Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008325.1 Hibiscus syriacus cultivar Beakdansim tig00111029_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: 165133
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:24687 original size:19 final size:19
Alignment explanation
Indices: 24643--24692 Score: 50
Period size: 19 Copynumber: 2.6 Consensus size: 19
24633 GTTCCGTCAA
*
24643 TATT-AAATAGAATACATAT
1 TATTAAAATA-AATAAATAT
24662 TATTAAAATAAATAAAT-T
1 TATTAAAATAAATAAATAT
*
24680 TATGTAAATTAAA
1 TAT-TAAAATAAA
24693 ATTTATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 4 0.15
19 18 0.67
20 5 0.19
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (19 bp):
TATTAAAATAAATAAATAT
Found at i:24731 original size:22 final size:22
Alignment explanation
Indices: 24693--24740 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
24683 GTAAATTAAA
*
24693 ATTTATATATTAAATAACTTTTT
1 ATTTATATATTAAATAA-ATTTT
*
24716 ATTTAT-TATTATATAAATTTT
1 ATTTATATATTAAATAAATTTT
24737 ATTT
1 ATTT
24741 TTAAGTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 8 0.35
22 9 0.39
23 6 0.26
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (22 bp):
ATTTATATATTAAATAAATTTT
Found at i:25937 original size:20 final size:20
Alignment explanation
Indices: 25843--26211 Score: 440
Period size: 20 Copynumber: 18.4 Consensus size: 20
25833 GATTTTCCAT
* ** *
25843 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
25863 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
25883 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
25903 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
25923 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
25943 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
25963 TATCGCAACGCATATCCGTA
1 AATCGCAACGCGTATCCGTA
25983 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
26003 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
26023 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
26043 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
26063 AATCGTAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
26083 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
26103 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
26123 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
26143 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
26163 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
26183 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
26203 AATCACAAC
1 AATCGCAAC
26212 ACTGAAATTT
Statistics
Matches: 301, Mismatches: 40, Indels: 16
0.84 0.11 0.04
Matches are distributed among these distances:
19 3 0.01
20 295 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:26933 original size:24 final size:24
Alignment explanation
Indices: 26894--26940 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
26884 AAATTTGGTC
26894 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
26918 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
26941 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:29441 original size:19 final size:19
Alignment explanation
Indices: 29419--29738 Score: 360
Period size: 19 Copynumber: 18.4 Consensus size: 19
29409 CGGAAAATAC
*
29419 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
29438 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
29452 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
29472 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
29486 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
29505 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
29524 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
29538 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
29557 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
29576 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
29595 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
*
29609 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
29628 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
29646 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
29660 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
29679 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
29693 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
29712 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
29731 AATCGCAA
1 AATCGCAA
29739 CGAGATAATC
Statistics
Matches: 260, Mismatches: 10, Indels: 62
0.78 0.03 0.19
Matches are distributed among these distances:
