Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003514.1 Hibiscus syriacus cultivar Beakdansim tig00007432_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: 93147
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:368 original size:12 final size:12
Alignment explanation
Indices: 351--375 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
341 ATATAATCCT
351 GAAGAAGAAAAA
1 GAAGAAGAAAAA
363 GAAGAAGAAAAA
1 GAAGAAGAAAAA
375 G
1 G
376 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:2674 original size:19 final size:19
Alignment explanation
Indices: 2652--2938 Score: 329
Period size: 19 Copynumber: 16.4 Consensus size: 19
2642 CGGAAAATAC
*
2652 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2671 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
2685 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
2705 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
2719 AATCGCAATGAGAAATGAA
1 AATCGCAATGCGAAATGAA
2738 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2757 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2776 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2795 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
*
2809 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
2828 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
2846 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
2860 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2879 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
2893 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2912 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
2931 AATCGCAA
1 AATCGCAA
2939 CGAGATAATC
Statistics
Matches: 232, Mismatches: 10, Indels: 52
0.79 0.03 0.18
Matches are distributed among these distances:
14 46 0.20
15 2 0.01
16 23 0.10
17 13 0.06
18 11 0.05
19 124 0.53
20 13 0.06
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:2739 original size:33 final size:33
Alignment explanation
Indices: 2652--2919 Score: 248
Period size: 33 Copynumber: 7.8 Consensus size: 33
2642 CGGAAAATAC
* *
2652 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAA
*
2685 AATCGCAATGCGGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGAGAA
*
2719 AATCGCAATGAGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
2757 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
* *
2795 AATCGCAA--CGACA-G--AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
2828 AATCGCAATGCGAAATG-AAATCGCAACGA-AA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAA
2859 GAATCGCAATGCGAAATGAAAATCGCAACGA-AA
1 -AATCGCAATGCGAAATGAAAATCGCAACGAGAA
2892 GAATCGCAATGCGAAATGAAAATCGCAA
1 -AATCGCAATGCGAAATGAAAATCGCAA
2920 TGCGAAATGA
Statistics
Matches: 213, Mismatches: 9, Indels: 26
0.86 0.04 0.10
Matches are distributed among these distances:
31 2 0.01
32 17 0.08
33 95 0.45
34 28 0.13
35 10 0.05
36 5 0.02
37 9 0.04
38 47 0.22
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAA
Found at i:2939 original size:52 final size:55
Alignment explanation
Indices: 2652--2960 Score: 317
Period size: 52 Copynumber: 5.9 Consensus size: 55
2642 CGGAAAATAC
* *
2652 AATCGCAACGCGAAATGAAAATCCCAA-C---ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAAGCGAAATG-AAATCGCAATGC-GAAATGAA
* *
2705 AATCGCAA--CG--A-GAGAATCGCAATGAGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA-GCGAAATG-AAATCGCAATGCGAAATGAA
*
2757 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAAAATCGCAA-GCGAAATG-AAATCGCAATGCGAAATGAA
*
2809 AATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAAATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAAAATCGCAA-GCGAAATGAAATCGCAATGCGAAATGAA
2860 AATCGCAATGCGAAATGAAAATCGCAA-CGAAA-G-AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAAGCGAAATGAAATCGCAATGCGAAATGAA
*
2912 AATCGCAATGCGAAATGAAAATCGCAA-CGAGAT--AATCGCAATGCGAAAT
1 AATCGCAATGCGAAATGAAAATCGCAAGCGAAATGAAATCGCAATGCGAAAT
2961 TATAAACGCA
Statistics
Matches: 230, Mismatches: 10, Indels: 33
0.84 0.04 0.12
Matches are distributed among these distances:
47 8 0.03
48 10 0.04
49 11 0.05
50 1 0.00
51 42 0.18
52 98 0.43
53 24 0.10
54 3 0.01
55 4 0.02
56 1 0.00
57 28 0.12
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (55 bp):
AATCGCAATGCGAAATGAAAATCGCAAGCGAAATGAAATCGCAATGCGAAATGAA
Found at i:2949 original size:33 final size:36
Alignment explanation
Indices: 2680--2960 Score: 239
Period size: 33 Copynumber: 8.1 Consensus size: 36
2670 AAATCCCAAC
2680 ATGAAAATCGCAATGCGGAAATGAAAATCGCAA--CG--
1 ATGAAAATCGCAA-GC-G-AATGAAAATCGCAATGCGAA
* *
2715 A-GAGAATCGCAATGAGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAA-GCG-AATGAAAATCGCAATGCGAA
2752 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAA-GCG-AATGAAAATCGCAATGCGAA
2790 ATGAAAATCGCAA-CGACA-G--AATCGCAATGCGAA
1 ATGAAAATCGCAAGCGA-ATGAAAATCGCAATGCGAA
*
2823 ATTAAAATCGCAATGCGAAATG-AAATCGCAA--CGAA
1 ATGAAAATCGCAA-GCG-AATGAAAATCGCAATGCGAA
2858 A-G--AATCGCAATGCGAAATGAAAATCGCAA--CGAA
1 ATGAAAATCGCAA-GCG-AATGAAAATCGCAATGCGAA
