Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008879.1 Hibiscus syriacus cultivar Beakdansim tig00112123_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: 283077
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
File 2 of 2
Found at i:251032 original size:52 final size:52
Alignment explanation
Indices: 250972--251224 Score: 262
Period size: 52 Copynumber: 4.8 Consensus size: 52
250962 CGGAAAATAC
* *
250972 AATCGCAACGCGA-AAT-GAAAATCCCAACATGAAAATCGCAACGCGAAATGAA
1 AATCGCAACGCGAGAATCG-AAATCCGAA-ATGAAAATCGCAATGCGAAATGAA
* * *
251024 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGCGAGAATCGAAATCCGAAATGAAAATCGCAATGCGAAATGAA
* * *
251076 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGCGAGAATCGAAATCCGAAATGAAAATCGCAATGCGAAATGAA
* * * * *
251128 AATCG-AAC-CGACATAATCGCAATGCGAAATTAAAATCGCAATACGAAATGAA
1 AATCGCAACGCG--AGAATCGAAATCCGAAATGAAAATCGCAATGCGAAATGAA
* * *
251180 AATCGCAATGCGAAATGAAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAACGCG--A-G-AATCGAAATCCGAAATGAAAATCGCAA
251225 CGAAAGAATC
Statistics
Matches: 180, Mismatches: 13, Indels: 12
0.88 0.06 0.06
Matches are distributed among these distances:
50 1 0.01
51 3 0.02
52 134 0.74
53 11 0.06
54 5 0.03
56 26 0.14
ACGTcount: A:0.47, C:0.19, G:0.20, T:0.14
Consensus pattern (52 bp):
AATCGCAACGCGAGAATCGAAATCCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:251269 original size:52 final size:53
Alignment explanation
Indices: 251038--251298 Score: 278
Period size: 52 Copynumber: 4.9 Consensus size: 53
251028 GCAACGAGAG
*
251038 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAAAATCGCAA--CGAAATG--AATCGCAATGCGAAATGAA
**
251090 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA----AAT-CGAACCGACA
1 AATCGCAATGCGAAATGAAAATCGCAA--CGAAATGAATCGCAATGCGAAATGA-A
*
251141 TAATCGCAATGCGAAATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAAATG-A
1 -AATCGCAATGCGAAATGAAAATCGC-A-ACGAAATG--AATCGCAATGCGAAATGAA
251198 AATCGCAATGCGAAATGAAAATCGCAACGAAA-GAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAAATGAATCGCAATGCGAAATGAA
*
251250 AATCGCAATGCGAAATGAAAATCGCAACGAGAT-AATCGCAATGCGAAAT
1 AATCGCAATGCGAAATGAAAATCGCAACGAAATGAATCGCAATGCGAAAT
251299 TATAAACGCA
Statistics
Matches: 185, Mismatches: 7, Indels: 34
0.82 0.03 0.15
Matches are distributed among these distances:
46 2 0.01
47 2 0.01
50 4 0.02
51 17 0.09
52 115 0.62
53 2 0.01
54 9 0.05
55 1 0.01
56 24 0.13
57 1 0.01
58 3 0.02
59 5 0.03
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (53 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAAATGAATCGCAATGCGAAATGAA
Found at i:251414 original size:19 final size:19
Alignment explanation
Indices: 251305--251406 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
251295 AAATTATAAA
251305 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
251324 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
251344 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
251360 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
251377 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
251396 CGCATTGCGAT
1 CGCATTGCGAT
251407 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:251546 original size:14 final size:14
Alignment explanation
Indices: 251513--251548 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
251503 CATCAATTAC
251513 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
251527 AC-AATCATCTTTT
1 ACAAATCAACTTTT
251540 ACAAATCAA
1 ACAAATCAA
251549 TTAAACAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.33
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:253526 original size:14 final size:14
Alignment explanation
Indices: 253507--253563 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
253497 GCGAAATGAA
*
253507 AATCGCAACGACAG
1 AATCGCAACGAAAG
253521 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
253538 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
253554 AATCGCAACG
1 AATCGCAACG
253564 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:253534 original size:33 final size:33
Alignment explanation
Indices: 253488--253579 Score: 166