14 56 0.22
15 3 0.01
16 26 0.10
17 15 0.06
18 12 0.05
19 135 0.52
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:29506 original size:33 final size:33
Alignment explanation
Indices: 29419--29719 Score: 234
Period size: 33 Copynumber: 8.8 Consensus size: 33
29409 CGGAAAATAC
* *
29419 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAA
*
29452 AATCGCAATGCGGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGAGAA
29486 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
*
29524 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
29557 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
* *
29595 AATCGCAA--CGACA-G--AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
29628 AATCGCAATGCGAAATG-AAATCGCAACGA-AA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAA
29659 GAATCGCAATGCGAAATGAAAATCGCAACGA-AA
1 -AATCGCAATGCGAAATGAAAATCGCAACGAGAA
29692 GAATCGCAATGCGAAATGAAAATCGCAA
1 -AATCGCAATGCGAAATGAAAATCGCAA
29720 TGCGAAATGA
Statistics
Matches: 241, Mismatches: 9, Indels: 36
0.84 0.03 0.13
Matches are distributed among these distances:
31 2 0.01
32 17 0.07
33 124 0.51
34 30 0.12
35 12 0.05
36 7 0.03
37 10 0.04
38 39 0.16
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.14
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAA
Found at i:29749 original size:33 final size:34
Alignment explanation
Indices: 29502--29760 Score: 238
Period size: 33 Copynumber: 7.6 Consensus size: 34
29492 AATGCGAAAT
29502 GAAAATCGCAATGCGAAATGAAAATCGCAA-CGA
1 GAAAATCGCAATGCGAAATGAAAATCGCAAGCGA
*
29535 GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAA
1 GAAAATCGCAATGCGAAATGAAAATCGCAA-GCG--A
29572 TGAAAATCGCAATGCGAAATGAAAATCGCAA-CGA
1 -GAAAATCGCAATGCGAAATGAAAATCGCAAGCGA
* * *
29606 CAGAATCGCAATGCGAAATTAAAATCGCAATGCGA
1 GAAAATCGCAATGCGAAATGAAAATCGCAA-GCGA
*
29641 AATGAAATCGCAA--CGAAA-G--AATCGCAATGCGAAA
1 GA--AAATCGCAATGCGAAATGAAAATCGCAA-GCG--A
29675 TGAAAATCGCAA--CGAAA-G--AATCGCAATGCGAAA
1 -GAAAATCGCAATGCGAAATGAAAATCGCAA-GCG--A
29708 TGAAAATCGCAATGCGAAATGAAAATCGCAA-CGA
1 -GAAAATCGCAATGCGAAATGAAAATCGCAAGCGA
*
29742 GATAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
29761 TATAAACGCA
Statistics
Matches: 199, Mismatches: 10, Indels: 34
0.82 0.04 0.14
Matches are distributed among these distances:
32 12 0.06
33 116 0.58
34 3 0.02
35 17 0.09
36 5 0.03
37 9 0.05
38 37 0.19
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (34 bp):
GAAAATCGCAATGCGAAATGAAAATCGCAAGCGA
Found at i:29776 original size:52 final size:52
Alignment explanation
Indices: 29447--29760 Score: 419
Period size: 52 Copynumber: 6.0 Consensus size: 52
29437 AAATCCCAAC
29447 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
29500 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* * * *
29552 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGA-AAT-GAAAAT-CGCA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-CAATGCGAA
* * *
29602 ACGACAGAATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAAATCGCAA--CGAA
1 ATGA-A-AATCGCAATGCGAAATGAAAATCGCAA--CGAGA-G-AATCGCAATGCGAA
*
29658 A-G--AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
29707 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
29759 AT
1 AT
29761 TATAAACGCA
Statistics
Matches: 233, Mismatches: 14, Indels: 29
0.84 0.05 0.11
Matches are distributed among these distances:
47 8 0.03
48 1 0.00
49 10 0.04
50 8 0.03
51 33 0.14
52 144 0.62
53 16 0.07
54 2 0.01
55 1 0.00
56 4 0.02
57 5 0.02
58 1 0.00
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:29876 original size:19 final size:19
Alignment explanation
Indices: 29767--29868 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
29757 AAATTATAAA
29767 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
29786 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
29806 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
29822 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
29839 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
29858 CGCATTGCGAT
1 CGCATTGCGAT
29869 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:29994 original size:14 final size:14
Alignment explanation
Indices: 29975--30011 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
29965 CATCAATTAC
29975 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
29989 ACAAATCATCTTTT
1 ACAAATCAACTTTT
30003 ACAAATCAA
1 ACAAATCAA
30012 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:32013 original size:14 final size:14
