Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003718.1 Hibiscus syriacus cultivar Beakdansim tig00007951_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: 295015
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 2 of 2
Found at i:254884 original size:52 final size:52
Alignment explanation
Indices: 254797--255075 Score: 372
Period size: 52 Copynumber: 5.2 Consensus size: 52
254787 AAATCCCAAC
254797 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
254850 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
254902 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
254954 ATTAAAATCGCAATGCGAAGA-GAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA-ATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
*
255011 ATGAAAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
255063 ATGAAAATCGCAA
1 ATGAAAATCGCAA
255076 CGAGATAATC
Statistics
Matches: 215, Mismatches: 5, Indels: 13
0.92 0.02 0.06
Matches are distributed among these distances:
52 162 0.75
53 17 0.08
54 4 0.02
55 4 0.02
56 1 0.00
57 27 0.13
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:254920 original size:71 final size:71
Alignment explanation
Indices: 254836--255075 Score: 357
Period size: 71 Copynumber: 3.4 Consensus size: 71
254826 GCAACGAGAG
*
254836 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
254901 AATGAA
66 AATGAA
* *
254907 AATCGCAATGCGAAATGAAAATCGCAA--CGACA-G--AATCGCAATGCGAAATTAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG-AA--AGAATCGCAA
254967 TGCGAAGA-GAA
61 TGCGAA-ATGAA
254978 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
255043 AATGAA
66 AATGAA
255049 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
255076 CGAGATAATC
Statistics
Matches: 152, Mismatches: 5, Indels: 24
0.84 0.03 0.13
Matches are distributed among these distances:
66 8 0.05
68 3 0.02
69 5 0.03
70 1 0.01
71 117 0.77
72 1 0.01
73 6 0.04
74 3 0.02
76 8 0.05
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.14
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
AATGAA
Found at i:255021 original size:142 final size:138
Alignment explanation
Indices: 254769--255113 Score: 527
Period size: 142 Copynumber: 2.5 Consensus size: 138
254759 CGGAAAATAC
* * *
254769 AATCGCAACGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAA--CG
1 AATCGCAATGCGAAATGAAAATCGCAAC--GAAAATCGCAATGC-GAAATTAAAATCGCAATGCG
*
254832 -AGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAA
63 AAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAA
254896 TGCGAAATGAA
128 TGCGAAATGAA
254907 AATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAAATTAAAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-A-AATCGCAATGCGAAATTAAAATCGCAATGCGA
254972 AGAGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCA
64 AGAG--AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCA
255037 ATGCGAAATGAA
127 ATGCGAAATGAA
*
255049 AATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAATTATAAA-CGCATTGCG
1 AATCGCAATGCGAAATGAAAATCGCAACGA-A-AATCGCAATGCGAAATTA-AAATCGCAATGCG
255113 A
63 A
255114 TTTTCATTTC
Statistics
Matches: 192, Mismatches: 7, Indels: 12
0.91 0.03 0.06
Matches are distributed among these distances:
136 2 0.01
137 16 0.08
138 37 0.19
139 2 0.01
140 4 0.02
142 128 0.67
143 3 0.02
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.14
Consensus pattern (138 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAAAATCGCAATGCGAAATTAAAATCGCAATGCGAAG
AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGC
GAAATGAA
Found at i:255076 original size:52 final size:54
Alignment explanation
Indices: 254769--255097 Score: 303
Period size: 52 Copynumber: 6.3 Consensus size: 54
254759 CGGAAAATAC
* *
254769 AATCGCAACGCGAAATGAAAATCCCAA--C---ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GC-GAAA-G-A
*
254822 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAAA-G-A
*
254874 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAAA-G-A
* *
254926 AATCGCAA--CGACA-G--AATCGCAATGCGAAATTAAAATCGCAATGCGAAGAGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAA-AG-A
254978 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGAAAG-
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAAGA
255030 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-CG--AGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAAGA
255081 TAATCGCAATGCGAAAT
1 -AATCGCAATGCGAAAT
255098 TATAAACGCA
Statistics
Matches: 256, Mismatches: 5, Indels: 31
0.88 0.02 0.11
Matches are distributed among these distances:
48 9 0.04
49 1 0.00
50 3 0.01
51 2 0.01
52 177 0.69
53 25 0.10
54 8 0.03
55 5 0.02
57 26 0.10
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (54 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAAGA
Found at i:255194 original size:19 final size:19
Alignment explanation
Indices: 255104--255186 Score: 113
Period size: 20 Copynumber: 4.6 Consensus size: 19
255094 AAATTATAAA
255104 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
255123 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
255143 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
255159 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
