Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007764.1 Hibiscus syriacus cultivar Beakdansim tig00110035_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: 58257
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:17470 original size:32 final size:32
Alignment explanation
Indices: 17434--17494 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
17424 AGATTTCGGG
*
17434 TCGGGTTAATATCAGATCGATCGATTTTTGGA
1 TCGGGTTAATATCAAATCGATCGATTTTTGGA
* *
17466 TCGGGTTAATATCAAATCGGTTGATTTTT
1 TCGGGTTAATATCAAATCGATCGATTTTT
17495 AATTTGAGTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.25, C:0.11, G:0.23, T:0.41
Consensus pattern (32 bp):
TCGGGTTAATATCAAATCGATCGATTTTTGGA
Found at i:19215 original size:16 final size:19
Alignment explanation
Indices: 19193--19238 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 19
19183 TTTTAAGTTT
19193 GTTTAAATTAA-TTT-ATA
1 GTTTAAATTAACTTTGATA
*
19210 -TTTAAAATAACTTTGATA
1 GTTTAAATTAACTTTGATA
*
19228 GTTTGAATTAA
1 GTTTAAATTAA
19239 AGTGAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 9 0.39
17 3 0.13
18 3 0.13
19 8 0.35
ACGTcount: A:0.41, C:0.02, G:0.09, T:0.48
Consensus pattern (19 bp):
GTTTAAATTAACTTTGATA
Found at i:19754 original size:23 final size:24
Alignment explanation
Indices: 19718--19788 Score: 87
Period size: 23 Copynumber: 3.1 Consensus size: 24
19708 GTTTAAGTTA
19718 TTTTCGATTC-GGTTTGCTTT-AG
1 TTTTCGATTCGGGTTTGCTTTCAG
**
19740 TTTTTTATTCGGGTTT-CTTTCAG
1 TTTTCGATTCGGGTTTGCTTTCAG
*
19763 TTTTCGATTCGGG-TTGCTTTCGG
1 TTTTCGATTCGGGTTTGCTTTCAG
19786 TTT
1 TTT
19789 GAGTTAATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
22 14 0.34
23 27 0.66
ACGTcount: A:0.07, C:0.14, G:0.23, T:0.56
Consensus pattern (24 bp):
TTTTCGATTCGGGTTTGCTTTCAG
Found at i:20665 original size:21 final size:20
Alignment explanation
Indices: 20579--20736 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
20569 AAATGACCAA
**
20579 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
20598 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
20618 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
20638 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
20659 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
20680 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
20700 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
20721 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
20737 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:20952 original size:20 final size:20
Alignment explanation
Indices: 20703--20939 Score: 260
Period size: 20 Copynumber: 11.8 Consensus size: 20
20693 CGATTTTCCA
* ** *
20703 AAATCGCAACGCGAATATGA
1 AAATCGCAACGAGAATCCGT
* *
20723 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGAGAATC-CGT
* *
20743 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGAGAATCCGT
* * *
20763 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGAGAATCCGT
* * *
20783 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGAGAATCCGT
* * *
20803 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGAGAATCCGT
*
20823 AAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGT
*
20843 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGAGAATCCGT
*
20863 AAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGT
*
20883 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGAGAATCCGT
*
20903 AAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGT
20923 AAATCGCAACGAGAATC
1 AAATCGCAACGAGAATC
20940 TGAAAATCAC
Statistics
Matches: 189, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
20 188 0.99
21 1 0.01
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGAGAATCCGT
Found at i:21673 original size:24 final size:24
Alignment explanation
Indices: 21634--21680 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
21624 AAATTTGGTC
21634 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
21658 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
21681 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:21871 original size:12 final size:12
Alignment explanation
Indices: 21854--21878 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
21844 ATATAATCCT
21854 GAAGAAGAAAAA
1 GAAGAAGAAAAA
21866 GAAGAAGAAAAA
1 GAAGAAGAAAAA
21878 G
1 G
21879 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:24255 original size:19 final size:19
Alignment explanation
Indices: 24215--24312 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
24205 GATTCTCTCG
24215 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
24235 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
24254 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
24268 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
24287 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
24306 TTGCGAT
1 TTGCGAT
24313 AGTCAATTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:24309 original size:52 final size:53
