Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008050.1 Hibiscus syriacus cultivar Beakdansim tig00110545_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: 45658
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Found at i:531 original size:14 final size:15
Alignment explanation
Indices: 512--589 Score: 52
Period size: 14 Copynumber: 4.8 Consensus size: 15
502 CGGAAATGAA
512 AATCGCAA-CGAGAG
1 AATCGCAAGCGAGAG
*
526 AATCGCAATGCGAAATG
1 AATCGCAA-GCGAGA-G
*
543 AAATCGCAATGCGAAATGAA
1 -AATCGCAA-GCG--A-GAG
563 AATCGCAA-CGAGAG
1 AATCGCAAGCGAGAG
577 AATCGCAATGCGA
1 AATCGCAA-GCGA
590 AATGAAAATT
Statistics
Matches: 51, Mismatches: 4, Indels: 16
0.72 0.06 0.23
Matches are distributed among these distances:
14 18 0.35
15 1 0.02
16 7 0.14
17 3 0.06
18 12 0.24
19 8 0.16
20 1 0.02
21 1 0.02
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (15 bp):
AATCGCAAGCGAGAG
Found at i:567 original size:19 final size:19
Alignment explanation
Indices: 460--782 Score: 378
Period size: 19 Copynumber: 18.4 Consensus size: 19
450 ACGGAAATAC
460 AATCGCAA-GCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
478 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
492 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
512 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
526 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
544 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
563 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
577 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
596 AATTGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
615 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
629 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
648 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
667 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
686 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
705 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
723 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
737 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
756 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
775 AATCGCAA
1 AATCGCAA
783 CGAGATAATC
Statistics
Matches: 264, Mismatches: 14, Indels: 53
0.80 0.04 0.16
Matches are distributed among these distances:
14 50 0.19
15 4 0.02
16 17 0.06
17 7 0.03
18 37 0.14
19 136 0.52
20 13 0.05
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:819 original size:51 final size:52
Alignment explanation
Indices: 487--803 Score: 514
Period size: 52 Copynumber: 6.0 Consensus size: 52
477 AAATCCCAAC
487 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
540 ATG-AAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
591 ATGAAAATTGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
643 ATGAAAATCGCAATGCGAAATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGC-A-ACG--A-GAGAATCGCAATGCGAA
*
700 ATGAAAATCGCAATGCGAAATG-AAATCGCAACGAAAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
751 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGC-ATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
802 AT
1 AT
804 TATAAACGCA
Statistics
Matches: 248, Mismatches: 9, Indels: 16
0.91 0.03 0.06
Matches are distributed among these distances:
51 85 0.34
52 107 0.43
53 4 0.02
54 6 0.02
55 1 0.00
56 8 0.03
57 37 0.15
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:918 original size:19 final size:19
Alignment explanation
Indices: 810--910 Score: 158
Period size: 19 Copynumber: 5.6 Consensus size: 19
800 AAATTATAAA
810 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
829 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
*
848 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
864 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
881 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
900 CGCATTGCGAT
1 CGCATTGCGAT
911 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 10
0.86 0.02 0.11
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 55 0.73
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.45
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:1036 original size:14 final size:14
Alignment explanation
Indices: 1017--1053 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1007 CATCAATTAC
1017 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1031 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1045 ACAAATCAA
1 ACAAATCAA
1054 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:1065 original size:12 final size:12
Alignment explanation
Indices: 1048--1119 Score: 53
Period size: 12 Copynumber: 6.0 Consensus size: 12
1038 ATCTTTTACA
1048 AATCAATTAAAC
1 AATCAATTAAAC
*
1060 AATCAA--AAATTG
1 AATCAATTAAA--C
**
1072 AATCAACTTTTAC
1 AATCAA-TTAAAC
1085 AAATCAATTAAAC
1 A-ATCAATTAAAC
1098 AATCAA--AAAC
1 AATCAATTAAAC
1108 AATCAATTAAAC
1 AATCAATTAAAC
1120 TATTGAATCA
Statistics
Matches: 46, Mismatches: 6, Indels: 16
0.68 0.09 0.24
Matches are distributed among these distances:
10 13 0.28
12 21 0.46
13 6 0.13
14 5 0.11
15 1 0.02
ACGTcount: A:0.57, C:0.17, G:0.01, T:0.25
Consensus pattern (12 bp):
AATCAATTAAAC
Found at i:1082 original size:38 final size:38
Alignment explanation