2891 A-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAA-GCG-AATGAAAATCGCAATGCGAA
*
2926 ATGAAAATCGCAA-CG-A-GATAATCGCAATGCGAA
1 ATGAAAATCGCAAGCGAATGAAAATCGCAATGCGAA
2959 AT
1 AT
2961 TATAAACGCA
Statistics
Matches: 222, Mismatches: 7, Indels: 36
0.84 0.03 0.14
Matches are distributed among these distances:
32 17 0.08
33 102 0.46
34 13 0.06
35 18 0.08
36 8 0.04
37 9 0.04
38 55 0.25
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (36 bp):
ATGAAAATCGCAAGCGAATGAAAATCGCAATGCGAA
Found at i:3076 original size:19 final size:19
Alignment explanation
Indices: 2967--3068 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
2957 AAATTATAAA
2967 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
2986 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
3006 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
3022 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
3039 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
3058 CGCATTGCGAT
1 CGCATTGCGAT
3069 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:3194 original size:14 final size:14
Alignment explanation
Indices: 3175--3211 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
3165 CATCAATTAC
3175 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
3189 ACAAATCATCTTTT
1 ACAAATCAACTTTT
3203 ACAAATCAA
1 ACAAATCAA
3212 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:5173 original size:19 final size:20
Alignment explanation
Indices: 5133--5179 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
5123 TAGTTTACTT
* *
5133 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAACTCAAAA
5153 TCGCAACGCGAAAC-CAAAA
1 TCGCAACGCGAAACTCAAAA
5172 TCGCAACG
1 TCGCAACG
5180 ACAGAATCGC
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:0.45, C:0.30, G:0.15, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAACTCAAAA
Found at i:5189 original size:14 final size:14
Alignment explanation
Indices: 5170--5226 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
5160 GCGAAACCAA
*
5170 AATCGCAACGACAG
1 AATCGCAACGAAAG
5184 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
5201 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
5217 AATCGCAACG
1 AATCGCAACG
5227 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:5197 original size:33 final size:33
Alignment explanation
Indices: 5151--5243 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
5141 CGAAACTTAA
** *
5151 AATCGCAACGCGAAACCAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
5184 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
5217 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
5244 TGCGATTTTG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:5208 original size:19 final size:19
Alignment explanation
Indices: 5184--5248 Score: 86
Period size: 19 Copynumber: 3.7 Consensus size: 19
5174 GCAACGACAG
5184 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
5203 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
*
5217 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
5236 AATCGCAATGCGA
1 AATCGCAATGCGA
5249 TTTTGGTTTC
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
14 8 0.20
16 6 0.15
17 6 0.15
19 20 0.50
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.12
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:5266 original size:19 final size:19
Alignment explanation
Indices: 5244--5372 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
5234 AAAATCGCAA
5244 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
5263 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
5277 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
5296 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
5310 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
5329 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
5348 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
5368 TGCGA
1 TGCGA
5373 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:5286 original size:33 final size:33
Alignment explanation
Indices: 5244--5335 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
5234 AAAATCGCAA
5244 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
5277 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
5310 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
5336 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:5563 original size:93 final size:93
Alignment explanation
Indices: 5404--5870 Score: 918
Period size: 93 Copynumber: 5.0 Consensus size: 93
5394 GCAAATTGAA
5404 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
5469 GCAGAATTGGCAGCAACCGAACAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
5497 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
5562 GCAGAATTGGCAGCAACCGAACAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
5590 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
5655 GCAGAATTGGCAGCAACCGAACAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
5683 ACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
5747 GCAGAATTGGCAGCAACCGAACAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