Alignment explanation
Indices: 24196--24312 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
24186 GAAATGAAAA
24196 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
24249 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
24301 TCGCATTGCGAT
1 TCGCATTGCGAT
24313 AGTCAATTTT
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 30 0.47
53 34 0.53
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:24438 original size:14 final size:14
Alignment explanation
Indices: 24419--24455 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
24409 CATCAATTAC
24419 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
24433 ACAAATCATCTTTT
1 ACAAATCAACTTTT
24447 ACAAATCAA
1 ACAAATCAA
24456 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:26457 original size:14 final size:14
Alignment explanation
Indices: 26438--26494 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
26428 ACGAAATGAA
*
26438 AATCGCAACGACAG
1 AATCGCAACGAAAG
26452 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
26469 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
26485 AATCGCAACG
1 AATCGCAACG
26495 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:26466 original size:33 final size:33
Alignment explanation
Indices: 26419--26511 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
26409 GCGAAACCAA
* *
26419 AATCGCAACACGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
26452 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
26485 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
26512 TGCGATTTTG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.48, C:0.22, G:0.19, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:26476 original size:19 final size:19
Alignment explanation
Indices: 26382--26516 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
26372 TAGTTTACTT
* *
26382 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
26402 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
*
26421 TCGCAACACGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
26440 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
26454 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
26473 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
26487 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
26506 TCGCAATGCGA
1 TCGCAACGCGA
26517 TTTTGGTTTC
Statistics
Matches: 96, Mismatches: 9, Indels: 21
0.76 0.07 0.17
Matches are distributed among these distances:
14 16 0.17
16 11 0.11
17 11 0.11
19 46 0.48
20 12 0.12
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:26534 original size:19 final size:19
Alignment explanation
Indices: 26512--26640 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
26502 AAAATCGCAA
26512 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
26531 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
26545 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
26564 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
26578 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
26597 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
26616 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
26636 TGCGA
1 TGCGA
26641 GAGTAAACTA
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:26554 original size:33 final size:33
Alignment explanation
Indices: 26512--26603 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
26502 AAAATCGCAA
26512 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
26545 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
26578 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
26604 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:26843 original size:93 final size:93
Alignment explanation
Indices: 26684--27250 Score: 1098
Period size: 93 Copynumber: 6.1 Consensus size: 93
26674 TTGAATGGAT
26684 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
26749 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
26777 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTATAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
26842 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
26870 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
26935 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
26963 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTATAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
27028 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
27056 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
27121 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
27149 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATATAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
27214 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
27242 AAATTTACT
1 AAATTTACT
27251 AAGCAATCTA
Statistics
Matches: 468, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 468 1.00
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.23