Alignment explanation
Indices: 31994--32050 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
31984 GCGAAATGAA
*
31994 AATCGCAACGACAG
1 AATCGCAACGAAAG
32008 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
32025 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
32041 AATCGCAACG
1 AATCGCAACG
32051 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:32021 original size:33 final size:33
Alignment explanation
Indices: 31975--32067 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
31965 GCGAAACCAA
*
31975 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
32008 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
32041 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
32068 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:32032 original size:19 final size:19
Alignment explanation
Indices: 31938--32072 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
31928 TAGTTTACTT
* *
31938 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
31958 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
31977 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
31996 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
32010 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
32029 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
32043 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
32062 TCGCAATGCGA
1 TCGCAACGCGA
32073 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:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:32090 original size:19 final size:19
Alignment explanation
Indices: 32068--32196 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
32058 AAAATCGCAA
32068 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
32087 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
32101 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
32120 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
32134 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
32153 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
32172 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
32192 TGCGA
1 TGCGA
32197 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:0.16, G:0.29, T:0.47
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:32110 original size:33 final size:33
Alignment explanation
Indices: 32068--32159 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
32058 AAAATCGCAA
32068 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
32101 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
32134 TGCGATTTTTATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
32160 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:0.17, G:0.28, T:0.47
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:32502 original size:93 final size:93
Alignment explanation
Indices: 32228--32693 Score: 909
Period size: 93 Copynumber: 5.0 Consensus size: 93
32218 GCAAATTGAA
32228 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
32293 GCAGAATTGGCAGCAACCGAACAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
32321 ACTTTCAACCAAAAGACAAAAC-AAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
32385 GCAGAATTGGCAGCAACCGAACAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
32413 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
32478 GCAGAATTGGCAGCAACCGAACAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
32506 ACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
32570 GCAGAATTGGCAGCAACCGAACAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
32598 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
*
32663 GCAGAATTGGCAGCAACCGAATAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
32691 ACT
1 ACT
32694 AAGCAATCTA
Statistics
Matches: 370, Mismatches: 1, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
92 184 0.50
93 186 0.50
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
GCAGAATTGGCAGCAACCGAACAAATTT
Found at i:32545 original size:185 final size:185
Alignment explanation
Indices: 32228--32693 Score: 907
Period size: 185 Copynumber: 2.5 Consensus size: 185
32218 GCAAATTGAA
32228 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
32293 GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAGACAAATACTATT
66 GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAGACAAATACTATT
32358 TCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
131 TCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
32413 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
