Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006557.1 Hibiscus syriacus cultivar Beakdansim tig00016029_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: 84179
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:588 original size:23 final size:23
Alignment explanation
Indices: 559--603 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
549 AATTTGGTCT
559 TGGTCAATATC-CGGACTTTGATA
1 TGGTCAATA-CACGGACTTTGATA
*
582 TGGTCAATACACGGATTTTGAT
1 TGGTCAATACACGGACTTTGAT
604 GATGTTTCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 1 0.05
23 19 0.95
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.36
Consensus pattern (23 bp):
TGGTCAATACACGGACTTTGATA
Found at i:3188 original size:52 final size:53
Alignment explanation
Indices: 3075--3191 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
3065 CGAATGAAAA
3075 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
3128 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
3180 TCGCATTGCGAT
1 TCGCATTGCGAT
3192 AGTCATTTTG
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:3199 original size:19 final size:19
Alignment explanation
Indices: 3094--3191 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
3084 GATTCTCTCG
3094 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
3114 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
3133 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
3147 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3166 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3185 TTGCGAT
1 TTGCGAT
3192 AGTCATTTTG
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:3287 original size:14 final size:14
Alignment explanation
Indices: 3268--3321 Score: 63
Period size: 14 Copynumber: 3.6 Consensus size: 14
3258 GGAAATGAAA
3268 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
3282 AATCGCAATGCGAAATG
1 AATCGCAA--CGAGA-G
3299 AAATCGCAACGAGAG
1 -AATCGCAACGAGAG
3314 AATCGCAA
1 AATCGCAA
3322 TGCGAAATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
14 16 0.47
15 1 0.03
16 8 0.24
17 1 0.03
18 8 0.24
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:3308 original size:32 final size:33
Alignment explanation
Indices: 3249--3340 Score: 159
Period size: 32 Copynumber: 2.8 Consensus size: 33
3239 CCATTACATT
3249 TCGCAATGCGGAAATGAAAAATCGCAACGAGAGAA
1 TCGCAATGC-GAAATG-AAAATCGCAACGAGAGAA
3284 TCGCAATGCGAAATG-AAATCGCAACGAGAGAA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
3316 TCGCAATGCGAAATGAAAATCGCAA
1 TCGCAATGCGAAATGAAAATCGCAA
3341 TGCGAAATGA
Statistics
Matches: 56, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
32 32 0.57
33 9 0.16
34 6 0.11
35 9 0.16
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.13
Consensus pattern (33 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
Found at i:3338 original size:19 final size:19
Alignment explanation
Indices: 3249--3359 Score: 109
Period size: 19 Copynumber: 6.3 Consensus size: 19
3239 CCATTACATT
3249 TCGCAATGCGGAAATGAAAAA
1 TCGCAATGC-GAAATG-AAAA
*
3270 TCGCAA--CG--A-GAGAA
1 TCGCAATGCGAAATGAAAA
3284 TCGCAATGCGAAATG-AAA
1 TCGCAATGCGAAATGAAAA
*
3302 TCGCAA--CG--A-GAGAA
1 TCGCAATGCGAAATGAAAA
3316 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
3335 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
3354 TCGCAA
1 TCGCAA
3360 CGAGAATCGC
Statistics
Matches: 75, Mismatches: 4, Indels: 24
0.73 0.04 0.23
Matches are distributed among these distances:
13 1 0.01
14 18 0.24
15 1 0.01
16 7 0.09
18 11 0.15
19 31 0.41
21 6 0.08
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (19 bp):
TCGCAATGCGAAATGAAAA
Found at i:3442 original size:19 final size:19
Alignment explanation
Indices: 3400--3499 Score: 147
Period size: 19 Copynumber: 5.5 Consensus size: 19
3390 GCGATTCTCC
3400 CATTGCGATTTTCATTTCCG
1 CATTGCGATTTTCATTT-CG
3420 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
*
3439 CATTGCGA--TTC-TCTCG
1 CATTGCGATTTTCATTTCG
3455 --TTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
3472 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
3491 CATTGCGAT
1 CATTGCGAT
3500 AGTCAATTTT
Statistics
Matches: 73, 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 0.49
20 17 0.23
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (19 bp):
CATTGCGATTTTCATTTCG
Found at i:3496 original size:52 final size:53
Alignment explanation
Indices: 3383--3499 Score: 209
Period size: 53 Copynumber: 2.2 Consensus size: 53
3373 GAAATTAAAA
3383 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
* *
3436 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
3488 TCGCATTGCGAT
1 TCGCATTGCGAT
3500 AGTCAATTTT
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 30 0.48
53 32 0.52