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:28973 original size:14 final size:14
Alignment explanation
Indices: 28954--29043 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
28944 TTGAAATGAA
28954 AATCGCAACGAGAG
1 AATCGCAACGAGAG
28968 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
28985 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
29001 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
29020 AATCGCAACGAGAG
1 AATCGCAACGAGAG
29034 AATCGCAACG
1 AATCGCAACG
29044 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:28991 original size:33 final size:33
Alignment explanation
Indices: 28946--29060 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
28936 TCTTTTGGTT
28946 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
28979 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
29012 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
29045 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
29061 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:28992 original size:19 final size:18
Alignment explanation
Indices: 28953--29065 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
28943 GTTGAAATGA
28953 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
28968 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
28985 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
29001 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
29018 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
29034 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
29051 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
29066 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:29094 original size:19 final size:19
Alignment explanation
Indices: 29061--29179 Score: 95
Period size: 21 Copynumber: 6.3 Consensus size: 19
29051 AAAATCGCAA
** *
29061 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTCATTTCTCGT
*
29080 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCTCGT
29099 TGCGA--TTC---TCTCGT
1 TGCGATTTTCATTTCTCGT
29113 TGCGATTTTCATTTCTCTCGT
1 TGCGATTTTCA-TT-TCTCGT
***
29134 TGCGACAGTCATTCTCTCGT
1 TGCGATTTTCATT-TCTCGT
29154 TGCGATTTTCATTTATCTCGT
1 TGCGATTTTCA-TT-TCTCGT
29175 TGCGA
1 TGCGA
29180 CTCTTCTGCA
Statistics
Matches: 82, Mismatches: 10, Indels: 14
0.77 0.09 0.13
Matches are distributed among these distances:
14 10 0.12
16 3 0.04
17 3 0.04
19 22 0.27
20 17 0.21
21 27 0.33
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.45
Consensus pattern (19 bp):
TGCGATTTTCATTTCTCGT
Found at i:29160 original size:41 final size:41
Alignment explanation
Indices: 29103--29180 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
29093 TCGCGTTGCG
*
29103 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
29144 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
29181 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:29165 original size:20 final size:21
Alignment explanation
Indices: 29104--29179 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
29094 CGCGTTGCGA
29104 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
29125 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
29145 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
29166 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
29180 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:29306 original size:33 final size:33
Alignment explanation
Indices: 29259--29329 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
29249 AATACTAACT
* *
29259 TGAAAATCGGAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
29292 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
29325 TGAAA
1 TGAAA
29330 TCTAAGTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:29563 original size:22 final size:22
Alignment explanation
Indices: 29511--29565 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
29501 TGGTTGTGAG
**
29511 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
29533 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
29555 GGATTTCTTCG
1 GGATTTCTTCG
29566 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:29736 original size:20 final size:20
Alignment explanation
Indices: 29711--29904 Score: 212
Period size: 20 Copynumber: 9.7 Consensus size: 20
29701 CTTTAAATAT
29711 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
29731 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
* *
29753 -TCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
29772 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
29792 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
29812 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
29832 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
29852 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
29872 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
29892 CGCGTTGCGATTT
1 CGCGTTGCGATTT
29905 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:29898 original size:60 final size:60