32478 GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TAT
66 GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAAC-AAGACAAATACTAT
32542 TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
130 TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
32598 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
*
32663 GCAGAATTGGCAGCAACCGAATAAATTTACT
66 GCAGAATTGGCAGCAACCGAACAAATTTACT
32694 AAGCAATCTA
Statistics
Matches: 279, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
185 269 0.96
186 10 0.04
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (185 bp):
ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAGACAAATACTATT
TCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
Found at i:34414 original size:14 final size:14
Alignment explanation
Indices: 34395--34451 Score: 69
Period size: 14 Copynumber: 3.7 Consensus size: 14
34385 TTGAAATGAA
34395 AATCGCAACGAGAG
1 AATCGCAACGAGAG
34409 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
34426 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
34442 AATCGCAACG
1 AATCGCAACG
34452 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
14 18 0.47
16 6 0.16
17 6 0.16
19 8 0.21
ACGTcount: A:0.40, C:0.25, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:34432 original size:33 final size:33
Alignment explanation
Indices: 34387--34470 Score: 150
Period size: 33 Copynumber: 2.5 Consensus size: 33
34377 TCTTTTGGTT
34387 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
34420 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
34453 GAAATGAAAATCGCAACG
1 GAAATGAAAATCGCAACG
34471 CGAAATGAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.44, C:0.21, G:0.25, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:34433 original size:19 final size:19
Alignment explanation
Indices: 34409--34492 Score: 97
Period size: 19 Copynumber: 4.7 Consensus size: 19
34399 GCAACGAGAG
* *
34409 AATCGCAACGCGAGATGAC
1 AATCGCAACGCGAAATGAA
*
34428 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
34442 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
34461 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
34480 AATCGCAATGCGA
1 AATCGCAACGCGA
34493 TTTTGGTTTC
Statistics
Matches: 57, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 41 0.72
ACGTcount: A:0.43, C:0.23, G:0.24, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:34523 original size:14 final size:14
Alignment explanation
Indices: 34504--34558 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
34494 TTTGGTTTCG
34504 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
34518 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
34537 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
34551 CGTTGCGA
1 CGTTGCGA
34559 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:34536 original size:33 final size:33
Alignment explanation
Indices: 34488--34558 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
34478 AAAATCGCAA
**
34488 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
34521 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
34554 TGCGA
1 TGCGA
34559 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:34566 original size:33 final size:33
Alignment explanation
Indices: 34499--34580 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
34489 GCGATTTTGG
***
34499 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
34532 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
34565 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
34581 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:34585 original size:20 final size:20
Alignment explanation
Indices: 34511--34599 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
34501 TCGCGTTGCG
34511 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
34531 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
34544 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
34564 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
34584 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
34600 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:34721 original size:33 final size:33
Alignment explanation
Indices: 34679--34749 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
34669 AATACTAACT
*
34679 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
34712 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
34745 TGAAA
1 TGAAA
34750 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:34983 original size:22 final size:22