Period size: 33 Copynumber: 2.8 Consensus size: 33
253478 GCGAAACCAA
*
253488 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
253521 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
253554 AATCGCAACGCGAAATGAAAATCGCA
1 AATCGCAACGCGAAATGAAAATCGCA
253580 TTGCGATTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.47, C:0.22, G:0.21, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:253585 original size:19 final size:19
Alignment explanation
Indices: 253451--253579 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
253441 TAGTTTACTT
* *
253451 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
253471 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
253490 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
253509 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
253523 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
253542 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
253556 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
253575 TCGCA
1 TCGCA
253580 TTGCGATTTT
Statistics
Matches: 92, Mismatches: 7, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.17
16 11 0.12
17 11 0.12
19 42 0.46
20 12 0.13
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:253622 original size:33 final size:33
Alignment explanation
Indices: 253580--253672 Score: 152
Period size: 33 Copynumber: 2.8 Consensus size: 33
253570 GAAAATCGCA
253580 TTGCGATTTTCATTTCGCGTTGCGA-TCTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTC-TGTCG
**
253613 TTGCGATTTTGGTTTCGCGTTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
253646 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
253673 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
33 53 0.96
34 2 0.04
ACGTcount: A:0.09, C:0.19, G:0.26, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:253701 original size:20 final size:19
Alignment explanation
Indices: 253575--253709 Score: 105
Period size: 19 Copynumber: 7.6 Consensus size: 19
253565 GAAATGAAAA
*
253575 TCGCATTGCGATTTTCA-TT
1 TCGCGTTGCGATTTT-AGTT
*
253594 TCGCGTTGCGATCTT-G--
1 TCGCGTTGCGATTTTAGTT
*
253610 T--CGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTAGTT
*
253627 TCGCGTTGCGATTCT-G--
1 TCGCGTTGCGATTTTAGTT
253643 T--CGTTGCGATTTTCA-TT
1 TCGCGTTGCGATTTT-AGTT
*
253660 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTAGTT
253679 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTT-AGTT
*
253699 TCGTGTTGCGA
1 TCGCGTTGCGA
253710 AAGTAAACTA
Statistics
Matches: 94, Mismatches: 8, Indels: 27
0.73 0.06 0.21
Matches are distributed among these distances:
14 22 0.23
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 53 0.56
20 13 0.14
ACGTcount: A:0.10, C:0.19, G:0.27, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTAGTT
Found at i:253912 original size:93 final size:93
Alignment explanation
Indices: 253753--254225 Score: 921
Period size: 93 Copynumber: 5.1 Consensus size: 93
253743 TTGAATGGAT
253753 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
253818 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
253846 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
253911 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
253939 AAATTTACTTTCAACCAAAAGATAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
254004 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
254032 AAATTTACTTTCAACCAAAAGACAAAACAACGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
254096 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
254124 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
254189 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
254217 AAATTTACT
1 AAATTTACT
254226 AAGCAATCTA
Statistics
Matches: 375, Mismatches: 4, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
92 91 0.24
93 284 0.76
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:254179 original size:185 final size:186
Alignment explanation
Indices: 253753--254225 Score: 921
Period size: 185 Copynumber: 2.5 Consensus size: 186
253743 TTGAATGGAT
253753 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