Alignment explanation
Indices: 29711--29904 Score: 244
Period size: 60 Copynumber: 3.2 Consensus size: 60
29701 CTTTAAATAT
** *
29711 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
29772 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
29832 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
29892 CGCGTTGCGATTT
1 CGCGTTGCGATTT
29905 TGGAAAATCG
Statistics
Matches: 111, Mismatches: 22, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:29921 original size:21 final size:21
Alignment explanation
Indices: 29891--29973 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
29881 ATTTTCATAT
*
29891 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
29912 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
29933 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
29954 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
29974 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:29964 original size:42 final size:43
Alignment explanation
Indices: 29871--29969 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
29861 ATTTATGTGT
* *
29871 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
29912 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
29954 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
29970 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:30414 original size:2 final size:2
Alignment explanation
Indices: 30407--30438 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
30397 TATTTTTAAA
30407 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30439 TAATTAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37649 original size:38 final size:38
Alignment explanation
Indices: 37572--37649 Score: 86
Period size: 38 Copynumber: 2.1 Consensus size: 38
37562 ATTGAACCTG
* * * *
37572 ATATATTTTTATATAAATTATGTTTAAGTAAAATTTTA
1 ATATATTTTTAAATAAATTATGTTAAAATAAAATATTA
**
37610 ATATACTTTTTAAATAAATTATG-TAAAATTTAATATTA
1 ATATA-TTTTTAAATAAATTATGTTAAAATAAAATATTA
37648 AT
1 AT
37650 TAAAATTAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
38 17 0.52
39 16 0.48
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.50
Consensus pattern (38 bp):
ATATATTTTTAAATAAATTATGTTAAAATAAAATATTA
Found at i:37725 original size:15 final size:15
Alignment explanation
Indices: 37705--37738 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
37695 ATTATCGATG
37705 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
37720 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
37735 AATT
1 AATT
37739 AGAATTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:43626 original size:29 final size:30
Alignment explanation
Indices: 43563--43627 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 30
43553 TTTCATGTTA
* * *
43563 GGGGGGACGAACTTGAACTTAAAAATTTTT
1 GGGGGGACAAACTTAAACTTAAAAATTTCT
*
43593 AGGGGG-CAAACTTAAACTTATAAAA-TTCT
1 GGGGGGACAAACTTAAACTTA-AAAATTTCT
43622 GGGGGG
1 GGGGGG
43628 GGCGAAAACA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
29 20 0.69
30 9 0.31
ACGTcount: A:0.34, C:0.11, G:0.29, T:0.26
Consensus pattern (30 bp):
GGGGGGACAAACTTAAACTTAAAAATTTCT
Found at i:51399 original size:19 final size:20
Alignment explanation
Indices: 51375--51424 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
51365 AACGCGATCC
51375 CCAGAATCGCAAATCAG-TT
1 CCAGAATCGCAAATCAGTTT
51394 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
51414 CCA-AATCGCAA
1 CCAGAATCGCAA
51425 CGCGATTCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 25 0.83
20 5 0.17
ACGTcount: A:0.38, C:0.28, G:0.14, T:0.20
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:51442 original size:21 final size:20
Alignment explanation
Indices: 51411--51512 Score: 69
Period size: 21 Copynumber: 5.0 Consensus size: 20
51401 CGCAAATCAG
*
51411 TTTCCAAATCGCAACGCGAT
1 TTTCAAAATCGCAACGCGAT
* * *
51431 TCTTGAAAATCGCGATGCGAT
1 T-TTCAAAATCGCAACGCGAT
* * * **
51452 AGTACAAATTCGCATTGCGAT
1 -TTTCAAAATCGCAACGCGAT
*
51473 TTTCCAAAATCGCAACGCGAA
1 TTT-CAAAATCGCAACGCGAT
* *
51494 TATGAAAATCGCAACGCGA
1 TTTCAAAATCGCAACGCGA
51513 ACACATAAAT
Statistics
Matches: 61, Mismatches: 18, Indels: 6
0.72 0.21 0.07
Matches are distributed among these distances:
20 17 0.28
21 44 0.72
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.24
Consensus pattern (20 bp):
TTTCAAAATCGCAACGCGAT
Found at i:51541 original size:20 final size:20
Alignment explanation
Indices: 51479--51670 Score: 194
Period size: 20 Copynumber: 9.7 Consensus size: 20
51469 CGATTTTCCA
* ** *
51479 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
51499 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
51519 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
51539 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
51559 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
51579 AAAT--CAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* *