Alignment explanation
Indices: 34931--34985 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
34921 TGGTTGTGAG
**
34931 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
34953 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
34975 GGATTTCTTCG
1 GGATTTCTTCG
34986 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:35156 original size:20 final size:20
Alignment explanation
Indices: 35131--35323 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
35121 CTTTAAATAT
35131 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
35151 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
35173 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
35192 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
35212 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
35232 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
35252 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
35272 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
35292 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
35312 CGCGTTGCGATT
1 CGCGTTGCGATT
35324 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:35318 original size:60 final size:60
Alignment explanation
Indices: 35131--35323 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
35121 CTTTAAATAT
**
35131 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
35192 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
35252 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
35312 CGCGTTGCGATT
1 CGCGTTGCGATT
35324 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:35404 original size:20 final size:20
Alignment explanation
Indices: 35379--35430 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
35369 AAGAATCGCG
*
35379 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
35399 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
35419 TTGCGATTCTGG
1 TTGCGATTCTGG
35431 GGGATCGCGT
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:56844 original size:202 final size:194
Alignment explanation
Indices: 56480--56857 Score: 469
Period size: 202 Copynumber: 1.9 Consensus size: 194
56470 CATTGATATC
** * *
56480 TCATCAGTGGGAGGCTCAGGATATTGTCTATATGTACGTTACTTGTTTTCATAATTATTAACAGC
1 TCATCAGTGGGAGGCTCAGGATATTGTCTATATCAAAGTTACTTGTCTTCATAATTATTAACAGC
* *
56545 GTTCGCCTGCCTAGAGTTTGAAGCAGACAAATCCTCCTCCATCTTTCATGGCCATATTCTCATTC
66 ATTCGCCTGCCTA-AGTTTGAAGCAGACAAATCCTCCACCATCTTTCATGGCCATATTCTCATTC
* *
56610 TCCGTTTTTCTTCTCTATTTGTTTTTCTACGAGGTGGTGACACCTTCATTACTTTCTCTTCTGTA
130 TCCGTTTTTCTTCTCTATTTGCTTTTCTACGAGGCGGTGACACCTTCATTACTTTCTCTTCTGTA
* *
56675 TCATCAGTGGGAGGCTCGGGATCATTGTCTATATCCAAAGTTATTTG-CTTCATAATTATT-ACA
1 TCATCAGTGGGAGGCTCAGGAT-ATTGTCTATAT-CAAAGTTACTTGTCTTCATAATTATTAACA
* ** *
56738 GCATTCGCTTGCCT-AGTTTGAAGTGGACAAATCAGAACTTCCACCATCTTTCTTGGCCATATTC
64 GCATTCGCCTGCCTAAGTTTGAAGCAGACAAATC----C-TCCACCATCTTTCATGGCCATATT-
56802 CTCA-TCTTCACTGGTTTTTCTTCTCT-TGTTGCTTTTCTACGAGGCGGTGACACCTT
123 CTCATTC-TC-C--GTTTTTCTTCTCTAT-TTGCTTTTCTACGAGGCGGTGACACCTT
56858 TGGCACTTTC
Statistics
Matches: 156, Mismatches: 14, Indels: 19
0.83 0.07 0.10
Matches are distributed among these distances:
193 17 0.11
195 36 0.23
196 23 0.15
197 9 0.06
198 24 0.15
199 6 0.04
200 1 0.01
201 1 0.01
202 39 0.25
ACGTcount: A:0.20, C:0.23, G:0.17, T:0.39
Consensus pattern (194 bp):
TCATCAGTGGGAGGCTCAGGATATTGTCTATATCAAAGTTACTTGTCTTCATAATTATTAACAGC
ATTCGCCTGCCTAAGTTTGAAGCAGACAAATCCTCCACCATCTTTCATGGCCATATTCTCATTCT
CCGTTTTTCTTCTCTATTTGCTTTTCTACGAGGCGGTGACACCTTCATTACTTTCTCTTCTGTA
Found at i:62322 original size:88 final size:87
Alignment explanation
Indices: 62217--62378 Score: 236
Period size: 87 Copynumber: 1.9 Consensus size: 87
62207 AGGAGAGTGT
* * *
62217 TCACCAAATAAGTTCATAAAAATGAAAATTTAAAACAAATTTAAAGCAATT-AAATTCTACATTA
1 TCACCAAATAAGTTCATAAAAATGAAAA-TTAAAACAAA-TCAAAGCAATTAAAAATATACATTA
62281 AACGAATTCAAAATGCGTTCACCA
64 AACGAATTCAAAATGCGTTCACCA
* ** *
62305 TCACCAAATAAGTTCATAAAAATGACAATTAAAGTAAATCAAAGCAATTAAAAATATACATTAAC
1 TCACCAAATAAGTTCATAAAAATGAAAATTAAAACAAATCAAAGCAATTAAAAATATACATTAAA
62370 CGAATTCAA
66 CGAATTCAA
62379 TTTGGATGCA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
86 10 0.15
87 29 0.44
88 27 0.41
ACGTcount: A:0.52, C:0.15, G:0.07, T:0.26
Consensus pattern (87 bp):
TCACCAAATAAGTTCATAAAAATGAAAATTAAAACAAATCAAAGCAATTAAAAATATACATTAAA
CGAATTCAAAATGCGTTCACCA
Found at i:66511 original size:18 final size:19
Alignment explanation
