Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003385.1 Hibiscus syriacus cultivar Beakdansim tig00007124_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: 59906
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:6913 original size:38 final size:39
Alignment explanation
Indices: 6832--6914 Score: 91
Period size: 38 Copynumber: 2.2 Consensus size: 39
6822 TATAAGTTAG
* * * *
6832 AAAATATTTATATATTTTCTTTAAAAAATTTAAATTCCT
1 AAAAAATTTATATATTTTCTTTAAAAAATTAAAAATCAT
*
6871 -AAAAATTTATATAATTTT-TTTACAAAATTAAAAAT-AT
1 AAAAAATTTATAT-ATTTTCTTTAAAAAATTAAAAATCAT
6908 AAAAAAT
1 AAAAAAT
6915 GTTTAATAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
37 1 0.03
38 31 0.84
39 5 0.14
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (39 bp):
AAAAAATTTATATATTTTCTTTAAAAAATTAAAAATCAT
Found at i:10653 original size:29 final size:29
Alignment explanation
Indices: 10593--10649 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
10583 GAATAGAGTT
10593 TTGTTGTTGTTGTTAAGTCATTTTTGTTG
1 TTGTTGTTGTTGTTAAGTCATTTTTGTTG
10622 TTGTTGTTGTTGTTAAGTCA-TTTTGTTG
1 TTGTTGTTGTTGTTAAGTCATTTTTGTTG
10650 GTTGATTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 8 0.29
29 20 0.71
ACGTcount: A:0.11, C:0.04, G:0.25, T:0.61
Consensus pattern (29 bp):
TTGTTGTTGTTGTTAAGTCATTTTTGTTG
Found at i:15336 original size:23 final size:23
Alignment explanation
Indices: 15303--15347 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
15293 ATTGTTGATT
15303 CAATTTCACAT-TCTTAAATTTTA
1 CAATTTCACATCT-TTAAATTTTA
*
15326 CAATTTTACATCTTTAAATTTT
1 CAATTTCACATCTTTAAATTTT
15348 TAATATAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.33, C:0.16, G:0.00, T:0.51
Consensus pattern (23 bp):
CAATTTCACATCTTTAAATTTTA
Found at i:26090 original size:60 final size:60
Alignment explanation
Indices: 26019--26188 Score: 268
Period size: 60 Copynumber: 2.8 Consensus size: 60
26009 ATCAGGTAAA
*
26019 TATTTTGTAATTTTTAATAATCGAGGGACTCAACAAAATAACATTCTATAGTTAGGGGAT
1 TATTTTATAATTTTTAATAATCGAGGGACTCAACAAAATAACATTCTATAGTTAGGGGAT
*
26079 TATTTTATAATTTTTAATAATCGAGGGACTCAACAAAATAATATTCTATAGTTAGGGGAT
1 TATTTTATAATTTTTAATAATCGAGGGACTCAACAAAATAACATTCTATAGTTAGGGGAT
* * * * * *
26139 TGTTTTATAACTTTTAATAATTGAGGGACTCAATAAAGTAACATCCTATA
1 TATTTTATAATTTTTAATAATCGAGGGACTCAACAAAATAACATTCTATA
26189 ATTGAAGGAC
Statistics
Matches: 101, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 101 1.00
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.38
Consensus pattern (60 bp):
TATTTTATAATTTTTAATAATCGAGGGACTCAACAAAATAACATTCTATAGTTAGGGGAT
Found at i:26471 original size:21 final size:21
Alignment explanation
Indices: 26447--26495 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
26437 AAAGTGTCAT
26447 AAAATAACAAAACCGATAGAA
1 AAAATAACAAAACCGATAGAA
* *
26468 AAAATAACAAAATCGGTAGAA
1 AAAATAACAAAACCGATAGAA
*
26489 ATAATAA
1 AAAATAA
26496 TATTTTTGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.65, C:0.10, G:0.10, T:0.14
Consensus pattern (21 bp):
AAAATAACAAAACCGATAGAA
Found at i:26951 original size:21 final size:20
Alignment explanation
Indices: 26925--27022 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
26915 ATCAGTTTCC
26925 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTG
* **
26946 AAAATCGCAATGCGATAGT-
1 AAAATCGCAACGCGATTTTG
** *
26965 ACAAATTCGCATTGCGATTTTCA
1 A-AAA-TCGCAACGCGATTTT-G
* *
26988 AAAATCGCAACGCGAATATG
1 AAAATCGCAACGCGATTTTG
27008 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
27023 ACACATAAAT
Statistics
Matches: 62, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
19 1 0.02
20 19 0.31
21 38 0.61
22 3 0.05
23 1 0.02
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.21
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTG
Found at i:27051 original size:20 final size:20