Indices: 1034--1106 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
1024 AACTTTTACA
*
1034 AATCATCTTTTACAAATCAATTAAACAATCAAAAATTG
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
1072 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
1107 CAATCAATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.53, C:0.16, G:0.01, T:0.29
Consensus pattern (38 bp):
AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
Found at i:2953 original size:19 final size:19
Alignment explanation
Indices: 2913--3047 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
2903 TAGTTTACTT
* *
2913 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
2933 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
2952 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2971 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
2985 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
3004 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
3018 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
3037 TCGCAATGCGA
1 TCGCAACGCGA
3048 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:2988 original size:14 final size:14
Alignment explanation
Indices: 2969--3025 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2959 GCGAAATGAA
*
2969 AATCGCAACGACAG
1 AATCGCAACGAAAG
2983 AATCGCAACGCGAAATG
1 AATCGCAA--CGAAA-G
3000 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
3016 AATCGCAACG
1 AATCGCAACG
3026 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:0.25, G:0.21, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:2992 original size:33 final size:33
Alignment explanation
Indices: 2950--3042 Score: 177
Period size: 33 Copynumber: 2.8 Consensus size: 33
2940 GCGAAACCAA
*
2950 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
2983 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
3016 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
3043 TGCGATTTTG
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.47, C:0.23, G:0.20, T:0.10
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:3039 original size:52 final size:54
Alignment explanation
Indices: 2913--3047 Score: 131
Period size: 52 Copynumber: 2.5 Consensus size: 54
2903 TAGTTTACTT
*
2913 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAA
1 TCGCAAC-CGAAA-TGAAAATCGCAACGCGAAACCAAAATCGCAAC-CGAAATG-AAA
* **
2971 TCGCAA-CGACA-G--AATCGCAACGCGAAATGAAAATCGCAA-CGAAA-G-AA
1 TCGCAACCGAAATGAAAATCGCAACGCGAAACCAAAATCGCAACCGAAATGAAA
*
3018 TCGCAACGCGAAATGAAAATCGCAATGCGA
1 TCGCAAC-CGAAATGAAAATCGCAACGCGA
3048 TTTTGGTTTC
Statistics
Matches: 66, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
47 8 0.12
49 5 0.08
50 6 0.09
52 37 0.56
56 4 0.06
58 6 0.09
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.10
Consensus pattern (54 bp):
TCGCAACCGAAATGAAAATCGCAACGCGAAACCAAAATCGCAACCGAAATGAAA
Found at i:3065 original size:19 final size:19
Alignment explanation
Indices: 3043--3171 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
3033 AAAATCGCAA
3043 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
3062 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
3076 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
3095 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
3109 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
3128 TGCAATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
3147 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
3167 TGCGA
1 TGCGA
3172 AAGTAAACTA
Statistics
Matches: 88, Mismatches: 11, Indels: 21
0.73 0.09 0.17
Matches are distributed among these distances:
14 22 0.25
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 46 0.52
20 13 0.15
ACGTcount: A:0.09, C:0.17, G:0.28, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:3085 original size:33 final size:33
Alignment explanation
Indices: 3043--3130 Score: 142
Period size: 33 Copynumber: 2.7 Consensus size: 33
3033 AAAATCGCAA
3043 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
3076 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
3109 TGCGATTTTCATTTCGCGTTGC
1 TGCGATTTTGGTTTCGCGTTGC
3131 AATTTTGGTT
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
33 50 0.96
34 2 0.04
ACGTcount: A:0.07, C:0.19, G:0.28, T:0.45
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:3499 original size:91 final size:93
Alignment explanation
Indices: 3215--3591 Score: 717
Period size: 92 Copynumber: 4.1 Consensus size: 93
3205 TTGAATGGAT
3215 AAATTTACTTTCAACC-AAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
3279 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
3307 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
3372 AGTTTAGCAGAATTGGCAGCAA-CGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
3399 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
3463 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
3491 AAA-TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
3555 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
3583 AAATTTACT
1 AAATTTACT
3592 AAGCAATCTA
Statistics
Matches: 280, Mismatches: 1, Indels: 7
0.97 0.00 0.02
Matches are distributed among these distances:
91 82 0.29
92 123 0.44
93 75 0.27
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:5314 original size:14 final size:14