ACGTcount: A:0.15, C:0.25, G:0.17, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:3639 original size:14 final size:14
Alignment explanation
Indices: 3606--3641 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
3596 CATCAATTAC
3606 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
3620 AC-AATCATCTTTT
1 ACAAATCAACTTTT
3633 ACAAATCAA
1 ACAAATCAA
3642 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:5631 original size:14 final size:14
Alignment explanation
Indices: 5612--5668 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
5602 GCGAAATGAA
*
5612 AATCGCAACGACAG
1 AATCGCAACGAAAG
5626 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
5643 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
5659 AATCGCAACG
1 AATCGCAACG
5669 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:5644 original size:33 final size:33
Alignment explanation
Indices: 5593--5685 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
5583 GCGAAACCAA
* *
5593 AATCACAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
5626 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
5659 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
5686 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:5650 original size:19 final size:19
Alignment explanation
Indices: 5556--5690 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
5546 TAGTTTACTT
* *
5556 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
5576 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
*
5595 TCACAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
5614 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
5628 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
5647 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
5661 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
5680 TCGCAATGCGA
1 TCGCAACGCGA
5691 TTTTGGTTTC
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 16 0.17
16 11 0.12
17 11 0.12
19 45 0.47
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:5708 original size:19 final size:19
Alignment explanation
Indices: 5686--5814 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
5676 AAAATCGCAA
5686 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
5705 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
5719 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
5738 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
5752 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
5771 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
5790 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
5810 TGCGA
1 TGCGA
5815 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:5728 original size:33 final size:33
Alignment explanation
Indices: 5686--5777 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
5676 AAAATCGCAA
5686 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
5719 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
5752 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
5778 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:5996 original size:92 final size:93
Alignment explanation
Indices: 5858--6326 Score: 876
Period size: 92 Copynumber: 5.1 Consensus size: 93
5848 TTGAATGGAT
5858 AAATTTACTTTCAACC-AAAGAC-AAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
5921 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
5949 AAATTTACTTTCAACCAAAAGACAAAAC-AAGACAAATACTATTTCACAGTGTTATAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
6013 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
6041 AAATTTACTTTCAACC-AAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
6105 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
6133 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
6198 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
6226 -AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
* *
6290 AGTTTAGCATAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
6318 AAATTTACT
1 AAATTTACT
6327 AAGCAATCTA
Statistics
Matches: 369, Mismatches: 4, Indels: 8
0.97 0.01 0.02
Matches are distributed among these distances:
91 27 0.07
92 254 0.69
93 88 0.24
ACGTcount: A:0.45, C:0.19, G:0.13, T:0.23
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:6289 original size:185 final size:184
Alignment explanation
Indices: 5858--6326 Score: 879
Period size: 185 Copynumber: 2.5 Consensus size: 184
5848 TTGAATGGAT
5858 AAATTTACTTTCAACCAAAGAC-AAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
1 AAATTTACTTTCAACCAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
5922 GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAGACAAATA
66 GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAGACAAATA
*
5987 CTATTTCACAGTGTTATAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 CTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
6041 AAATTTACTTTCAACCAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
1 AAATTTACTTTCAACCAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
6106 GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAAT
66 GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAAC-AAGACAAAT
6171 ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
130 ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
6226 -AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACC-AAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
* *
6290 AGTTTAGCATAATTGGCAGCAACCGAATAAATTTACT
65 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
6327 AAGCAATCTA
Statistics
Matches: 280, Mismatches: 3, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
183 22 0.08
184 112 0.40
185 146 0.52
ACGTcount: A:0.45, C:0.19, G:0.13, T:0.23
Consensus pattern (184 bp):
AAATTTACTTTCAACCAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAGACAAATA
CTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:8047 original size:14 final size:14
Alignment explanation
Indices: 8028--8115 Score: 77
Period size: 14 Copynumber: 5.6 Consensus size: 14
8018 TTGAAATGAA
8028 AATCGCAACGAGAG
1 AATCGCAACGAGAG
8042 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
8059 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
8075 AATCGCAACGCGAAATGAC
1 AATCGCAA--CG--A-GAG
8094 AATCGCAACGAGAG
1 AATCGCAACGAGAG
8108 AATCGCAA
1 AATCGCAA
8116 TGCGAAATGA
Statistics
Matches: 62, Mismatches: 2, Indels: 20
0.74 0.02 0.24
Matches are distributed among these distances:
14 26 0.42
15 1 0.02
16 8 0.13
17 8 0.13
18 1 0.02
19 18 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:8065 original size:33 final size:33
Alignment explanation
Indices: 8020--8134 Score: 194
Period size: 33 Copynumber: 3.5 Consensus size: 33
8010 TCTTTTGGTT
8020 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
8053 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
8086 GAAATGACAATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
8119 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
8135 TGCGATTTTG
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 77 1.00
ACGTcount: A:0.44, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:8066 original size:19 final size:19
Alignment explanation
Indices: 8042--8108 Score: 81
Period size: 19 Copynumber: 3.8 Consensus size: 19
8032 GCAACGAGAG
8042 AATCGCAACGCGAGATGAC
1 AATCGCAACGCGAGATGAC
8061 AATCGCAA--CGAGA-G--
1 AATCGCAACGCGAGATGAC
*
8075 AATCGCAACGCGAAATGAC
1 AATCGCAACGCGAGATGAC
*
8094 AATCGCAACGAGAGA
1 AATCGCAACGCGAGA
8109 ATCGCAATGC
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
14 8 0.20
16 5 0.12
17 6 0.15
19 21 0.52
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAGATGAC
Found at i:8132 original size:19 final size:19
Alignment explanation
Indices: 8075--8139 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 19
8065 GCAACGAGAG
* *
8075 AATCGCAACGCGAAATGAC
1 AATCGCAATGCGAAATGAA
*
8094 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
8108 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
8127 AATCGCAATGCGA
1 AATCGCAATGCGA
8140 TTTTGGTTTC
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 10 0.26
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 23 0.59
ACGTcount: A:0.43, C:0.22, G:0.23, T:0.12
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:8170 original size:14 final size:14
Alignment explanation
Indices: 8151--8207 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
8141 TTTGGTTTCG
8151 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
8165 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
8184 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
8198 CGTTGCGATT
1 CGTTGCGATT
8208 GTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:8183 original size:33 final size:33
Alignment explanation
Indices: 8135--8215 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
8125 AAAATCGCAA
**
8135 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
8168 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
*
8201 TGCGATTGTCATTTC
1 TGCGATTTTCATTTC
8216 TCTCGTTGCG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.09, C:0.22, G:0.23, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:8218 original size:21 final size:21
Alignment explanation
Indices: 8192--8267 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
8182 CGCGTTGCGA
8192 TTCTCTCGTTGCGATTGTCAT
1 TTCTCTCGTTGCGATTGTCAT
**
8213 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTGTCAT
*
8233 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTGTCAT
*
8254 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