Alignment explanation
Indices: 26989--27258 Score: 269
Period size: 20 Copynumber: 13.5 Consensus size: 20
26979 CGATTTTCAA
* ** *
26989 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
27009 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
27029 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
27049 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
27069 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
27089 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
27109 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
27129 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
27149 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
27169 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
27189 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
27209 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
27229 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
27249 AAATCACAAC
1 AAATCGCAAC
27259 ACTGAAATTT
Statistics
Matches: 210, Mismatches: 32, Indels: 16
0.81 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 206 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:27979 original size:24 final size:24
Alignment explanation
Indices: 27940--27986 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
27930 AAATTTGGTC
27940 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
27964 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
27987 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:28178 original size:12 final size:12
Alignment explanation
Indices: 28161--28185 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28151 ATATAATCCT
28161 GAAGAAGAAAAA
1 GAAGAAGAAAAA
28173 GAAGAAGAAAAA
1 GAAGAAGAAAAA
28185 G
1 G
28186 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:28910 original size:20 final size:19
Alignment explanation
Indices: 28872--28918 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
28862 GCGATTCTGT
*
28872 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTTAGTTTCG
28891 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTT-AGTTTCG
*
28911 TGTTGCGA
1 CGTTGCGA
28919 AAGTAAACTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.11, C:0.15, G:0.30, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTAGTTTCG
Found at i:29083 original size:93 final size:93
Alignment explanation
Indices: 28966--29527 Score: 1090
Period size: 93 Copynumber: 6.1 Consensus size: 93
28956 ATGGATTGCA
28966 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
29030 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
*
29058 TTACTTTCAACCAAAAGTCAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
29123 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
*
29151 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTAACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
29216 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
29244 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
29309 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
29337 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
29402 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
29430 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
29495 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
29523 TTACT
1 TTACT
29528 AAGCAATCTA
Statistics
Matches: 464, Mismatches: 5, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
92 4 0.01
93 460 0.99
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:31253 original size:14 final size:14
Alignment explanation
Indices: 31234--31290 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
31224 TTGAAATGAA
31234 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
31248 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
31267 AATCGCAACTAGAG