Alignment explanation
Indices: 5295--5384 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
5285 TTGAAATGAA
5295 AATCGCAACGAGAG
1 AATCGCAACGAGAG
5309 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
5326 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
5342 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
5361 AATCGCAACGAGAG
1 AATCGCAACGAGAG
5375 AATCGCAACG
1 AATCGCAACG
5385 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:5332 original size:33 final size:33
Alignment explanation
Indices: 5287--5401 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
5277 TCTTTTGGTT
5287 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
5320 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
5353 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
5386 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
5402 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:5333 original size:19 final size:18
Alignment explanation
Indices: 5294--5406 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
5284 GTTGAAATGA
5294 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
5309 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
5326 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
5342 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
5359 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
5375 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
5392 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
5407 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:5437 original size:14 final size:14
Alignment explanation
Indices: 5418--5472 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
5408 TTTGGTTTCG
5418 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
5432 CGTTGCGATTTCCATTTCG
1 CGTTGCGA-TT-C---TCT
5451 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
5465 CGTTGCGA
1 CGTTGCGA
5473 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:5483 original size:20 final size:20
Alignment explanation
Indices: 5458--5513 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
5448 TCGCGTTGCG
5458 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGACAGTC
***
5478 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGACAGTC
*
5498 ATTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGAC
5514 TCTTCTGCAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.14, C:0.27, G:0.18, T:0.41
Consensus pattern (20 bp):
ATTCTCTCGTTGCGACAGTC
Found at i:5634 original size:33 final size:33
Alignment explanation
Indices: 5592--5662 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
5582 AATACTAACT
*
5592 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
5625 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
5658 TGAAA
1 TGAAA
5663 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:5896 original size:22 final size:22
Alignment explanation
Indices: 5844--5898 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
5834 TGGTTGTGAG
**
5844 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
5866 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
5888 GGATTTCTTCG
1 GGATTTCTTCG
5899 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:6069 original size:20 final size:20
Alignment explanation
Indices: 6044--6237 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
6034 CTTTAAATAT
6044 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
6064 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
6086 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
6105 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
6125 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
6145 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
6165 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
6185 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
6205 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
6225 CGCGTTGCGATTT
1 CGCGTTGCGATTT
6238 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:6231 original size:60 final size:60
Alignment explanation
Indices: 6044--6237 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
6034 CTTTAAATAT
**
6044 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
6105 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
6165 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
6225 CGCGTTGCGATTT
1 CGCGTTGCGATTT
6238 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:6254 original size:21 final size:20
Alignment explanation
Indices: 6230--6306 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 20
6220 ATATTCGCGT
6230 TGCGATTTTGGAAAATCGCAA
1 TGCGATTTTGGAAAATCGC-A
* * **
6251 TGCGAATTTGTACTATCGCA
1 TGCGATTTTGGAAAATCGCA
* *
6271 TCGCGATTTT-CAAGAATCGCGT
1 T-GCGATTTTGGAA-AATCGC-A
6293 TGCGATTTTGGAAA
1 TGCGATTTTGGAAA
6307 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:6317 original size:20 final size:20
Alignment explanation
Indices: 6292--6343 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
6282 AAGAATCGCG
*
6292 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
6312 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
6332 TTGCGATTCTGG
1 TTGCGATTCTGG
6344 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:10479 original size:29 final size:29