51597 ATATCGCAACGCGTATCCAT
1 AAATCGCAACGCGTATCCGT
* * *
51617 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
51637 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
51658 AAATCGCAACGCG
1 AAATCGCAACGCG
51671 ATATTTAAAG
Statistics
Matches: 142, Mismatches: 23, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
18 14 0.10
19 2 0.01
20 108 0.76
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:51603 original size:38 final size:39
Alignment explanation
Indices: 51518--51670 Score: 166
Period size: 38 Copynumber: 3.8 Consensus size: 39
51508 CGCGAACACA
*
51518 TAAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCG
1 TAAATCGCAACGCGTATCCGTAAATC-CAACGCGTATCCG
** *
51558 TAAATCGCAACGCGTATGGGTAAAT-CAATGCGTATCCG
1 TAAATCGCAACGCGTATCCGTAAATCCAACGCGTATCCG
* * * * *
51596 TATATCGCAACGCGTATCCATAAATCGCAACG-ATAATACA
1 TAAATCGCAACGCGTATCCGTAAATC-CAACGCGT-ATCCG
51636 TAAAATCGCAACGCGTATCCGTAAATCGCAACGCG
1 T-AAATCGCAACGCGTATCCGTAAATC-CAACGCG
51671 ATATTTAAAG
Statistics
Matches: 93, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
38 32 0.34
39 1 0.01
40 31 0.33
41 29 0.31
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (39 bp):
TAAATCGCAACGCGTATCCGTAAATCCAACGCGTATCCG
Found at i:52083 original size:33 final size:33
Alignment explanation
Indices: 52044--52114 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
52034 TTCACTTAGA
52044 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
52077 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
52110 TTTCA
1 TTTCA
52115 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:52254 original size:14 final size:14
Alignment explanation
Indices: 52235--52289 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
52225 AGAATGACTG
52235 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
52249 TCGCAACGCGAAATGGAAA
1 TCGCAA--CGAGA--G-AA
52268 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
52282 TCGCAACG
1 TCGCAACG
52290 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 16 0.47
15 1 0.03
16 4 0.12
17 4 0.12
18 1 0.03
19 8 0.24
ACGTcount: A:0.40, C:0.24, G:0.27, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:52302 original size:33 final size:33
Alignment explanation
Indices: 52235--52305 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
52225 AGAATGACTG
***
52235 TCGCAACGAGAGAATCGCAACGCGAAATGGAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
52268 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
52301 TCGCA
1 TCGCA
52306 TTGCGATTTT
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:0.42, C:0.25, G:0.24, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:52323 original size:19 final size:19
Alignment explanation
Indices: 52301--52398 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
52291 GAAACCAAAA
*
52301 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
52320 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
52334 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
52353 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
52367 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
52386 TCGCGTTGCGATT
1 TCGCGTTGCGATT
52399 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:52342 original size:14 final size:14
Alignment explanation
Indices: 52323--52412 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
52313 TTTCATTTCG
52323 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
52337 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
52356 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
52370 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
52387 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
52403 CGTTGCGATT
1 CGTTGCGATT
52413 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:52348 original size:33 final size:33
Alignment explanation
Indices: 52306--52420 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
52296 CAAAATCGCA
52306 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
52339 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
52372 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
52405 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
52421 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:54324 original size:92 final size:93
Alignment explanation
Indices: 54108--54485 Score: 735
Period size: 92 Copynumber: 4.1 Consensus size: 93
54098 TAGATTGCTT
54108 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
54173 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
54201 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
54265 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
54293 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
54358 TTTGTCTTTG-TTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
54385 AGTAAA-TTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
54449 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
54477 AGTAAATTT