255176 CGCATTGCGAT
1 CGCATTGCGAT
255187 AGTCATTTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
14 6 0.11
16 7 0.12
17 7 0.12
19 17 0.30
20 19 0.34
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.43
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:255312 original size:14 final size:14
Alignment explanation
Indices: 255293--255329 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
255283 CATCAATTAC
255293 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
255307 ACAAATCATCTTTT
1 ACAAATCAACTTTT
255321 ACAAATCAA
1 ACAAATCAA
255330 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:257292 original size:19 final size:19
Alignment explanation
Indices: 257247--257312 Score: 71
Period size: 19 Copynumber: 3.4 Consensus size: 19
257237 TAGTTTACTT
* *
257247 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
257267 T-GACAACGCGAAACCAAAA
1 TCG-CAACGCGAAACCAAAA
**
257286 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
257305 TCGCAACG
1 TCGCAACG
257313 ACAGAATCGC
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
19 28 0.70
20 12 0.30
ACGTcount: A:0.47, C:0.26, G:0.17, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:257322 original size:14 final size:14
Alignment explanation
Indices: 257303--257359 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
257293 GCGAAATGAA
*
257303 AATCGCAACGACAG
1 AATCGCAACGAAAG
257317 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
257334 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
257350 AATCGCAACG
1 AATCGCAACG
257360 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:257322 original size:33 final size:33
Alignment explanation
Indices: 257284--257376 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
257274 GCGAAACCAA
*
257284 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
257317 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
257350 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
257377 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:257341 original size:19 final size:18
Alignment explanation
Indices: 257282--257381 Score: 99
Period size: 19 Copynumber: 5.8 Consensus size: 18
257272 ACGCGAAACC
257282 AAAATCGCAACGCGAAATG
1 AAAATCGCAA-GCGAAATG
*
257301 AAAATCGCAA-CGACA-G
1 AAAATCGCAAGCGAAATG
257317 --AATCGCAATGCGAAATG
1 AAAATCGCAA-GCGAAATG
257334 AAAATCGCAA-CGAAA-G
1 AAAATCGCAAGCGAAATG
257350 --AATCGCAACGCGAAATG
1 AAAATCGCAA-GCGAAATG
257367 AAAATCGCAATGCGA
1 AAAATCGCAA-GCGA
257382 TTTTGGTTTC
Statistics
Matches: 68, Mismatches: 3, Indels: 20
0.75 0.03 0.22
Matches are distributed among these distances:
14 16 0.24
16 11 0.16
17 11 0.16
19 30 0.44
ACGTcount: A:0.47, C:0.21, G:0.21, T:0.11
Consensus pattern (18 bp):
AAAATCGCAAGCGAAATG
Found at i:257399 original size:19 final size:19
Alignment explanation
Indices: 257377--257505 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
257367 AAAATCGCAA
257377 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
257396 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
257410 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
257429 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
257443 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
257462 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
257481 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
257501 TGCGA
1 TGCGA
257506 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:257419 original size:33 final size:33
Alignment explanation
Indices: 257377--257468 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
257367 AAAATCGCAA
257377 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
257410 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
257443 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
257469 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:257708 original size:93 final size:93
Alignment explanation
Indices: 257549--258114 Score: 1116
Period size: 93 Copynumber: 6.1 Consensus size: 93
257539 TTGAATGGAT
257549 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
257614 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
257642 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
257707 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
257735 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
257800 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
257828 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
257893 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
257921 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
257985 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
258013 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
258078 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
258106 AAATTTACT
1 AAATTTACT
258115 AAGCAATCTA
Statistics
Matches: 471, Mismatches: 1, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
92 92 0.20
93 379 0.80
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:259837 original size:14 final size:14
Alignment explanation
Indices: 259818--259907 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
259808 TTGAAATGAA