Alignment explanation
Indices: 10437--10496 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
10427 TTCCGTGTGA
* *
10437 CTCGATCCCACGACTTCAAGGTTAAAAAC
1 CTCGATCCCACGACCTCAAAGTTAAAAAC
*
10466 CTCGATCCCACGACCTCAAAGTTAAGAAC
1 CTCGATCCCACGACCTCAAAGTTAAAAAC
10495 CT
1 CT
10497 TATGATCTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.33, C:0.33, G:0.13, T:0.20
Consensus pattern (29 bp):
CTCGATCCCACGACCTCAAAGTTAAAAAC
Found at i:28548 original size:19 final size:20
Alignment explanation
Indices: 28526--28570 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
28516 AAGATAATTA
*
28526 TAATAATACTCAT-TTTTTT
1 TAATAATACTCATATTTTTC
* *
28545 TAATTATATTCATATTTTTC
1 TAATAATACTCATATTTTTC
28565 TAATAA
1 TAATAA
28571 AAATAATTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.56
Consensus pattern (20 bp):
TAATAATACTCATATTTTTC
Found at i:32438 original size:230 final size:228
Alignment explanation
Indices: 32031--32480 Score: 794
Period size: 230 Copynumber: 2.0 Consensus size: 228
32021 GTAAATTATC
* * *
32031 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
*
32096 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATTT
32161 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
*
32226 AAACATAAATTACATAAGTTTTAAAAAAAGTATA
196 AAACATAAATTACATAA-CTTTAAAAAAAGTATA
32260 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTAG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
32325 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAAT-ATAAT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAT-AT
* *
32389 TTTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAAT
129 TTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAT
32454 TGAAACATAAATTACATAACTTTAAAA
194 TGAAACATAAATTACATAACTTTAAAA
32481 GCAGTTTTAA
Statistics
Matches: 211, Mismatches: 8, Indels: 4
0.95 0.04 0.02
Matches are distributed among these distances:
229 45 0.21
230 166 0.79
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (228 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
AAACATAAATTACATAACTTTAAAAAAAGTATA
Found at i:32567 original size:20 final size:20
Alignment explanation
Indices: 32544--32588 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 20
32534 CGATATACCA
32544 GGTAA-AAATATGATAAAACC
1 GGTAACAAA-ATGATAAAACC
32564 GGTAACAAAATGATAAAACC
1 GGTAACAAAATGATAAAACC
32584 GGTAA
1 GGTAA
32589 TTTAAAAGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 21 0.88
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.18, T:0.18
Consensus pattern (20 bp):
GGTAACAAAATGATAAAACC
Found at i:32733 original size:20 final size:19
Alignment explanation
Indices: 32710--32756 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
32700 CGATATAACA
32710 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
32730 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
32750 GGTAAAA
1 GGTAAAA
32757 TGATACCGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:32758 original size:17 final size:18
Alignment explanation
Indices: 32714--32761 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 18
32704 ATAACAGGTA
32714 AAAATATGATAAAACCGGT
1 AAAA-ATGATAAAACCGGT
32733 AACAAAATGATAAAACCGGT
1 -A-AAAATGATAAAACCGGT
32753 -AAAATGATA
1 AAAAATGATA
32762 CCGGATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 9 0.33
20 15 0.56
21 3 0.11
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.19
Consensus pattern (18 bp):
AAAAATGATAAAACCGGT
Found at i:35031 original size:21 final size:21
Alignment explanation
Indices: 34984--35048 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
34974 AAGACAATCA
* *
34984 AGAGTCGAAGAGAAACTTGATC
1 AGAGTCGAAGAGAAACTCGA-G
*
35006 A-AGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
* *
35026 AGAGTCGAAGATACACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
35047 AG
1 AG
35049 GAATAAGGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.29, T:0.15
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTCGAG
Found at i:35124 original size:33 final size:33
Alignment explanation
Indices: 35082--35147 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
35072 AAATAGATGG
*
35082 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
35115 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
35148 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:36979 original size:18 final size:19
Alignment explanation
Indices: 36935--36982 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
36925 AATGTCGAGT
36935 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
36954 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
36973 T-ATTTTGTAT
1 TAATTTTGTAT
36983 GTGAATAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 9 0.32
19 19 0.68
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.56
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:38134 original size:197 final size:199
Alignment explanation
Indices: 37100--38859 Score: 3398
Period size: 197 Copynumber: 8.9 Consensus size: 199
37090 CAATATGGCC
* *
37100 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCAATCCCAAAATCATCGAAC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAAC
37165 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
