTAAAAAAATAAAT
1 TACTAAAAAAATAAAT
*
76914 TACTAAAAAATTAAA
1 TACTAAAAAAATAAA
76929 AAAACTAAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (16 bp):
TACTAAAAAAATAAAT
Found at i:77976 original size:2 final size:2
Alignment explanation
Indices: 77969--77995 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
77959 TTAATAACGC
77969 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
77996 TTAATCTGAC
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:78704 original size:14 final size:15
Alignment explanation
Indices: 78685--78714 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
78675 ATATTTTAAT
78685 TATATCCTC-AACTA
1 TATATCCTCAAACTA
78699 TATATCCTCAAACTA
1 TATATCCTCAAACTA
78714 T
1 T
78715 GATTCTCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.37, C:0.27, G:0.00, T:0.37
Consensus pattern (15 bp):
TATATCCTCAAACTA
Found at i:79338 original size:126 final size:126
Alignment explanation
Indices: 79182--79433 Score: 486
Period size: 126 Copynumber: 2.0 Consensus size: 126
79172 TACATACAAT
79182 TCTACAATACTTTTACCCTTAGATAAAGTATAAACAACACAATGATGGTCTATTATTTATCTAAA
1 TCTACAATACTTTTACCCTTAGATAAAGTATAAACAACACAATGATGGTCTATTATTTATCTAAA
79247 ACTACAGCTAGCAGCTACAAAATTGGCTAAACTTTTCATATTAACATATAATTATTAATTA
66 ACTACAGCTAGCAGCTACAAAATTGGCTAAACTTTTCATATTAACATATAATTATTAATTA
*
79308 TCTACAATACTTTTACCCTTAGATAAAGTATAAACAGCACAATGATGGTCTATTATTTATCTAAA
1 TCTACAATACTTTTACCCTTAGATAAAGTATAAACAACACAATGATGGTCTATTATTTATCTAAA
*
79373 ACTACAGCTAGCAGCTACAAAATTGGCTATACTTTTCATATTAACATATAATTATTAATTA
66 ACTACAGCTAGCAGCTACAAAATTGGCTAAACTTTTCATATTAACATATAATTATTAATTA
79434 CCAACAAAAA
Statistics
Matches: 124, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
126 124 1.00
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.35
Consensus pattern (126 bp):
TCTACAATACTTTTACCCTTAGATAAAGTATAAACAACACAATGATGGTCTATTATTTATCTAAA
ACTACAGCTAGCAGCTACAAAATTGGCTAAACTTTTCATATTAACATATAATTATTAATTA
Found at i:82981 original size:12 final size:12
Alignment explanation
Indices: 82964--82999 Score: 72
Period size: 12 Copynumber: 3.0 Consensus size: 12
82954 TATCATGTTC
82964 TCATATCACATA
1 TCATATCACATA
82976 TCATATCACATA
1 TCATATCACATA
82988 TCATATCACATA
1 TCATATCACATA
83000 AATATATGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.42, C:0.25, G:0.00, T:0.33
Consensus pattern (12 bp):
TCATATCACATA
Found at i:83493 original size:64 final size:64
Alignment explanation
Indices: 83359--83520 Score: 211
Period size: 64 Copynumber: 2.5 Consensus size: 64
83349 TTATTGCTGG
* * *
83359 GATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCACTATTAATGT
1 GATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTTTCACTATTAAAGA
* * *
83423 GATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTCTTTA-TTTTAAA-A
1 GATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGT-TTCACTATTAAAGA
** *
83486 GAGTGCATCGATGCACTACCAATGCATCGGTGCAC
1 GA-TGCATCGATGCACTACTTATGCATCGATGCAC
83521 ATTCAAACAA
Statistics
Matches: 87, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
63 2 0.02
64 82 0.94
65 3 0.03
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (64 bp):
GATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTTTCACTATTAAAGA
Done.