8268 CTCTTCTGCA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
20 17 0.35
21 31 0.65
ACGTcount: A:0.12, C:0.25, G:0.18, T:0.45
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTGTCAT
Found at i:8248 original size:41 final size:41
Alignment explanation
Indices: 8191--8268 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
8181 TCGCGTTGCG
*
8191 ATTCTCTCGTTGCGATTGTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTGTCATTTATCTCGTTGCGACAGTC
*
8232 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTGTCATTTATCTCGTTGCGAC
8269 TCTTCTGCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.13, C:0.26, G:0.18, T:0.44
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTGTCATTTATCTCGTTGCGACAGTC
Found at i:8394 original size:33 final size:33
Alignment explanation
Indices: 8347--8417 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
8337 AATACTAACT
* *
8347 TGAAAATCGGAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
8380 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
8413 TGAAA
1 TGAAA
8418 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:8652 original size:22 final size:22
Alignment explanation
Indices: 8600--8654 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
8590 TGGTTGTGAG
**
8600 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
8622 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
8644 GGATTTCTTCG
1 GGATTTCTTCG
8655 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:8820 original size:39 final size:40
Alignment explanation
Indices: 8777--8858 Score: 96
Period size: 40 Copynumber: 2.1 Consensus size: 40
8767 TATGCGTAGC
*
8777 GATTATAATGGCGCTTTA-A-ATATCGCGTTGCGATTTACG
1 GATTATAATGGCGATTTACAGAT-TCGCGTTGCGATTTACG
** * *
8816 GATTATCGTTGCGATTTACAGATTCTCGTTGCGATTTACG
1 GATTATAATGGCGATTTACAGATTCGCGTTGCGATTTACG
8856 GAT
1 GAT
8859 ACGCGTTGCG
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
39 14 0.39
40 20 0.56
41 2 0.06
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.38
Consensus pattern (40 bp):
GATTATAATGGCGATTTACAGATTCGCGTTGCGATTTACG
Found at i:8993 original size:20 final size:20
Alignment explanation
Indices: 8800--8992 Score: 219
Period size: 20 Copynumber: 9.7 Consensus size: 20
8790 CTTTAAATAT
8800 CGCGTTGCGATTTACGGATTA
1 CGCGTTGCGATTTACGGA-TA
* * *
8821 -TCGTTGCGATTTACAGATT
1 CGCGTTGCGATTTACGGATA
*
8840 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
8860 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
8880 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
8900 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
8920 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
8940 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
8960 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
8980 CGCGTTGCGATTT
1 CGCGTTGCGATTT
8993 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
19 1 0.01
20 145 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:9009 original size:21 final size:21
Alignment explanation
Indices: 8979--9061 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
8969 ATTTTCATAT
*
8979 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
9000 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
9021 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
9042 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
9062 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:9052 original size:42 final size:43
Alignment explanation
Indices: 8959--9057 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
8949 ATTTATGTGT
* *
8959 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
9000 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
9042 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
9058 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:16533 original size:61 final size:59
Alignment explanation
Indices: 16398--16536 Score: 140
Period size: 61 Copynumber: 2.3 Consensus size: 59
16388 AAATATATAA
* **
16398 ATAG-TTGGGTGATCATTTTGTAACTTTTAATAGAAGATGACTCAACAAAGCAATATCTT
1 ATAGTTTGGG-GATCATTTTATAACTTTTAATAGAAGATGACTCAACAAAAAAATATCTT
* * ** *
16457 ATA-TTCGGAGAATCATTTTATAACTTTTTAATAGTCGGGA-GACTCAACAAAAAAATATTTT
1 ATAGTTTGG-GGATCATTTTATAAC-TTTTAATAG--AAGATGACTCAACAAAAAAATATCTT
16518 ATAGTTTGGGGATCATTTT
1 ATAGTTTGGGGATCATTTT
16537 TGTACTTTAC
Statistics
Matches: 64, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
59 18 0.28
60 10 0.16
61 30 0.47
62 6 0.09
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.37
Consensus pattern (59 bp):
ATAGTTTGGGGATCATTTTATAACTTTTAATAGAAGATGACTCAACAAAAAAATATCTT
Found at i:18400 original size:52 final size:48
Alignment explanation
Indices: 18318--18426 Score: 114
Period size: 52 Copynumber: 2.2 Consensus size: 48