5775 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
*
5840 GCAGAATTGGCAGCAACCGAATAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
5868 ACT
1 ACT
5871 AAGCAATCTA
Statistics
Matches: 372, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 92 0.25
93 280 0.75
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
GCAGAATTGGCAGCAACCGAACAAATTT
Found at i:5841 original size:185 final size:186
Alignment explanation
Indices: 5404--5870 Score: 918
Period size: 185 Copynumber: 2.5 Consensus size: 186
5394 GCAAATTGAA
5404 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
5469 GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAT
66 GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAT
5534 TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
131 TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
5590 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
5655 GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TAT
66 GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAT
5719 TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
131 TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
5775 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
*
5840 GCAGAATTGGCAGCAACCGAATAAATTTACT
66 GCAGAATTGGCAGCAACCGAACAAATTTACT
5871 AAGCAATCTA
Statistics
Matches: 280, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
185 154 0.55
186 126 0.45
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAT
TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
Found at i:7591 original size:14 final size:14
Alignment explanation
Indices: 7572--7661 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
7562 TTGAAATGAA
7572 AATCGCAACGAGAG
1 AATCGCAACGAGAG
7586 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
7603 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
7619 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
7638 AATCGCAACGAGAG
1 AATCGCAACGAGAG
7652 AATCGCAACG
1 AATCGCAACG
7662 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:7609 original size:33 final size:33
Alignment explanation
Indices: 7564--7678 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
7554 TCTTTTGGTT
7564 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
7597 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
7630 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
7663 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
7679 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:7610 original size:19 final size:18
Alignment explanation
Indices: 7571--7683 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
7561 GTTGAAATGA
7571 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
7586 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
7603 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
7619 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
7636 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
7652 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
7669 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
7684 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:7714 original size:14 final size:14
Alignment explanation
Indices: 7695--7749 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
7685 TTTGGTTTCG
7695 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
7709 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
7728 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
7742 CGTTGCGA
1 CGTTGCGA
7750 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:7727 original size:33 final size:33
Alignment explanation
Indices: 7679--7749 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
7669 AAAATCGCAA
**
7679 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
7712 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
7745 TGCGA
1 TGCGA
7750 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:7757 original size:33 final size:33
Alignment explanation
Indices: 7690--7771 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
7680 GCGATTTTGG
***
7690 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
7723 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
7756 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
7772 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:7776 original size:20 final size:20
Alignment explanation
Indices: 7702--7790 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
7692 TCGCGTTGCG
7702 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
7722 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
7735 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
7755 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
7775 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
7791 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:7912 original size:33 final size:33
Alignment explanation
Indices: 7870--7940 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
7860 AATACTAACT
*
7870 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