1 AGTAAATTT
54486 ATCCATTCAA
Statistics
Matches: 282, Mismatches: 0, Indels: 6
0.98 0.00 0.02
Matches are distributed among these distances:
91 68 0.24
92 138 0.49
93 76 0.27
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:54337 original size:185 final size:184
Alignment explanation
Indices: 54108--54485 Score: 731
Period size: 185 Copynumber: 2.0 Consensus size: 184
54098 TAGATTGCTT
54108 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
54173 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTG-TTTGTCTTTTGGTTGAAAGTAAA-TTGTTCGGTTGCTGCCAATTCTGCTAAACT
54238 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
129 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
54293 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
54358 TTTGTCTTTGTTTGTCTTTTGGTTGAAAGTAAATTGTTCGGTTGCTGCCAATTCTGCTAAACTGT
66 TTTGTCTTTGTTTGTCTTTTGGTTGAAAGTAAATTGTTCGGTTGCTGCCAATTCTGCTAAACTGT
54423 GTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
54477 AGTAAATTT
1 AGTAAATTT
54486 ATCCATTCAA
Statistics
Matches: 192, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
183 55 0.29
184 62 0.32
185 75 0.39
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (184 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTGTCTTTTGGTTGAAAGTAAATTGTTCGGTTGCTGCCAATTCTGCTAAACTGT
GTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:54569 original size:19 final size:19
Alignment explanation
Indices: 54529--54657 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
54519 TAGTTTACTT
* *
54529 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
54549 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
54568 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
54587 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
54601 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
54620 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
54634 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
54653 TCGCA
1 TCGCA
54658 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:54608 original size:33 final size:32
Alignment explanation
Indices: 54565--54657 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
54555 CGCGAAACCA
**
54565 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
54597 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
54630 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
54658 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:54655 original size:52 final size:52
Alignment explanation
Indices: 54529--54657 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
54519 TAGTTTACTT
**
54529 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
54581 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
54634 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
54658 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:54675 original size:19 final size:19
Alignment explanation
Indices: 54653--54787 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
54643 GAAACCAAAA
*
54653 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
54672 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
54688 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
54705 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
54721 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
54738 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
54757 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
54777 TCGTGTTGCGA
1 TCGCGTTGCGA
54788 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:54694 original size:14 final size:14
Alignment explanation
Indices: 54675--54731 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
54665 TTTCATTTCG
54675 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
54689 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
54706 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
54722 CGTTGCGATT
1 CGTTGCGATT
54732 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:54700 original size:33 final size:33
Alignment explanation
Indices: 54658--54750 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
54648 CAAAATCGCA
*
54658 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
54691 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
54724 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
54751 TTGGTTTCGC
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:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:56643 original size:14 final size:14
Alignment explanation
Indices: 56624--56659 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
56614 GATGTTTAAT
56624 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
56638 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
56652 TGATTTGT
1 TGATTTGT
56660 GTAATTGATG
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:56782 original size:19 final size:19
Alignment explanation
Indices: 56766--56867 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