37230 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAA
37295 TGGAA
195 TGGAA
37300 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
37365 CAAAAGTATAATATAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
37430 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
37495 GGAA
196 GGAA
37499 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
37564 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
37629 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
37694 GGAA
196 GGAA
37698 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
37763 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGG-TTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
37827 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTT-CCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
37891 GGAA
196 GGAA
37895 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
37960 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
38025 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
38090 GG-A
196 GGAA
38093 AACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
38157 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
38222 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTATCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
38287 GG-A
196 GGAA
38290 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
38355 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
38420 AATATGTCT-AATAATGTGTCGACACTAATATAGTTTGTGTCGATAC-TTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
38483 GGAA
196 GGAA
38487 AACAAGGTGCACCCATAAAGTGTCGATCC--ATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
38550 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
38615 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
38680 GGAA
196 GGAA
38684 AACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
38748 C-AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
38812 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACT
38860 AATTTAAATA
Statistics
Matches: 1546, Mismatches: 6, Indels: 19
0.98 0.00 0.01
Matches are distributed among these distances:
195 108 0.07
196 56 0.04
197 557 0.36
198 295 0.19
199 496 0.32
200 34 0.02
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.31
Consensus pattern (199 bp):
AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
GGAA
Found at i:40335 original size:3 final size:3
Alignment explanation
Indices: 40327--40398 Score: 72
Period size: 3 Copynumber: 24.0 Consensus size: 3
40317 TGAAGCTGAC
* * * ** * *
40327 GAT GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA GAT GAT GAC GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
*
40375 GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT
40399 CCAAACAAGT
Statistics
Matches: 54, Mismatches: 15, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.35, C:0.06, G:0.35, T:0.25
Consensus pattern (3 bp):
GAT
Found at i:40356 original size:27 final size:27
Alignment explanation
Indices: 40315--40397 Score: 103
Period size: 27 Copynumber: 3.0 Consensus size: 27
40305 CGGCGCAGAA
*
40315 GATGAAGCTGACGATGATGATGATGAC
1 GATGAAGCTGACGATGAAGATGATGAC
*
40342 GATGAAGCTGGCGATGAAGATGATGAC
1 GATGAAGCTGACGATGAAGATGATGAC
* *
40369 GATGATGATGATGATGATGAAGATGATGA
1 GATGA--A-GCTGACGATGAAGATGATGA
40398 TCCAAACAAG
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
27 30 0.62
29 1 0.02
30 17 0.35
ACGTcount: A:0.35, C:0.07, G:0.35, T:0.23
Consensus pattern (27 bp):
GATGAAGCTGACGATGAAGATGATGAC
Found at i:44743 original size:23 final size:23
Alignment explanation
Indices: 44717--44771 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
44707 GTAAACTATG
44717 ATGTAATAGGTAGCCCTTATATA
1 ATGTAATAGGTAGCCCTTATATA
* **
44740 ATGTAATAGGTATCGTTTATATA
1 ATGTAATAGGTAGCCCTTATATA
44763 ATGTAATAG
1 ATGTAATAG
44772 TAGTGGTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.36, C:0.07, G:0.18, T:0.38
Consensus pattern (23 bp):
ATGTAATAGGTAGCCCTTATATA
Found at i:45166 original size:23 final size:23
Alignment explanation
Indices: 45135--45198 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
45125 ATAGGTAAAC
*
45135 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
45158 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
45181 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
45199 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:45205 original size:23 final size:23
Alignment explanation
Indices: 45135--45207 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
45125 ATAGGTAAAC
* **
45135 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
45158 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
45181 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
45204 ATAT
1 ATAT
45208 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:45235 original size:20 final size:20
Alignment explanation
Indices: 45210--45248 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
45200 GGTTATATTG
* *
45210 TAAAGTGTCTATCCTTTTTA
1 TAAAGTGTCCATACTTTTTA
45230 TAAAGTGTCCATACTTTTT
1 TAAAGTGTCCATACTTTTT
45249 TCACTGTGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.15, G:0.10, T:0.49
Consensus pattern (20 bp):
TAAAGTGTCCATACTTTTTA
Done.