18308 CTACTATTAT
* *
18318 TATATACTATATTTTCATTATTATTATATTTTGTTCCTTTATTAATATATATA
1 TATATA-TATATTTTCATTATTATTATATTTT-AT--TTTATT-ATACATATA
*
18371 TATATATATATTTT-ATGTA-TATTTTTATTTTATTTTATTATACATATA
1 TATATATATATTTTCAT-TATTA-TTATATTTTATTTTATTATACATATA
18419 TATATATA
1 TATATATA
18427 CATATAATCA
Statistics
Matches: 51, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
48 16 0.31
49 6 0.12
51 5 0.10
52 18 0.35
53 6 0.12
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.60
Consensus pattern (48 bp):
TATATATATATTTTCATTATTATTATATTTTATTTTATTATACATATA
Found at i:20175 original size:10 final size:10
Alignment explanation
Indices: 20160--20193 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
20150 TTCATTTACC
20160 ATTTATTTTT
1 ATTTATTTTT
20170 ATTTATTTTT
1 ATTTATTTTT
* *
20180 ATCTATTTCT
1 ATTTATTTTT
20190 ATTT
1 ATTT
20194 TACTAACGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.74
Consensus pattern (10 bp):
ATTTATTTTT
Found at i:30558 original size:105 final size:105
Alignment explanation
Indices: 30376--30869 Score: 961
Period size: 105 Copynumber: 4.7 Consensus size: 105
30366 AGGTTTCACC
30376 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTACAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTACAGACAACGCAAGTTCAACTTCACG
30441 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
30481 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTACAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTACAGACAACGCAAGTTCAACTTCACG
30546 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
30586 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTACAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTACAGACAACGCAAGTTCAACTTCACG
*
30651 ATGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
30691 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTACAGACAACGCAAGTTCAACTTCACG
30756 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
30796 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTACAGACAACGCAAGTTCAACTTCACG
30861 ACGAAGGGA
66 ACGAAGGGA
30870 AACAATTCTC
Statistics
Matches: 386, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
105 386 1.00
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.21
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTACAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
Found at i:32681 original size:19 final size:17
Alignment explanation
Indices: 32657--32691 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 17
32647 GGTCCCTACT
32657 ATTATTATACTATATTTTC
1 ATTATTAT--TATATTTTC
32676 ATTATTATTATATTTT
1 ATTATTATTATATTTT
32692 GTTCCTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
19 8 0.50
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (17 bp):
ATTATTATTATATTTTC
Found at i:33001 original size:137 final size:136
Alignment explanation
Indices: 32768--33018 Score: 348
Period size: 137 Copynumber: 1.8 Consensus size: 136
32758 ATATATACAT
* * *
32768 ATAATCATCGTTATTTTTATTATTTTAAGTATCATTGATAGCGTATATAAACATATATTTTTTTC
1 ATAACCATCGTTAATTTTATTATTTTAAGTATCATCGATAGCGTATATAAACATATATTTTTTTC
32833 CTTTTATTATTATATGTATATTCTTTATATTT-T-TTCATTTGCTTTATGTATTTATTTTATTTA
66 CTTTTATTATTATATGTATA---TTTATATTTCTATTCATTTGCTTTATGTATTTATTTTATTTA
32896 TCTCTATAC
128 TCTCTATAC
*
32905 ATAACCATCGTTAATTTTATTATTTTAAGTATTATCGATAGCGTATATAAACATATATTTTTTTT
1 ATAACCATCGTTAATTTTATTATTTTAAGTATCATCGATAGCGTATATAAACATATA--TTTTTT
* *
32970 TCTTTCTTTTATTATTATCTGTATA-TT-TATTTCTATTCATTTGTTTTAT
64 TC---CTTTTATTATTATATGTATATTTATATTTCTATTCATTTGCTTTAT
33019 TTAATAATAT
Statistics
Matches: 101, Mismatches: 6, Indels: 12
0.85 0.05 0.10
Matches are distributed among these distances:
137 58 0.57
138 3 0.03
139 21 0.21
142 19 0.19
ACGTcount: A:0.27, C:0.10, G:0.06, T:0.57
Consensus pattern (136 bp):
ATAACCATCGTTAATTTTATTATTTTAAGTATCATCGATAGCGTATATAAACATATATTTTTTTC
CTTTTATTATTATATGTATATTTATATTTCTATTCATTTGCTTTATGTATTTATTTTATTTATCT
CTATAC
Found at i:38669 original size:2 final size:2
Alignment explanation
Indices: 38662--38705 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
38652 TACACAACTC
38662 AT AT AT AT AT 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 AT AT AT AT AT
38704 AT
1 AT
38706 TATCAATTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43530 original size:25 final size:25
Alignment explanation
Indices: 43502--43554 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
43492 TATTTTGAAT
* *
43502 TCAAAGCAGCCCCTTAATTTGAAAA
1 TCAAACCAACCCCTTAATTTGAAAA
*
43527 TC-AACCAACCCCTTAGTTTGAAAA
1 TCAAACCAACCCCTTAATTTGAAAA
43551 TCAA
1 TCAA
43555 CCGGCCTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 21 0.88
25 3 0.12
ACGTcount: A:0.40, C:0.26, G:0.09, T:0.25
Consensus pattern (25 bp):