56756 AAAAATGACT
56766 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
56785 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
56804 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
56818 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
56837 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
56857 ATCGCAATGCG
1 ATCGCAATGCG
56868 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:56886 original size:19 final size:18
Alignment explanation
Indices: 56858--57168 Score: 204
Period size: 19 Copynumber: 17.9 Consensus size: 18
56848 GAAATGAAAA
* *
56858 TCGCAATGCGTTTATAATT
1 TCGCATTGCGTTT-TCATT
* *
56877 TCGCATTGCG-ATT-ATC
1 TCGCATTGCGTTTTCATT
56893 TCG--TTGCGATTTTCATT
1 TCGCATTGCG-TTTTCATT
56910 TCGCATTGCGATTTTCATT
1 TCGCATTGCG-TTTTCATT
*
56929 TCGCATTGCG-ATTC--T
1 TCGCATTGCGTTTTCATT
*
56944 TCG--TTGCGATTTCATT
1 TCGCATTGCGTTTTCATT
56960 TCGCATTGCGATTTTCATT
1 TCGCATTGCG-TTTTCATT
56979 TCGCATTGCGATTTTCATT
1 TCGCATTGCG-TTTTCATT
* * *
56998 TCGTATTGCGATTTAATT
1 TCGCATTGCGTTTTCATT
57016 TCGCATTGCG-----ATT
1 TCGCATTGCGTTTTCATT
*
57029 GTCG-GTT-CGATTTTCATT
1 -TCGCATTGCG-TTTTCATT
57047 TCGCATTGCGATTTTCATT
1 TCGCATTGCG-TTTTCATT
* *
57066 TCGCATTGCG-ATTC-TC
1 TCGCATTGCGTTTTCATT
57082 TCG--TTGCGATTTTCATT
1 TCGCATTGCG-TTTTCATT
57099 TCGCATTGCGATTTTCA-T
1 TCGCATTGCG-TTTTCATT
* *
57117 TCGCATTGCG-ATTC-TC
1 TCGCATTGCGTTTTCATT
57133 TCG--TTGCGATTTTCATT
1 TCGCATTGCG-TTTTCATT
57150 TCCGCATTGCGATTTTCAT
1 T-CGCATTGCG-TTTTCAT
57169 GTTGGGATTT
Statistics
Matches: 238, Mismatches: 22, Indels: 63
0.74 0.07 0.20
Matches are distributed among these distances:
12 2 0.01
13 10 0.04
14 21 0.09
15 4 0.02
16 27 0.11
17 21 0.09
18 39 0.16
19 101 0.42
20 13 0.05
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (18 bp):
TCGCATTGCGTTTTCATT
Found at i:57055 original size:137 final size:136
Alignment explanation
Indices: 56864--57196 Score: 471
Period size: 137 Copynumber: 2.4 Consensus size: 136
56854 AAAATCGCAA
*
56864 TGCG-TTTATAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCAT
1 TGCGATTT-TAATTTCGCATTGCGATTATCACGTTGCGATTTTCATTTCGCATTGCGATTTTCAT
56928 TTCGCATTGCGATTCT-TCGTTGCGA-TTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGAT
65 TTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCA-TTCGCATTGCGA-
*
56991 TTTCATTTCGTAT
128 -TTC-TCTCG--T
* *
57004 TGCGA-TTTAATTTCGCATTGCGATTGTC-GGTT-CGATTTTCATTTCGCATTGCGATTTTCATT
1 TGCGATTTTAATTTCGCATTGCGATTATCACGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
57066 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTCGCATTGCGATTC
66 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTCGCATTGCGATTC
57131 TCTCGT
131 TCTCGT
* * * * *
57137 TGCGATTTTCATTTCCGCATTGCGATTTTCATGTTGGGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTAATTT-CGCATTGCGATTATCACGTTGCGATTTTCATTTCGCATTGCGATT
57197 GTATTTTCCG
Statistics
Matches: 178, Mismatches: 8, Indels: 17
0.88 0.04 0.08
Matches are distributed among these distances:
133 6 0.03
134 7 0.04
135 18 0.10
136 6 0.03
137 67 0.38
138 24 0.13
139 44 0.25
140 6 0.03
ACGTcount: A:0.15, C:0.20, G:0.19, T:0.46
Consensus pattern (136 bp):
TGCGATTTTAATTTCGCATTGCGATTATCACGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTCGCATTGCGATTC
TCTCGT
Found at i:57090 original size:14 final size:15
Alignment explanation
Indices: 57070--57143 Score: 53
Period size: 18 Copynumber: 4.6 Consensus size: 15
57060 TTCATTTCGC
57070 ATTGCGATTCTCTCG
1 ATTGCGATTCTCTCG
*
57085 -TTGCGATTTTCATTTCG
1 ATTGCGA--TTC-TCTCG
*
57102 CATTGCGATTTTCATTCG
1 -ATTGCGATTCTC--TCG
57120 CATTGCGATTCTCTCG
1 -ATTGCGATTCTCTCG
57136 -TTGCGATT
1 ATTGCGATT
57144 TTCATTTCCG
Statistics
Matches: 48, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
14 14 0.29
16 7 0.15
17 6 0.12
18 15 0.31
19 6 0.12
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.45
Consensus pattern (15 bp):
ATTGCGATTCTCTCG
Found at i:57141 original size:51 final size:52
Alignment explanation
Indices: 56896--57168 Score: 316
Period size: 50 Copynumber: 5.2 Consensus size: 52
56886 GATTATCTCG
*
56896 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC--TTCG--
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
* *
56947 TTGCGA-TTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
* * *
57003 TTGCGA-TTTAATTTCGCATTGCGATTGTC-GGTT-CGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
57052 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
57104 TTGCGATTTTCA-TTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCA
57156 TTGCGATTTTCAT
1 TTGCGATTTTCAT
57169 GTTGGGATTT
Statistics
Matches: 203, Mismatches: 8, Indels: 20
0.88 0.03 0.09
Matches are distributed among these distances:
49 21 0.10
50 60 0.30
51 44 0.22
52 48 0.24
53 1 0.00
54 6 0.03
56 23 0.11
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.47
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
Done.