253818 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
253883 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
*
253939 AAATTTACTTTCAACCAAAAGATAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
254004 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAACGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
254069 TA-TATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
254124 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
254189 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
254226 AAGCAATCTA
Statistics
Matches: 284, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
185 154 0.54
186 130 0.46
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:255950 original size:14 final size:14
Alignment explanation
Indices: 255931--256020 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
255921 TTGAAATGAA
255931 AATCGCAACGAGAG
1 AATCGCAACGAGAG
255945 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
255962 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
255978 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
255997 AATCGCAACGAGAG
1 AATCGCAACGAGAG
256011 AATCGCAACG
1 AATCGCAACG
256021 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:255968 original size:33 final size:33
Alignment explanation
Indices: 255923--256037 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
255913 TCTTTTGGTT
255923 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
255956 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
255989 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
256022 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
256038 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:255969 original size:19 final size:18
Alignment explanation
Indices: 255930--256042 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
255920 GTTGAAATGA
255930 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
255945 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
255962 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
255978 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
255995 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
256011 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
256028 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
256043 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:256073 original size:14 final size:14
Alignment explanation
Indices: 256054--256108 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
256044 TTTGGTTTCG
256054 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
256068 CGTTGCGATTTCCATTTCG
1 CGTTGCGA-TT-C---TCT
256087 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
256101 CGTTGCGA
1 CGTTGCGA
256109 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 2 0.06
16 1 0.03
17 1 0.03
18 2 0.06
19 10 0.29
ACGTcount: A:0.09, C:0.27, G:0.24, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:256271 original size:33 final size:33
Alignment explanation
Indices: 256229--256299 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
256219 AATACTAACT
*
256229 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
256262 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
256295 TGAAA
1 TGAAA
256300 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:256532 original size:22 final size:22
Alignment explanation
Indices: 256480--256534 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
256470 TGGTTGTGAG
**
256480 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
256502 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
256524 GGATTTCTTCG
1 GGATTTCTTCG
256535 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:256705 original size:20 final size:20
Alignment explanation
Indices: 256680--256873 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
256670 CTTTAAATAT
256680 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
256700 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
256722 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
256741 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