7903 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
7936 TGAAA
1 TGAAA
7941 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:8346 original size:20 final size:20
Alignment explanation
Indices: 8321--8513 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
8311 CTTTAAATAT
8321 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
8341 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
8363 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
8382 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
8402 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
8422 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
8442 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
8462 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
8482 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
8502 CGCGTTGCGATT
1 CGCGTTGCGATT
8514 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:8508 original size:60 final size:60
Alignment explanation
Indices: 8321--8513 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
8311 CTTTAAATAT
**
8321 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
8382 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
8442 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
8502 CGCGTTGCGATT
1 CGCGTTGCGATT
8514 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:8594 original size:20 final size:20
Alignment explanation
Indices: 8569--8620 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
8559 AAGAATCGCG
*
8569 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
8589 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
8609 TTGCGATTCTGG
1 TTGCGATTCTGG
8621 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:9691 original size:2 final size:2
Alignment explanation
Indices: 9684--9715 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
9674 AGATTATTTG
9684 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9716 AATGTAAAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11189 original size:35 final size:35
Alignment explanation
Indices: 11143--11218 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
11133 AAAACAATCA
* *
11143 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
11178 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
11213 TCAATT
1 TCAATT
11219 AAATTCAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.39, C:0.24, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:11760 original size:130 final size:130
Alignment explanation
Indices: 11615--11862 Score: 415
Period size: 130 Copynumber: 1.9 Consensus size: 130
11605 TATTTATATA
* **
11615 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* *
11680 TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
11745 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* * * *
11810 TTAACACATGATCATGATATATGTTATTGGTGACACGTGTCACCACCTAATTA
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTA
11863 GATGAAAATT
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 109 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.35
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:11893 original size:130 final size:129
Alignment explanation
Indices: 11629--11893 Score: 309
Period size: 130 Copynumber: 2.0 Consensus size: 129
11619 ATTTGGTCCT
* ** *
11629 AAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* ** * * **** *
11694 TGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATTATGAAAATAAGCTATCAAAGAAGT-CA
11759 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* * * * *
11824 TGATATATGTTATTGGTGACACGTGTCACCACCTAATTAGATGAAAATTAAGTTA-CAAAGAAGT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATT--ATGAAAA-TAAGCTATCAAAGAAGT
11888 -A
128 CA
11889 AAATT
1 AAATT
11894 TGGGTCTTGG
Statistics
Matches: 113, Mismatches: 19, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
130 99 0.88
132 9 0.08
133 5 0.04
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.34
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
TGACACATGTCATTGGTGACACATGTCACCACCTAATTATGAAAATAAGCTATCAAAGAAGTCA
Found at i:12220 original size:28 final size:27
Alignment explanation
Indices: 12189--12251 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
12179 AGTTGATACA
*
12189 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
12217 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
12245 ATATTTT
1 ATATTTT
12252 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:12359 original size:17 final size:17
Alignment explanation
Indices: 12333--12365 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
12323 ATTTCTTATT
12333 AAAAATAAAT-ATTCAA
1 AAAAATAAATGATTCAA
12349 AAAATATAAATGATTCA
1 AAAA-ATAAATGATTCA
12366 TACATTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 6 0.40
18 5 0.33
ACGTcount: A:0.64, C:0.06, G:0.03, T:0.27
Consensus pattern (17 bp):
AAAAATAAATGATTCAA
Found at i:18854 original size:52 final size:52
Alignment explanation
Indices: 18772--18878 Score: 160
Period size: 52 Copynumber: 2.1 Consensus size: 52