TCAAACCAACCCCTTAATTTGAAAA
Found at i:43538 original size:24 final size:24
Alignment explanation
Indices: 43511--43556 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
43501 TTCAAAGCAG
43511 CCCCTTAATTTGAAAATCAACCAA
1 CCCCTTAATTTGAAAATCAACCAA
*
43535 CCCCTTAGTTTGAAAATCAACC
1 CCCCTTAATTTGAAAATCAACC
43557 GGCCTTCTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.37, C:0.30, G:0.07, T:0.26
Consensus pattern (24 bp):
CCCCTTAATTTGAAAATCAACCAA
Found at i:58034 original size:26 final size:26
Alignment explanation
Indices: 58005--58059 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
57995 ATTCATGTCA
*
58005 CAGAATTACATAAATGAAAATTCCAT
1 CAGAATTACAGAAATGAAAATTCCAT
58031 CAGAATTACAGAAATGAAAATTCCAT
1 CAGAATTACAGAAATGAAAATTCCAT
58057 CAG
1 CAG
58060 TTCTTTCATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.49, C:0.16, G:0.11, T:0.24
Consensus pattern (26 bp):
CAGAATTACAGAAATGAAAATTCCAT
Found at i:60878 original size:17 final size:18
Alignment explanation
Indices: 60842--60879 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
60832 TATTGAATTT
* *
60842 TATAAATATATTGTTTTA
1 TATAAATATATTATTGTA
60860 TATAAA-ATATTATTGTA
1 TATAAATATATTATTGTA
60877 TAT
1 TAT
60880 TTTTAATGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (18 bp):
TATAAATATATTATTGTA
Found at i:61065 original size:29 final size:29
Alignment explanation
Indices: 61008--61066 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
60998 GATTTATCAG
* * *
61008 AAAAAGTATAAATTTATTTATTTTGAATA
1 AAAAAGCATAAATTTATTAATTATGAATA
61037 AAAAAGCATAAATTTATTAAATTAT-AATA
1 AAAAAGCATAAATTTATT-AATTATGAATA
61066 A
1 A
61067 TAATTTCATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.39
Consensus pattern (29 bp):
AAAAAGCATAAATTTATTAATTATGAATA
Found at i:61658 original size:35 final size:35
Alignment explanation
Indices: 61612--61686 Score: 125
Period size: 35 Copynumber: 2.1 Consensus size: 35
61602 AAACAATCCC
*
61612 CAATTTCATTCTAAACCC-AAATTTCCAAAGTAATT
1 CAATTTCATTCTAAACCCTAAA-TTCCAAAATAATT
61647 CAATTTCATTCTAAACCCTAAATTCCAAAATAATT
1 CAATTTCATTCTAAACCCTAAATTCCAAAATAATT
61682 CAATT
1 CAATT
61687 AAATTCAATT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
35 35 0.92
36 3 0.08
ACGTcount: A:0.41, C:0.23, G:0.01, T:0.35
Consensus pattern (35 bp):
CAATTTCATTCTAAACCCTAAATTCCAAAATAATT
Found at i:62234 original size:128 final size:126
Alignment explanation
Indices: 62071--62325 Score: 420
Period size: 128 Copynumber: 2.0 Consensus size: 126
62061 TTCAATCTTT
* **
62071 ATTATTTATATAATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGG
1 ATTATTTATATAATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGG
* *
62136 ATCTGACATGTGTTAGCACATGATCATGACATGTGTCATTGGTGACACATGTCACCACCTA
66 ATCTGACATGTGTTAACACATGATCATGACATATGTCATTGGTGACACATGTCACCACCTA
*
62197 ATTATTTATATGCTATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCA
1 ATTATTTATAT--AATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCA
* *
62262 GGATCTGACATGTGTTAACACATGATCATGATATATGTTATTGGTGACACATGTCACCACCTA
64 GGATCTGACATGTGTTAACACATGATCATGACATATGTCATTGGTGACACATGTCACCACCTA
62325 A
1 A
62326 GTAGAAGAAA
Statistics
Matches: 119, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
126 11 0.09
128 108 0.91
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (126 bp):
ATTATTTATATAATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGG
ATCTGACATGTGTTAACACATGATCATGACATATGTCATTGGTGACACATGTCACCACCTA
Found at i:62681 original size:28 final size:26
Alignment explanation
Indices: 62650--62710 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
62640 AGTTGATACA
*
62650 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTT-AAA-AATAAATTTAAGAATT
* * *
62678 ATATTTTTAAACTAAATTTAATAATT
1 ATATTTTAAAAATAAATTTAAGAATT
62704 ATATTTT
1 ATATTTT
62711 TCATATTTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 20 0.69
27 2 0.07
28 7 0.24
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (26 bp):
ATATTTTAAAAATAAATTTAAGAATT
Found at i:62808 original size:16 final size:18
Alignment explanation
Indices: 62787--62820 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
62777 ATTTCTTATT
62787 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
62803 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
62821 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:74444 original size:20 final size:21
Alignment explanation
Indices: 74415--74455 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
74405 AAATCGTTTA
74415 AATTGGATTT-TGGTTTATTT
1 AATTGGATTTATGGTTTATTT
* *
74435 AATTGTATTTATTGTTTATTT
1 AATTGGATTTATGGTTTATTT
74456 TTTTCTTATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.22, C:0.00, G:0.15, T:0.63
Consensus pattern (21 bp):
AATTGGATTTATGGTTTATTT
Done.