1 AATCGCAACGAGAG
31281 AATCGCAACG
1 AATCGCAACG
31291 CGAAATGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
15 1 0.03
16 2 0.06
17 1 0.03
18 1 0.03
19 10 0.29
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:31266 original size:33 final size:33
Alignment explanation
Indices: 31226--31340 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
31216 TCTTTTGGTT
31226 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
31259 GAAATGAAAATCGCAACTAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
31292 GAAATGAAAATCGCAACGAGAGAATCACAATGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
31325 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
31341 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:0.48, C:0.19, G:0.22, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:31272 original size:19 final size:18
Alignment explanation
Indices: 31226--31345 Score: 75
Period size: 19 Copynumber: 7.1 Consensus size: 18
31216 TCTTTTGGTT
31226 GAAATGAAAATCGCAA-C
1 GAAATGAAAATCGCAAGC
*
31243 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAA-GC
31259 GAAATGAAAATCGCAA-C
1 GAAATGAAAATCGCAAGC
* *
31276 --TA-GAGAATCGCAACGC
1 GAAATGAAAATCGCAA-GC
31292 GAAATGAAAATCGCAA-C
1 GAAATGAAAATCGCAAGC
* *
31309 G--A-GAGAATCACAATGC
1 GAAATGAAAATCGCAA-GC
31325 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAA-GC
31344 GA
1 GA
31346 TTTTGGTTTC
Statistics
Matches: 78, Mismatches: 10, Indels: 28
0.67 0.09 0.24
Matches are distributed among these distances:
14 29 0.37
15 3 0.04
16 5 0.06
17 4 0.05
18 3 0.04
19 34 0.44
ACGTcount: A:0.47, C:0.19, G:0.23, T:0.12
Consensus pattern (18 bp):
GAAATGAAAATCGCAAGC
Found at i:31421 original size:41 final size:41
Alignment explanation
Indices: 31364--31441 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
31354 TCGCGTTGCG
*
31364 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
31405 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
31442 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:31426 original size:20 final size:21
Alignment explanation
Indices: 31365--31440 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
31355 CGCGTTGCGA
31365 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
31386 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
31406 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
31427 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
31441 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:31562 original size:33 final size:33
Alignment explanation
Indices: 31520--31590 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
31510 AATACTAACT
*
31520 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
31553 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
31586 TGAAA
1 TGAAA
31591 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:31824 original size:22 final size:22
Alignment explanation
Indices: 31772--31826 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
31762 TGGTTGTGAG
**
31772 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
31794 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
31816 GGATTTCTTCG
1 GGATTTCTTCG
31827 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:31998 original size:20 final size:20
Alignment explanation
Indices: 31973--32126 Score: 168
Period size: 20 Copynumber: 7.7 Consensus size: 20
31963 CTTTAAATAT
31973 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
31993 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
32015 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
32034 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
32054 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
32074 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
32094 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