Indices: 66488--66525 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
66478 ACCTATAATA
*
66488 AATTTTTTATAAT-TTTAT
1 AATTTTGTATAATGTTTAT
*
66506 AATTTTGTATCATGTTTAT
1 AATTTTGTATAATGTTTAT
66525 A
1 A
66526 TAACTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.61
Consensus pattern (19 bp):
AATTTTGTATAATGTTTAT
Found at i:68677 original size:19 final size:19
Alignment explanation
Indices: 68653--68693 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
68643 TTTCGAACTG
68653 AGTTGATATTAGAATAATT
1 AGTTGATATTAGAATAATT
68672 AGTTGATATTAGAATAATT
1 AGTTGATATTAGAATAATT
68691 AGT
1 AGT
68694 AGCATTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.17, T:0.41
Consensus pattern (19 bp):
AGTTGATATTAGAATAATT
Found at i:69059 original size:22 final size:23
Alignment explanation
Indices: 69033--69076 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
69023 TAAACTTAAA
69033 TAAAAAT-ATTA-AATTAAATTT
1 TAAAAATAATTAGAATTAAATTT
*
69054 TAAAAATAATTAGACTTAAATTT
1 TAAAAATAATTAGAATTAAATTT
69077 GTTTTTGTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 4 0.20
23 9 0.45
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (23 bp):
TAAAAATAATTAGAATTAAATTT
Found at i:70318 original size:54 final size:53
Alignment explanation
Indices: 70238--70348 Score: 143
Period size: 54 Copynumber: 2.1 Consensus size: 53
70228 CAAACATCTG
* * *
70238 TTATTGGATTTAGGGTTGTTGGGCAGTGAACTCGGAACTTAATTAACCGGGGT
1 TTATTGGATTCAGGGTTGTTGGGCAGTGAACTAGGAACTTAATTAACCAGGGT
* * *
70291 TTATTGTATTCAGGGTT-TTGGGTGCAGTGAACTAGGAACTTAGTTAATCAGGGT
1 TTATTGGATTCAGGGTTGTT-GG-GCAGTGAACTAGGAACTTAATTAACCAGGGT
70345 TTAT
1 TTAT
70349 AAGATTTAGG
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
52 2 0.04
53 17 0.34
54 31 0.62
ACGTcount: A:0.23, C:0.10, G:0.30, T:0.37
Consensus pattern (53 bp):
TTATTGGATTCAGGGTTGTTGGGCAGTGAACTAGGAACTTAATTAACCAGGGT
Found at i:74133 original size:31 final size:31
Alignment explanation
Indices: 74097--74159 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
74087 TAATTTTTAT
74097 TATCACCCCTGAAATTTAAATAAAATATCAA
1 TATCACCCCTGAAATTTAAATAAAATATCAA
*
74128 TATCACCCCTGAAATTTAAATAGAATATCAA
1 TATCACCCCTGAAATTTAAATAAAATATCAA
74159 T
1 T
74160 TTGATATTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.46, C:0.19, G:0.05, T:0.30
Consensus pattern (31 bp):
TATCACCCCTGAAATTTAAATAAAATATCAA
Found at i:74610 original size:21 final size:20
Alignment explanation
Indices: 74584--74623 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
74574 CTTTTAGATA
74584 TATTATTAAAATTAAAATAAT
1 TATTATTAAAA-TAAAATAAT
*
74605 TATTATTTAAATAAAATAA
1 TATTATTAAAATAAAATAA
74624 AAATACAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TATTATTAAAATAAAATAAT
Found at i:74619 original size:26 final size:28
Alignment explanation
Indices: 74590--74652 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 28
74580 GATATATTAT
*
74590 TAAAATTAAAAT-A-ATTATTATTTAAA
1 TAAAATAAAAATAATATTATTATTTAAA
*
74616 TAAAATAAAAATACAATATTTTTATTTAAA
1 TAAAATAAAAAT--AATATTATTATTTAAA
74646 TAAAATA
1 TAAAATA
74653 GATAAATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 11 0.35
29 1 0.03
30 19 0.61
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (28 bp):
TAAAATAAAAATAATATTATTATTTAAA
Found at i:74750 original size:2 final size:2
Alignment explanation
Indices: 74743--74797 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
74733 ATCAATTCAT
74743 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
74785 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
74798 GGATTAATCA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:77226 original size:29 final size:28
Alignment explanation
Indices: 77189--77338 Score: 151
Period size: 29 Copynumber: 5.2 Consensus size: 28
77179 CTGTTGACCG
* * *
77189 GGTGGTATTTTTGTAATTATTTTGAAAA
1 GGTGATATTTTCGTAATTATTTTTAAAA
* *
77217 TGGTGCTATTTTTGTAATT-TTTTTAAAA
1 -GGTGATATTTTCGTAATTATTTTTAAAA
*
77245 -GTGATAATTTCGTAATTATTTTTTAAAA
1 GGTGATATTTTCGTAATTA-TTTTTAAAA
**
77273 AATGATATTTTCGTAATTATTTTTAAAA
1 GGTGATATTTTCGTAATTATTTTTAAAA
* *
77301 GGGTGACATTTTCGTAAATATTTCTTAAAA
1 -GGTGATATTTTCGTAATTATTT-TTAAAA
77331 GGGTGATA
1 -GGTGATA
77339 ATTGTGTAAA
Statistics
Matches: 104, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
26 14 0.13
28 26 0.25
29 51 0.49
30 13 0.12
ACGTcount: A:0.32, C:0.04, G:0.16, T:0.48
Consensus pattern (28 bp):
GGTGATATTTTCGTAATTATTTTTAAAA
Found at i:84501 original size:29 final size:28
Alignment explanation
Indices: 84439--84524 Score: 93