259818 AATCGCAACGAGAG
1 AATCGCAACGAGAG
259832 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
259849 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
259865 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
259884 AATCGCAACGAGAG
1 AATCGCAACGAGAG
259898 AATCGCAACG
1 AATCGCAACG
259908 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:259855 original size:33 final size:33
Alignment explanation
Indices: 259810--259924 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
259800 TCTTTTGGTT
259810 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
259843 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
259876 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
259909 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
259925 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:259856 original size:19 final size:18
Alignment explanation
Indices: 259817--259929 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
259807 GTTGAAATGA
259817 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
259832 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
259849 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
259865 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
259882 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
259898 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
259915 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
259930 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:259973 original size:33 final size:33
Alignment explanation
Indices: 259925--259995 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
259915 AAAATCGCAA
**
259925 TGCGATTTTGGTTTCGCGTTGCGATTATCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
*
259958 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
259991 TGCGA
1 TGCGA
259996 CAGTCATTCT
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:0.10, C:0.21, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
Found at i:260003 original size:33 final size:33
Alignment explanation
Indices: 259936--260017 Score: 110
Period size: 33 Copynumber: 2.5 Consensus size: 33
259926 GCGATTTTGG
***
259936 TTTCGCGTTGCGATTATCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTATCTCGTTGCGACAGTCA
*
259969 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTATCTCGTTGCGACAGTCA
*
260002 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
260018 TTCATTTATC
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 31 0.72
34 12 0.28
ACGTcount: A:0.11, C:0.24, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTATCTCGTTGCGACAGTCA
Found at i:260158 original size:33 final size:33
Alignment explanation
Indices: 260116--260186 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
260106 AATACTAACT
*
260116 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
260149 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
260182 TGAAA
1 TGAAA
260187 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:260420 original size:22 final size:22
Alignment explanation
Indices: 260368--260422 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
260358 TGGTTGTGAG
**
260368 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
260390 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
260412 GGATTTCTTCG
1 GGATTTCTTCG
260423 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:260593 original size:20 final size:20
Alignment explanation
Indices: 260568--260760 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
260558 CTTTAAATAT
260568 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
260588 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
260610 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
260629 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
260649 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
260669 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
260689 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
260709 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
260729 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
260749 CGCGTTGCGATT
1 CGCGTTGCGATT
260761 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:260755 original size:60 final size:60
Alignment explanation
Indices: 260568--260760 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
260558 CTTTAAATAT
**
260568 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
260629 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
260689 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
260749 CGCGTTGCGATT
1 CGCGTTGCGATT
260761 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:260841 original size:20 final size:20
Alignment explanation
Indices: 260816--260867 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
260806 AAGAATCGCG
*
260816 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
260836 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
260856 TTGCGATTCTGG
1 TTGCGATTCTGG
260868 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:265247 original size:59 final size:60
Alignment explanation
Indices: 265155--265274 Score: 145
Period size: 59 Copynumber: 2.0 Consensus size: 60