18762 TAGAGGTATC
***
18772 CAATTGGTGCACTGAGATTGGTTTGGTGCATGAACAAGACAGTTTTTAATTG
1 CAATTGGTGCACTGAGATTGGTTCAATGCATGAACAAGACAGTTTTTAATTG
* * *
18824 CAATTGGTGCACTGGGATTGGTTCAATGCATGAACAATATAGTTTTTAATTG
1 CAATTGGTGCACTGAGATTGGTTCAATGCATGAACAAGACAGTTTTTAATTG
18876 CAA
1 CAA
18879 GTTTCAACAA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.35
Consensus pattern (52 bp):
CAATTGGTGCACTGAGATTGGTTCAATGCATGAACAAGACAGTTTTTAATTG
Found at i:19222 original size:31 final size:32
Alignment explanation
Indices: 19187--19246 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 32
19177 TGTGATATCA
*
19187 TAATAAATTTTAA-AATAATTTTATAACATAG
1 TAATAAATTTTAATAATAATTTCATAACATAG
*
19218 TAATAAATTTTAATAATTATTTCATAACA
1 TAATAAATTTTAATAATAATTTCATAACA
19247 AAAATTGTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 13 0.50
32 13 0.50
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (32 bp):
TAATAAATTTTAATAATAATTTCATAACATAG
Found at i:26648 original size:35 final size:35
Alignment explanation
Indices: 26602--26713 Score: 143
Period size: 35 Copynumber: 3.2 Consensus size: 35
26592 AAAATAGTCC
* *
26602 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
* *
26637 TCAATTTCATTCTAAACCCTAAATTCCAAAATATT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
** * * *
26672 TCAATTAAATTTTAAACCCCAAATTCTAAAATACT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
26707 TCAATTT
1 TCAATTT
26714 AAGGTTTAGA
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 66 1.00
ACGTcount: A:0.40, C:0.22, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:26777 original size:35 final size:35
Alignment explanation
Indices: 26709--26783 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 35
26699 AAAATACTTC
* * *
26709 AATTTAAGGTTTAGAATGTAATTGAATTATTTTGG
1 AATTTAAGGTTTAGAATGAAATTGAAGTATTTTGA
* *
26744 AATTTAGGGTTTAGAATGAAATT-AAGGTGTTTTGA
1 AATTTAAGGTTTAGAATGAAATTGAA-GTATTTTGA
26779 AATTT
1 AATTT
26784 TGAACATGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
34 2 0.06
35 32 0.94
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (35 bp):
AATTTAAGGTTTAGAATGAAATTGAAGTATTTTGA
Found at i:34490 original size:2 final size:2
Alignment explanation
Indices: 34483--34507 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
34473 AGCATCAAAT
34483 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
34508 TAAAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40093 original size:16 final size:16
Alignment explanation
Indices: 40072--40104 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
40062 AATAGTTAGA
40072 CTATAACTGTAACTTC
1 CTATAACTGTAACTTC
40088 CTATAACTGTAACTTC
1 CTATAACTGTAACTTC
40104 C
1 C
40105 GTATCCCATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.27, G:0.06, T:0.36
Consensus pattern (16 bp):
CTATAACTGTAACTTC
Found at i:42342 original size:14 final size:14
Alignment explanation
Indices: 42323--42350 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
42313 AAGGTGTTAC
42323 TTTGGATTGCATTA
1 TTTGGATTGCATTA
42337 TTTGGATTGCATTA
1 TTTGGATTGCATTA
42351 GCAGTTGCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.07, G:0.21, T:0.50
Consensus pattern (14 bp):
TTTGGATTGCATTA
Found at i:48135 original size:12 final size:12
Alignment explanation
Indices: 48118--48146 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
48108 GTTAATATCA
48118 ACATCACGAATG
1 ACATCACGAATG
48130 ACATCACGAATG
1 ACATCACGAATG
48142 ACATC
1 ACATC
48147 TAAATTAGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.41, C:0.28, G:0.14, T:0.17
Consensus pattern (12 bp):
ACATCACGAATG
Found at i:61451 original size:11 final size:11
Alignment explanation
Indices: 61435--61459 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
61425 ACTACATCTG
61435 GCCCAAATTCT
1 GCCCAAATTCT
61446 GCCCAAATTCT
1 GCCCAAATTCT
61457 GCC
1 GCC
61460 GTGTTTCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.40, G:0.12, T:0.24
Consensus pattern (11 bp):
GCCCAAATTCT
Found at i:64604 original size:35 final size:35
Alignment explanation
Indices: 64558--64633 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
64548 AAAACACTCA
* *
64558 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
64593 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
64628 TCAATT
1 TCAATT
64634 AAATTCAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.39, C:0.24, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:65181 original size:128 final size:126
Alignment explanation
Indices: 65018--65275 Score: 408
Period size: 128 Copynumber: 2.0 Consensus size: 126
65008 TTCAGTCTTT
* **
65018 ATTATTTATATAATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGG
1 ATTATTTATATAATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGG
* *
65083 ATCTGACATGTGTTAGCACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTA
66 ATCTGACATGTGTTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTA
*
65144 ATTATTTATATGCTATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCA
1 ATTATTTATAT--AATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCA
* * * *
65209 GGATCTGACATGTGTTAACACATGATCATGATATATGTTATTGGTGACACGTGTCACCACCTA
64 GGATCTGACATGTGTTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTA
65272 ATTA
1 ATTA
65276 GAAGAAAATT
Statistics
Matches: 120, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
126 11 0.09
128 109 0.91
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (126 bp):
ATTATTTATATAATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGG
ATCTGACATGTGTTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTA
Found at i:65634 original size:28 final size:27
Alignment explanation
Indices: 65603--65665 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
65593 AGTTGATACA
*
65603 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
65631 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
65659 ATATTTT
1 ATATTTT
65666 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:65763 original size:15 final size:16
Alignment explanation
Indices: 65739--65775 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
65729 TTTAATTTCT
65739 TATT-AAAAATA-AAA
1 TATTCAAAAATATAAA
65753 TATTCAAAAATATAAA
1 TATTCAAAAATATAAA
65769 TGATTCA
1 T-ATTCA
65776 TACATTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.20
15 7 0.35
16 4 0.20
17 5 0.25
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.32
Consensus pattern (16 bp):
TATTCAAAAATATAAA
Found at i:68551 original size:28 final size:26
Alignment explanation
Indices: 68492--68553 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
68482 TATTTTAAGT
* *
68492 TTTAATTTAATATATTATACATAAAC
1 TTTAATTTAATACATTATACATAAAA
* *
68518 TTTAATTTTATACATTATATATATAAA
1 TTTAATTTAATACATTATACATA-AAA
68545 TTCTAATTT
1 TT-TAATTT
68554 GATAAGAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 20 0.67
27 4 0.13
28 6 0.20
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (26 bp):
TTTAATTTAATACATTATACATAAAA
Found at i:72214 original size:52 final size:52
Alignment explanation
Indices: 72132--72238 Score: 160
Period size: 52 Copynumber: 2.1 Consensus size: 52
72122 TAGAGGTATC
***
72132 CAATTGGTGCACTGAGATTGGTTTGGTGCATGAACAAGACAGTTTTTAATTG
1 CAATTGGTGCACTGAGATTGGTTCAATGCATGAACAAGACAGTTTTTAATTG
* * *
72184 CAATTGGTGCACTGGGATTGGTTCAATGCATGAACAATATAGTTTTTAATTG
1 CAATTGGTGCACTGAGATTGGTTCAATGCATGAACAAGACAGTTTTTAATTG
72236 CAA
1 CAA
72239 GTTTCAACAA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.35
Consensus pattern (52 bp):
CAATTGGTGCACTGAGATTGGTTCAATGCATGAACAAGACAGTTTTTAATTG
Found at i:72582 original size:31 final size:32
Alignment explanation
Indices: 72547--72606 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 32
72537 TGTGATATCA
*
72547 TAATAAATTTTAA-AATAATTTTATAACATAG
1 TAATAAATTTTAATAATAATTTCATAACATAG
*
72578 TAATAAATTTTAATAATTATTTCATAACA
1 TAATAAATTTTAATAATAATTTCATAACA
72607 AAAATTGTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 13 0.50
32 13 0.50
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (32 bp):
TAATAAATTTTAATAATAATTTCATAACATAG
Found at i:80004 original size:35 final size:35
Alignment explanation
Indices: 79958--80069 Score: 143
Period size: 35 Copynumber: 3.2 Consensus size: 35
79948 AAAATAGTCC
* *
79958 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
* *
79993 TCAATTTCATTCTAAACCCTAAATTCCAAAATATT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
** * * *
80028 TCAATTAAATTTTAAACCCCAAATTCTAAAATACT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
80063 TCAATTT
1 TCAATTT
80070 AAGGTTTAGA
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 66 1.00
ACGTcount: A:0.40, C:0.22, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:80133 original size:35 final size:35
Alignment explanation
Indices: 80065--80139 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 35
80055 AAAATACTTC
* * *
80065 AATTTAAGGTTTAGAATGTAATTGAATTATTTTGG
1 AATTTAAGGTTTAGAATGAAATTGAAGTATTTTGA
* *
80100 AATTTAGGGTTTAGAATGAAATT-AAGGTGTTTTGA
1 AATTTAAGGTTTAGAATGAAATTGAA-GTATTTTGA
80135 AATTT
1 AATTT
80140 TGAACATGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
34 2 0.06
35 32 0.94
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (35 bp):
AATTTAAGGTTTAGAATGAAATTGAAGTATTTTGA
Found at i:87839 original size:2 final size:2
Alignment explanation
Indices: 87832--87862 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
87822 AGCATCAAAT
87832 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
87863 TAAAAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:88188 original size:39 final size:38
Alignment explanation
Indices: 88126--88201 Score: 116
Period size: 39 Copynumber: 2.0 Consensus size: 38
88116 AAACATATAT
* *
88126 ATAATTCCAATTGAATTGGGTAAAGCCAGTTTAGATTA
1 ATAAATCCAATTGAATTGCGTAAAGCCAGTTTAGATTA
*
88164 ATAAATCCAAATTGAATTGCGTAAAGCCCGTTTAGATT
1 ATAAATCC-AATTGAATTGCGTAAAGCCAGTTTAGATT
88202 GAATTAGATT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 7 0.21
39 27 0.79
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (38 bp):
ATAAATCCAATTGAATTGCGTAAAGCCAGTTTAGATTA
Done.