Period size: 29 Copynumber: 3.0 Consensus size: 28
84429 TGACCGGGTG
* * *
84439 GTATTTTTGTAATTATTTTGAAATTGGTT
1 GTATTTTCGTAATTATTTTGAAAAT-GAT
*
84468 GTATTTTGGTAATTATTTTGAAAATGAT
1 GTATTTTCGTAATTATTTTGAAAATGAT
*
84496 GCTATTTTCGTAATT-TTTTTAAAAGTGAT
1 G-TATTTTCGTAATTATTTTGAAAA-TGAT
84525 AATTTATTAA
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
28 11 0.22
29 39 0.78
ACGTcount: A:0.28, C:0.02, G:0.16, T:0.53
Consensus pattern (28 bp):
GTATTTTCGTAATTATTTTGAAAATGAT
Found at i:84545 original size:30 final size:29
Alignment explanation
Indices: 84509--84571 Score: 92
Period size: 29 Copynumber: 2.1 Consensus size: 29
84499 ATTTTCGTAA
84509 TTTTTTTAAAAGTGATAATTTAT-TAATTAT
1 TTTTTTTAAAA-TGAT-ATTTATGTAATTAT
*
84539 TTTTTTTAAAATGATATTTTTGTAATTAT
1 TTTTTTTAAAATGATATTTATGTAATTAT
84568 TTTT
1 TTTT
84572 AAAAGGGTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
28 5 0.16
29 15 0.48
30 11 0.35
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (29 bp):
TTTTTTTAAAATGATATTTATGTAATTAT
Found at i:84586 original size:29 final size:29
Alignment explanation
Indices: 84441--84609 Score: 86
Period size: 29 Copynumber: 5.9 Consensus size: 29
84431 ACCGGGTGGT
* * * *
84441 ATTTTTGTAATTATTTTGAAATTGGTTG-T
1 ATTTTTGTAATTATTTTTAAA-AGGGTGAC
* * * *
84470 ATTTTGGTAATTATTTTGAAAATGATG-C
1 ATTTTTGTAATTATTTTTAAAAGGGTGAC
* *
84498 TATTTTCGTAATT-TTTTTAAAA--GTGATA
1 -ATTTTTGTAATTATTTTTAAAAGGGTGA-C
* *
84526 ATTTAT-TAATTATTTTTTTTAAAA---TGAT
1 ATTTTTGTAATTA---TTTTTAAAAGGGTGAC
84554 ATTTTTGTAATTATTTTTAAAAGGGTGAC
1 ATTTTTGTAATTATTTTTAAAAGGGTGAC
* *
84583 ATTTTCGTAAATATTTCTTAAAAGGGT
1 ATTTTTGTAATTATTT-TTAAAAGGGT
84610 AATAATTGTG
Statistics
Matches: 112, Mismatches: 16, Indels: 23
0.74 0.11 0.15
Matches are distributed among these distances:
26 16 0.14
27 4 0.04
28 16 0.14
29 57 0.51
30 19 0.17
ACGTcount: A:0.31, C:0.03, G:0.14, T:0.52
Consensus pattern (29 bp):
ATTTTTGTAATTATTTTTAAAAGGGTGAC
Found at i:84623 original size:30 final size:28
Alignment explanation
Indices: 84559--84623 Score: 67
Period size: 30 Copynumber: 2.2 Consensus size: 28
84549 ATGATATTTT
* * * *
84559 TGTAATTATTTTTAAAAGGGTGACATTT
1 TGTAAATATTTTTAAAAGGGTAAAATTG
84587 TCGTAAATATTTCTTAAAAGGGTAATAATTG
1 T-GTAAATATTT-TTAAAAGGGTAA-AATTG
84618 TGTAAA
1 TGTAAA
84624 ATGGTTGATC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
28 1 0.03
29 9 0.30
30 16 0.53
31 4 0.13
ACGTcount: A:0.37, C:0.05, G:0.17, T:0.42
Consensus pattern (28 bp):
TGTAAATATTTTTAAAAGGGTAAAATTG
Found at i:87613 original size:3 final size:3
Alignment explanation
Indices: 87605--87637 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
87595 ATGTAAACTC
87605 TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
87638 TTAATTTACA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:89086 original size:33 final size:31
Alignment explanation
Indices: 89032--89099 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 31
89022 GGCAATGTTT
*
89032 CCGACCCGATATGACACTTAAAAAAACTCGAC
1 CCGACCCGATATCACACTTAAAAAAAC-CGAC
*
89064 CCGACCCGAATATCACACTTAAAAAATCCGAC
1 CCGACCCG-ATATCACACTTAAAAAAACCGAC
89096 CCGA
1 CCGA
89100 ACAAAATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 16 0.48
33 17 0.52
ACGTcount: A:0.40, C:0.34, G:0.12, T:0.15
Consensus pattern (31 bp):
CCGACCCGATATCACACTTAAAAAAACCGAC
Found at i:89088 original size:32 final size:32
Alignment explanation
Indices: 89032--89099 Score: 95
Period size: 32 Copynumber: 2.1 Consensus size: 32
89022 GGCAATGTTT
*
89032 CCGACCCGATATGACACTTAAAAAAA-CTCGAC
1 CCGACCCGATATCACACTTAAAAAAATC-CGAC
89064 CCGACCCGAATATCACACTT-AAAAAATCCGAC
1 CCGACCCG-ATATCACACTTAAAAAAATCCGAC
89096 CCGA
1 CCGA
89100 ACAAAATAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
32 22 0.67
33 11 0.33
ACGTcount: A:0.40, C:0.34, G:0.12, T:0.15
Consensus pattern (32 bp):
CCGACCCGATATCACACTTAAAAAAATCCGAC
Found at i:91711 original size:150 final size:150
Alignment explanation
Indices: 91440--91739 Score: 543
Period size: 150 Copynumber: 2.0 Consensus size: 150
91430 GTTTGGAGTT
91440 GTGTTTAACCTAGAAGGATATTTAATTTAGAATATTAAAAAAGATACGTCATTTAAGGGAAAAAA
1 GTGTTTAACCTAGAAGGATATTTAATTTAGAATATTAAAAAAGATACGTCATTTAAGGGAAAAAA
*
91505 TTTAATTATAGGGGTAAAATATATGCAAACCCCCTGAAGGACCCGATAGTCTAGGCATTCGCGTC
66 ATTAATTATAGGGGTAAAATATATGCAAACCCCCTGAAGGACCCGATAGTCTAGGCATTCGCGTC
91570 GTGCGGGTACGCCCCCAACC
131 GTGCGGGTACGCCCCCAACC
91590 GTGTTTAACCTAGAAGGATATTTAATTTAGAATATTAAAAAAGATACGTCACATTTAAGGGAAAA