256761 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
256781 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
256801 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
256821 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
256841 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
256861 CGCGTTGCGATTT
1 CGCGTTGCGATTT
256874 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:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:256867 original size:60 final size:60
Alignment explanation
Indices: 256680--256873 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
256670 CTTTAAATAT
**
256680 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
256741 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
256801 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
256861 CGCGTTGCGATTT
1 CGCGTTGCGATTT
256874 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:256890 original size:21 final size:20
Alignment explanation
Indices: 256866--256942 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 20
256856 ATATTCGCGT
256866 TGCGATTTTGGAAAATCGCAA
1 TGCGATTTTGGAAAATCGC-A
* * **
256887 TGCGAATTTGTACTATCGCA
1 TGCGATTTTGGAAAATCGCA
* *
256907 TCGCGATTTT-CAAGAATCGCGT
1 T-GCGATTTTGGAA-AATCGC-A
256929 TGCGATTTTGGAAA
1 TGCGATTTTGGAAA
256943 CTGATTTGCG
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
20 3 0.07
21 36 0.86
22 3 0.07
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (20 bp):
TGCGATTTTGGAAAATCGCA
Found at i:256953 original size:20 final size:20
Alignment explanation
Indices: 256928--256979 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
256918 AAGAATCGCG
*
256928 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
256948 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
256968 TTGCGATTCTGG
1 TTGCGATTCTGG
256980 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:259219 original size:14 final size:15
Alignment explanation
Indices: 259187--259220 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
259177 TAGATACGAT
259187 TATTTAAATATAAAA
1 TATTTAAATATAAAA
*
259202 TATTTAAATA-ATAA
1 TATTTAAATATAAAA
259216 TATTT
1 TATTT
259221 TTTAACTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TATTTAAATATAAAA
Found at i:270097 original size:21 final size:21
Alignment explanation
Indices: 270073--270136 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
270063 GCAAATTCGC
270073 GTTGCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
* **
270094 GTTGAAAATCGCGTTGCGAT-
1 GTTGCATTTCGCGTTGCGATA
* *
270114 TTTCCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
270135 GT
1 GT
270137 CTACAGTTGT
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
20 15 0.45
21 18 0.55
ACGTcount: A:0.17, C:0.19, G:0.27, T:0.38
Consensus pattern (21 bp):
GTTGCATTTCGCGTTGCGATA
Found at i:270893 original size:22 final size:22
Alignment explanation
Indices: 270868--270955 Score: 94
Period size: 22 Copynumber: 4.1 Consensus size: 22
270858 GAAAATCACG
270868 ACGACAA-TCGTAGACTATCGCA
1 ACGACAACT-GTAGACTATCGCA
*
270890 ACGATAACTGTAGACTATCGCA
1 ACGACAACTGTAGACTATCGCA
* * **
270912 ACG--AA-TTTGGAAAATCGCA
1 ACGACAACTGTAGACTATCGCA
270931 ACGACAACTGTAGACTATCGCA
1 ACGACAACTGTAGACTATCGCA
270953 ACG
1 ACG
270956 CGAAATGAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
19 13 0.25
20 2 0.04
21 2 0.04
22 35 0.66
23 1 0.02
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (22 bp):
ACGACAACTGTAGACTATCGCA
Found at i:270966 original size:41 final size:42
Alignment explanation
Indices: 270884--270974 Score: 125
Period size: 41 Copynumber: 2.2 Consensus size: 42
270874 ATCGTAGACT
* *
270884 ATCGCAACGATAACTGTAGACTATCGCAACGAATTTGG-AAA
1 ATCGCAACGACAACTGTAGACTATCGCAACGAATATGGAAAA
270925 ATCGCAACGACAACTGTAGACTATCGCAACGCGAA-AT-GAAAA
1 ATCGCAACGACAACTGTAGACTATCGCAA--CGAATATGGAAAA
270967 ATCGCAAC
1 ATCGCAAC
270975 ACGAATTTGC
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
41 29 0.64
42 12 0.27
43 4 0.09
ACGTcount: A:0.41, C:0.23, G:0.19, T:0.18
Consensus pattern (42 bp):
ATCGCAACGACAACTGTAGACTATCGCAACGAATATGGAAAA
Found at i:270979 original size:63 final size:63