32114 CGCGTTGCGATTT
1 CGCGTTGCGATTT
32127 TGGAAACTGA
Statistics
Matches: 113, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.02
20 94 0.83
21 15 0.13
22 2 0.02
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:32100 original size:40 final size:40
Alignment explanation
Indices: 31972--32126 Score: 186
Period size: 40 Copynumber: 3.9 Consensus size: 40
31962 GCTTTAAATA
*
31972 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTGT
** * *
32013 TATCGTTGCGATTTACGGATACGCGTTGCGATATACG-GAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTG-T
* *
32053 ACACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
* ** *
32093 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTT
32127 TGGAAACTGA
Statistics
Matches: 96, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
40 66 0.69
41 30 0.31
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.37
Consensus pattern (40 bp):
TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
Found at i:32355 original size:16 final size:16
Alignment explanation
Indices: 32322--32362 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
32312 GGTTACTTTA
32322 GAATGATT-AAACGCT
1 GAATGATTCAAACGCT
*
32337 GAATGATTCAAATGCT
1 GAATGATTCAAACGCT
*
32353 GAACGATTCA
1 GAATGATTCA
32363 GAGGTTCTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.27
Consensus pattern (16 bp):
GAATGATTCAAACGCT
Found at i:35156 original size:41 final size:42
Alignment explanation
Indices: 35060--35452 Score: 302
Period size: 41 Copynumber: 9.6 Consensus size: 42
35050 CATGTAGCAA
* *
35060 CGTTTATATAACAAACGCCACAA-AATGGT-A-ACTTTAGCGG
1 CGTTTTTATAACAAACGCCGCAATAA-GGTAATACTTTAGCGG
* * *
35100 CATTTTTATAA-AAACGCCGCAATAAGGTAAT-CTATAGTGG
1 CGTTTTTATAACAAACGCCGCAATAAGGTAATACTTTAGCGG
*
35140 CGTTTTTTTAACAAACGCCGCAA-AAGAGTAATAC-TTAGCGG
1 CGTTTTTATAACAAACGCCGCAATAAG-GTAATACTTTAGCGG
*
35181 CGTTTTTAT-ACAAACGCCGCAAT-AGAGTAGTACTTTAGCGG
1 CGTTTTTATAACAAACGCCGCAATAAG-GTAATACTTTAGCGG
*
35222 CGTTTTTAT-ACAAACGCCGCAAT-AGAGTATTACTTTAGCGG
1 CGTTTTTATAACAAACGCCGCAATAAG-GTAATACTTTAGCGG
* * * * * *
35263 CGTTTTTAT-ACAAATGCCACAATAGGGTTCAT-CTGTAGTGG
1 CGTTTTTATAACAAACGCCGCAATAAGG-TAATACTTTAGCGG
* * * *
35304 TGGTTTTT-CAACAAACGCCGCAAT-AGAGTAGTACTTTAGTGG
1 -CGTTTTTATAACAAACGCCGCAATAAG-GTAATACTTTAGCGG
** * * *
35346 CGTTTTTATAA-AAACGCCATAATAGGGTTCAT-CTTTAGTGG
1 CGTTTTTATAACAAACGCCGCAATAAGG-TAATACTTTAGCGG
* * * * *
35387 CATTTTT-TCAACAAACACCGTAATAAAGTAGTACTTTAGCGG
1 CGTTTTTAT-AACAAACGCCGCAATAAGGTAATACTTTAGCGG
* *
35429 CATTTTTAT-ACAAAAGCCGCAATA
1 CGTTTTTATAACAAACGCCGCAATA
35453 GTTTGGTATG
Statistics
Matches: 287, Mismatches: 45, Indels: 41
0.77 0.12 0.11
Matches are distributed among these distances:
39 13 0.05
40 54 0.19
41 156 0.54
42 63 0.22
43 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.31
Consensus pattern (42 bp):
CGTTTTTATAACAAACGCCGCAATAAGGTAATACTTTAGCGG
Found at i:35339 original size:83 final size:82
Alignment explanation
Indices: 35090--35453 Score: 412
Period size: 83 Copynumber: 4.4 Consensus size: 82
35080 CAAAATGGTA
* * * * * * *
35090 ACTTTAGCGGCATTTTTATAAAAACGCCGCAATAAGGTAATCTATAGTGGCGTTTTTTTAACAAA
1 ACTTTAGCGGCGTTTTTATACAAACGCCGCAATAGGGTCATCTTTAGTGGCGGTTTTTCAACAAA
* *
35155 CGCCGCAAAAGAGTAAT
66 CGCCGCAATAGAGTAGT
* *
35172 AC-TTAGCGGCGTTTTTATACAAACGCCGCAATAGAGT-AGTACTTTAGCGGC-GTTTTT-ATAC
1 ACTTTAGCGGCGTTTTTATACAAACGCCGCAATAGGGTCA-T-CTTTAGTGGCGGTTTTTCA-AC
*
35233 AAACGCCGCAATAGAGTATT
63 AAACGCCGCAATAGAGTAGT
* * * *
35253 ACTTTAGCGGCGTTTTTATACAAATGCCACAATAGGGTTCATCTGTAGTGGTGGTTTTTCAACAA
1 ACTTTAGCGGCGTTTTTATACAAACGCCGCAATAGGG-TCATCTTTAGTGGCGGTTTTTCAACAA
35318 ACGCCGCAATAGAGTAGT
65 ACGCCGCAATAGAGTAGT
* * ** **
35336 ACTTTAGTGGCGTTTTTATAAAAACGCCATAATAGGGTTCATCTTTAGTGGCATTTTTTCAACAA