265145 TCCCTAACTT
* * *
265155 TAAGATATTGCTTTATTAAACCCCCTGACTATTAAAAGTTATAAAATAATC-CCCGACTA
1 TAAGAAATTGCTTTATTAAACCCCATGACTATTAAAAATTATAAAATAATCACCCGACTA
* * * * *
265214 TAAGAAATTGCTTTGTT-AACTCCATCGACTATTAAAAATTATAGAATGATCACCTGACTA
1 TAAGAAATTGCTTTATTAAACCCCAT-GACTATTAAAAATTATAAAATAATCACCCGACTA
265274 T
1 T
265275 TTATTATGTT
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
58 6 0.12
59 37 0.73
60 8 0.16
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.33
Consensus pattern (60 bp):
TAAGAAATTGCTTTATTAAACCCCATGACTATTAAAAATTATAAAATAATCACCCGACTA
Found at i:270632 original size:23 final size:24
Alignment explanation
Indices: 270596--270645 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
270586 CTATACAAGG
270596 AAAATGTTCAAAAACTCATCCAAA
1 AAAATGTTCAAAAACTCATCCAAA
*
270620 AAAATGTTC-AAAACTCATCTAAA
1 AAAATGTTCAAAAACTCATCCAAA
270643 AAA
1 AAA
270646 CTATCTTTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 16 0.64
24 9 0.36
ACGTcount: A:0.56, C:0.18, G:0.04, T:0.22
Consensus pattern (24 bp):
AAAATGTTCAAAAACTCATCCAAA
Found at i:284711 original size:23 final size:23
Alignment explanation
Indices: 284669--284757 Score: 74
Period size: 23 Copynumber: 4.0 Consensus size: 23
284659 GAGTCGAGGG
* * *
284669 TTCTACGCGGTTATTTGGGACAA
1 TTCTACGTGGTCATTCGGGACAA
* *
284692 TTCTACGTGGTCCTTCGGGACAT
1 TTCTACGTGGTCATTCGGGACAA
* *
284715 TTCTACGCGATCATTCGGGA-AA
1 TTCTACGTGGTCATTCGGGACAA
* * *
284737 -TCTATGTGGTCTTTTGGGACA
1 TTCTACGTGGTCATTCGGGACA
284758 TTTTATGTCG
Statistics
Matches: 51, Mismatches: 14, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
21 14 0.27
22 2 0.04
23 35 0.69
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (23 bp):
TTCTACGTGGTCATTCGGGACAA
Found at i:284756 original size:44 final size:46
Alignment explanation
Indices: 284669--284760 Score: 116
Period size: 44 Copynumber: 2.0 Consensus size: 46
284659 GAGTCGAGGG
* * *
284669 TTCTACGCGGTTATTTGGGACAATTCTACGTGGTCCTTCGGGACAT
1 TTCTACGCGATCATTCGGGACAATTCTACGTGGTCCTTCGGGACAT
* * *
284715 TTCTACGCGATCATTCGGGA-AA-TCTATGTGGTCTTTTGGGACAT
1 TTCTACGCGATCATTCGGGACAATTCTACGTGGTCCTTCGGGACAT
284759 TT
1 TT
284761 TATGTCGCAC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
44 21 0.52
45 2 0.05
46 17 0.43
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.37
Consensus pattern (46 bp):
TTCTACGCGATCATTCGGGACAATTCTACGTGGTCCTTCGGGACAT
Found at i:287532 original size:29 final size:29
Alignment explanation
Indices: 287491--287566 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
287481 TAATTTTTTT
287491 TTCGAAAAAGGTGATATTCTAAGAACTAA
1 TTCGAAAAAGGTGATATTCTAAGAACTAA
* * * * *
287520 TTTGAAAATGGTGATATTTTAGGAATTAA
1 TTCGAAAAAGGTGATATTCTAAGAACTAA
* *
287549 TTCGAAAAGGGTGCTATT
1 TTCGAAAAAGGTGATATT
287567 TTGGTAATTA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.38, C:0.07, G:0.21, T:0.34
Consensus pattern (29 bp):
TTCGAAAAAGGTGATATTCTAAGAACTAA
Found at i:287567 original size:29 final size:28
Alignment explanation
Indices: 287439--287576 Score: 87
Period size: 29 Copynumber: 4.6 Consensus size: 28
287429 TTAATTCTTT
* *
287439 GGTGCTATTCTGGGAATTAATTCGAAATG
1 GGTGCTATT-TTGGAATTAATTCGAAAAG
* ** *
287468 GGTGCTATATTGGTAATTTTTTTTTCGAAAAA
1 GGTGCTATTTTGG-AA---TTAATTCGAAAAG
* ** * * *
287500 GGTGATATTCTAAGAACTAATTTGAAAAT
1 GGTGCTATT-TTGGAATTAATTCGAAAAG
*
287529 GGTGATATTTTAGGAATTAATTCGAAAAG
1 GGTGCTATTTT-GGAATTAATTCGAAAAG
287558 GGTGCTATTTTGGTAATTA
1 GGTGCTATTTTGG-AATTA
287577 TTTAAAAAAA
Statistics
Matches: 81, Mismatches: 21, Indels: 14
0.70 0.18 0.12
Matches are distributed among these distances:
28 6 0.07
29 55 0.68
32 18 0.22
33 2 0.02
ACGTcount: A:0.32, C:0.07, G:0.22, T:0.39
Consensus pattern (28 bp):
GGTGCTATTTTGGAATTAATTCGAAAAG
Found at i:294789 original size:29 final size:29
Alignment explanation
Indices: 294726--294823 Score: 96
Period size: 29 Copynumber: 3.5 Consensus size: 29
294716 TTAATTCGGT
* * *
294726 TATTTTGGTAATT-TTTC-AAAAA-GTGA
1 TATTTTGGGAATTAATTCGAAAAATGTGC
* * *
294752 TATTCTGGGAATTAATTTG-AAATTGGTGC
1 TATTTTGGGAATTAATTCGAAAAAT-GTGC
294781 TATTTTGGGAATTAATTCGAAAAATGTGC
1 TATTTTGGGAATTAATTCGAAAAATGTGC
*
294810 TATTTTGGTAATTA
1 TATTTTGGGAATTA
294824 TTTAAAAAAA
Statistics
Matches: 57, Mismatches: 10, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
26 11 0.19
27 5 0.09
29 37 0.65
30 4 0.07
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.44
Consensus pattern (29 bp):
TATTTTGGGAATTAATTCGAAAAATGTGC
Found at i:294832 original size:29 final size:29
Alignment explanation
Indices: 294743--294833 Score: 78
Period size: 29 Copynumber: 3.2 Consensus size: 29
294733 GTAATTTTTC
* * *
294743 AAAAA-GTGATATTCTGGGAATTAATT-T
1 AAAAATGTGCTATTTTGGGAATTAATTAA
* * **
294770 GAAATTGGTGCTATTTTGGGAATTAATTCG
1 AAAAAT-GTGCTATTTTGGGAATTAATTAA
* *
294800 AAAAATGTGCTATTTTGGTAATTATTTAA
1 AAAAATGTGCTATTTTGGGAATTAATTAA
294829 AAAAA
1 AAAAA
294834 GGGTGTTATT
Statistics
Matches: 50, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
27 3 0.06
29 43 0.86
30 4 0.08
ACGTcount: A:0.38, C:0.04, G:0.19, T:0.38
Consensus pattern (29 bp):
AAAAATGTGCTATTTTGGGAATTAATTAA
Done.