Alignment explanation
Indices: 270847--270983 Score: 163
Period size: 63 Copynumber: 2.2 Consensus size: 63
270837 TTAACTATCA
* * * **
270847 CAACGAATTTGGAAAATCACGACGACAATCGTAGACTATCGCAACGATAACTGTAGACTATCG
1 CAACGAATTTGGAAAATCACAACGACAATCGTAGACTATCGCAACGAGAAATGTAGAAAATCG
* *
270910 CAACGAATTTGGAAAATCGCAACGACAA-CTGTAGACTATCGCAACGCGAAATG-A-AAAATCG
1 CAACGAATTTGGAAAATCACAACGACAATC-GTAGACTATCGCAACGAGAAATGTAGAAAATCG
270971 CAACACGAATTTG
1 C-A-ACGAATTTG
270984 CGATAGTGGA
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
61 6 0.09
62 3 0.05
63 55 0.86
ACGTcount: A:0.40, C:0.22, G:0.19, T:0.19
Consensus pattern (63 bp):
CAACGAATTTGGAAAATCACAACGACAATCGTAGACTATCGCAACGAGAAATGTAGAAAATCG
Found at i:271158 original size:19 final size:16
Alignment explanation
Indices: 271112--271162 Score: 57
Period size: 16 Copynumber: 3.0 Consensus size: 16
271102 TTATTTTCTC
*
271112 ATATTATAATTATATA
1 ATATTATAATTATAAA
*
271128 ATATTTTAATTATAAA
1 ATATTATAATTATAAA
271144 AGTTCATTATAATTATAAA
1 A--T-ATTATAATTATAAA
271163 GCTAATTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
16 15 0.52
18 1 0.03
19 13 0.45
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (16 bp):
ATATTATAATTATAAA
Found at i:271469 original size:21 final size:21
Alignment explanation
Indices: 271421--271466 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
271411 GTTGGATATA
* * *
271421 AGGTTAGGGTTTATGGTTTAG
1 AGGTTATGCTTTATGGTGTAG
271442 AGGTTATGCTTTATGGTGTAG
1 AGGTTATGCTTTATGGTGTAG
271463 -GGTT
1 AGGTT
271467 TATAATTTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.17, C:0.02, G:0.37, T:0.43
Consensus pattern (21 bp):
AGGTTATGCTTTATGGTGTAG
Found at i:271491 original size:13 final size:14
Alignment explanation
Indices: 271460--271493 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
271450 CTTTATGGTG
*
271460 TAGGGTTTATAATT
1 TAGGGTTTATAAGT
271474 TAGGGTTT-TAAGT
1 TAGGGTTTATAAGT
271487 TAGGGTT
1 TAGGGTT
271494 AGGGTATAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.24, C:0.00, G:0.29, T:0.47
Consensus pattern (14 bp):
TAGGGTTTATAAGT
Found at i:276693 original size:219 final size:219
Alignment explanation
Indices: 276314--276755 Score: 866
Period size: 219 Copynumber: 2.0 Consensus size: 219
276304 TAAGATGAAT
276314 GTGGATGGAGCTGTTAGTAGTGTGGGTATGATTACTGGAATTGGGGGTATTCTGAGAGATTGGAA
1 GTGGATGGAGCTGTTAGTAGTGTGGGTATGATTACTGGAATTGGGGGTATTCTGAGAGATTGGAA
276379 TCAGAATAAGCTTCTTTCTTTTTCAGAAAATGTTGGTCCTACTCCTATCATTCTAGCAGAGTTGA
66 TCAGAATAAGCTTCTTTCTTTTTCAGAAAATGTTGGTCCTACTCCTATCATTCTAGCAGAGTTGA
276444 AAGCTATAAAAAAAGGCATAAACATCTTTCTCTCTTCAGATTGGGTATCAAAGGAAAGGCTCATT
131 AAGCTATAAAAAAAGGCATAAACATCTTTCTCTCTTCAGATTGGGTATCAAAGGAAAGGCTCATT
276509 GTGGAAAGTGATAGTAAGTTAGCA
196 GTGGAAAGTGATAGTAAGTTAGCA
*
276533 GTGGATGGAGCTGTTAGTAGTGTGGGTATGATTACTGGAATTGGGGGTATTTTGAGAGATTGGAA
1 GTGGATGGAGCTGTTAGTAGTGTGGGTATGATTACTGGAATTGGGGGTATTCTGAGAGATTGGAA
276598 TCAGAATAAGCTTCTTTCTTTTTCAGAAAATGTTGGTCCTACTCCTATCATTCTAGCAGAGTTGA
66 TCAGAATAAGCTTCTTTCTTTTTCAGAAAATGTTGGTCCTACTCCTATCATTCTAGCAGAGTTGA
*
276663 AAGCTATAAAAAAAGGCATAAACATCTTTCTCTCTTCAGATTGGGTATCAAAGGGAAGGCTCATT
131 AAGCTATAAAAAAAGGCATAAACATCTTTCTCTCTTCAGATTGGGTATCAAAGGAAAGGCTCATT
276728 GTGGAAAGTGATAGTAAGTTAGCA
196 GTGGAAAGTGATAGTAAGTTAGCA
276752 GTGG
1 GTGG
276756 GTTGGATGAA
Statistics
Matches: 221, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
219 221 1.00
ACGTcount: A:0.30, C:0.12, G:0.26, T:0.32
Consensus pattern (219 bp):
GTGGATGGAGCTGTTAGTAGTGTGGGTATGATTACTGGAATTGGGGGTATTCTGAGAGATTGGAA
TCAGAATAAGCTTCTTTCTTTTTCAGAAAATGTTGGTCCTACTCCTATCATTCTAGCAGAGTTGA
AAGCTATAAAAAAAGGCATAAACATCTTTCTCTCTTCAGATTGGGTATCAAAGGAAAGGCTCATT
GTGGAAAGTGATAGTAAGTTAGCA
Found at i:278003 original size:11 final size:11
Alignment explanation
Indices: 277987--278013 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
277977 CATGAATGGA
277987 GATGTGTTGAT
1 GATGTGTTGAT
277998 GATGTGTTGAT
1 GATGTGTTGAT
278009 GATGT
1 GATGT
278014 TCGATTGTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.37, T:0.44
Consensus pattern (11 bp):
GATGTGTTGAT
Done.