1 ACTTTAGCGGCGTTTTTATACAAACGCCGCAATAGGG-TCATCTTTAGTGGCGGTTTTTCAACAA
* * *
35401 ACACCGTAATAAAGTAGT
65 ACGCCGCAATAGAGTAGT
* *
35419 ACTTTAGCGGCATTTTTATACAAAAGCCGCAATAG
1 ACTTTAGCGGCGTTTTTATACAAACGCCGCAATAG
35454 TTTGGTATGT
Statistics
Matches: 241, Mismatches: 33, Indels: 15
0.83 0.11 0.05
Matches are distributed among these distances:
80 2 0.01
81 59 0.24
82 48 0.20
83 130 0.54
84 2 0.01
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.31
Consensus pattern (82 bp):
ACTTTAGCGGCGTTTTTATACAAACGCCGCAATAGGGTCATCTTTAGTGGCGGTTTTTCAACAAA
CGCCGCAATAGAGTAGT
Found at i:35435 original size:124 final size:121
Alignment explanation
Indices: 35090--35453 Score: 362
Period size: 124 Copynumber: 3.0 Consensus size: 121
35080 CAAAATGGTA
* * *
35090 ACTTTAGCGGCATTTTTATAAAAACGCCGCAATAAGG-TAATCTATAGTGGCGTTTTTTTAACAA
1 ACTTTAGCGGCGTTTTTATAAAAACGCCGCAATAGGGTTAATCTTTAGTGGC--TTTTTTAACAA
35154 ACGCCGCAA-AAGAGTAATAC-TTAGCGGCGTTTTTATACAAACGCCGCAATAGAGTAGT
64 ACGCCGCAATAA-AGT-ATACTTTAGCGGCGTTTTTATACAAACGCCGCAATAGAGTAGT
* * * * *
35212 ACTTTAGCGGCGTTTTTATACAAACGCCGCAATAGAG-TATTACTTTAGCGGCGTTTTTATACAA
1 ACTTTAGCGGCGTTTTTATAAAAACGCCGCAATAGGGTTAAT-CTTTAGTGGCTTTTTTA-ACAA
* * ** * * *
35276 ATGCCACAATAGGGT-TCATCTGTAGTGGTGGTTTTTCA-ACAAACGCCGCAATAGAGTAGT
64 ACGCCGCAATAAAGTAT-A-CTTTAGCGG-CGTTTTT-ATACAAACGCCGCAATAGAGTAGT
* ** *
35336 ACTTTAGTGGCGTTTTTATAAAAACGCCATAATAGGGTTCATCTTTAGTGGCATTTTTTCAACAA
1 ACTTTAGCGGCGTTTTTATAAAAACGCCGCAATAGGGTTAATCTTTAGTGGC-TTTTTT-AACAA
* * * *
35401 ACACCGTAATAAAGTAGTACTTTAGCGGCATTTTTATACAAAAGCCGCAATAG
64 ACGCCGCAATAAAGTA-TACTTTAGCGGCGTTTTTATACAAACGCCGCAATAG
35454 TTTGGTATGT
Statistics
Matches: 193, Mismatches: 35, Indels: 26
0.76 0.14 0.10
Matches are distributed among these distances:
120 1 0.01
121 7 0.04
122 50 0.26
123 15 0.08
124 89 0.46
125 28 0.15
126 2 0.01
127 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.31
Consensus pattern (121 bp):
ACTTTAGCGGCGTTTTTATAAAAACGCCGCAATAGGGTTAATCTTTAGTGGCTTTTTTAACAAAC
GCCGCAATAAAGTATACTTTAGCGGCGTTTTTATACAAACGCCGCAATAGAGTAGT
Found at i:38272 original size:3 final size:3
Alignment explanation
Indices: 38264--38291 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
38254 CATAACCTTC
38264 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
38292 TTTTAACAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:39533 original size:21 final size:22
Alignment explanation
Indices: 39509--39568 Score: 77
Period size: 21 Copynumber: 2.8 Consensus size: 22
39499 TGATTTATTA
*
39509 TTATGGATTTCAATTTTCTTG-
1 TTATGGATTTCAAGTTTCTTGT
* *
39530 TTATGGATTTTAAGTTTGTTGT
1 TTATGGATTTCAAGTTTCTTGT
*
39552 TTATGGATGTCAAGTTT
1 TTATGGATTTCAAGTTT
39569 ATTGGAAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
21 18 0.55
22 15 0.45
ACGTcount: A:0.20, C:0.05, G:0.20, T:0.55
Consensus pattern (22 bp):
TTATGGATTTCAAGTTTCTTGT
Found at i:40175 original size:15 final size:15
Alignment explanation
Indices: 40157--40190 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
40147 TTTGTTGACC
40157 CCCTTTTGATCAAGT
1 CCCTTTTGATCAAGT
* *
40172 CCCTTTTGTTTAAGT
1 CCCTTTTGATCAAGT
40187 CCCT
1 CCCT
40191 AACATGGCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.29, G:0.12, T:0.44
Consensus pattern (15 bp):
CCCTTTTGATCAAGT
Found at i:40289 original size:30 final size:31
Alignment explanation
Indices: 40236--40298 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 31
40226 ACAGCTGAGA
* *
40236 GACTAAAATCAAACGGATTGATAATATTAGG
1 GACTAAAATCAAACGGATCGATAACATTAGG
* * *
40267 GACT-AAATCGAATGGATCGATAACGTTAGG
1 GACTAAAATCAAACGGATCGATAACATTAGG
40297 GA
1 GA
40299 TCATTCCCTC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 23 0.85
31 4 0.15
ACGTcount: A:0.41, C:0.11, G:0.24, T:0.24
Consensus pattern (31 bp):
GACTAAAATCAAACGGATCGATAACATTAGG
Done.