1 GTGTTTAACCTAGAAGGATATTTAATTTAGAATATTAAAAAAGATACGT--CATTTAAGGGAAAA
91655 AAATTAATT-TAGGGGT-AAA-ATATGCAAACCCCCTGAAGGACCCGATAAGTCTAGGCATTCGC
64 AAATTAATTATAGGGGTAAAATATATGCAAACCCCCTGAAGGACCCGAT-AGTCTAGGCATTCGC
91717 GTCGTGCGGGTACGCCCCCAACC
128 GTCGTGCGGGTACGCCCCCAACC
91740 CCAATGAATT
Statistics
Matches: 146, Mismatches: 1, Indels: 6
0.95 0.01 0.04
Matches are distributed among these distances:
149 27 0.18
150 90 0.62
151 7 0.05
152 22 0.15
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (150 bp):
GTGTTTAACCTAGAAGGATATTTAATTTAGAATATTAAAAAAGATACGTCATTTAAGGGAAAAAA
ATTAATTATAGGGGTAAAATATATGCAAACCCCCTGAAGGACCCGATAGTCTAGGCATTCGCGTC
GTGCGGGTACGCCCCCAACC
Found at i:94844 original size:13 final size:13
Alignment explanation
Indices: 94826--94855 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
94816 TATAATTATA
94826 TTTAAGGTTAAGG
1 TTTAAGGTTAAGG
94839 TTTAAGGTTAAGG
1 TTTAAGGTTAAGG
94852 TTTA
1 TTTA
94856 GTAAGTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.27, T:0.43
Consensus pattern (13 bp):
TTTAAGGTTAAGG
Found at i:95649 original size:21 final size:21
Alignment explanation
Indices: 95614--95672 Score: 100
Period size: 21 Copynumber: 2.7 Consensus size: 21
95604 AATAAGAAAA
95614 TGACACCTTTTTCAAAAAAGTTT
1 TGACACC--TTTCAAAAAAGTTT
95637 TGACACCTTTCAAAAAAGTTT
1 TGACACCTTTCAAAAAAGTTT
95658 TGACACCTTTCAAAA
1 TGACACCTTTCAAAA
95673 TGACACCTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
21 29 0.81
23 7 0.19
ACGTcount: A:0.37, C:0.20, G:0.08, T:0.34
Consensus pattern (21 bp):
TGACACCTTTCAAAAAAGTTT
Found at i:95888 original size:24 final size:24
Alignment explanation
Indices: 95856--95903 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
95846 TCACCATCCT
95856 TTGTTTTTACCTACAGGCCTGCAA
1 TTGTTTTTACCTACAGGCCTGCAA
95880 TTGTTTTTACCTACAGGCCTGCAA
1 TTGTTTTTACCTACAGGCCTGCAA
95904 CTTCATTATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.38
Consensus pattern (24 bp):
TTGTTTTTACCTACAGGCCTGCAA
Found at i:105713 original size:23 final size:23
Alignment explanation
Indices: 105641--105705 Score: 130
Period size: 23 Copynumber: 2.8 Consensus size: 23
105631 AATAACATAT
105641 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATGTAA
105664 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATGTAA
105687 TAGGTAGCGCTTATATAAT
1 TAGGTAGCGCTTATATAAT
105706 AAAATAGGCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.34, C:0.09, G:0.22, T:0.35
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATGTAA
Found at i:109857 original size:201 final size:201
Alignment explanation
Indices: 109327--110154 Score: 924
Period size: 201 Copynumber: 4.1 Consensus size: 201
109317 TAATTTTAAA
* * * *
109327 AAGTATCGACACTAATTTAA-AAAGTGTTGATACATTATGTAGACCTATTTTCTCATAAAATCGG
1 AAGTATCGACAC-AAATGAATAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCGG
109391 TAAATTTAAACCAGTTACATTGTAAAGTGACCTATTACATTATAATTACGGGTTTCGATGTTTTT
65 TAAATTTAAACCAGTTACATTGTAAAGTGACCTATTACATTATAATTACGGGTTTCGATGTTTTT
* * * * **
109456 AGGATCGACACTTTTTCTAAATGTATCGACAC-TTTTTCGTGAACTT-GTTTCGAAAATTTATTA
130 GGGATCGACACTTGTTATAAATGTATCGACACTTTTTTCGTGAACTTGGTTT-GGAAATACATTA
109519 TGGACATA-
194 TGGACA-AC
* * * * * *
109527 AAGTTTCGACACAAATGTATAAAGTATCGATACATTATGTATACCT-TTTT-T-TTAATAACCGA
1 AAGTATCGACACAAATGAATAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAA-AACCGG
* * * * * * * *
109589 TATATTTAGACCGGTTACATTGTTATGTTACCTATTACATTATAATTATGTGTTTCGATGTTTTT
65 TAAATTTAAACCAGTTACATTGTAAAGTGACCTATTACATTATAATTACGGGTTTCGATGTTTTT
* *
109654 GGGATCGACACTTGTTATAAATGTATCGACACTTTTTTCGTGTACTTGGTTTGGAAATACATTCT
130 GGGATCGACACTTGTTATAAATGTATCGACACTTTTTTCGTGAACTTGGTTTGGAAATACATTAT
109719 GGACAAC
195 GGACAAC
* *
109726 ATGTATCGACACAAATGAATAAAGTGTCGATACA-TATTTTAGACCTATTTTCTCATAAAACCGG
1 AAGTATCGACACAAATGAATAAAGTGTCGATACATTA-TGTAGACCTATTTTCTCATAAAACCGG
* * * **
109790 TAAATTTAAACCAGTTACATTATAAAGTGACTTATTACATTATAGTTACAAGTTTCGATGTTTTT
65 TAAATTTAAACCAGTTACATTGTAAAGTGACCTATTACATTATAATTACGGGTTTCGATGTTTTT
* * * *
109855 GGGATCGACACTTGATATAAATGTATCGATACTTATTT-GTGAACTTGTTTTGGTTGGAAAATAC
130 GGGATCGACACTTGTTATAAATGTATCGACACTTTTTTCGTGAACTTG----GTTTGG-AAATAC
109919 ATTATGGAC-AC
190 ATTATGGACAAC
* * * * *
109930 AAAGTATCGACACAAATGTATAAAGTGTCGATGCTTTATGTATACCTCTTTTCTCAT-AAACCGG
1 -AAGTATCGACACAAATGAATAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCGG
* * * * ** * * * *
109994 TATATTTAGACCGGTTACATTGTTATTTTACCTATTACATTATAATTATGGGTCTCGATATTTTT
65 TAAATTTAAACCAGTTACATTGTAAAGTGACCTATTACATTATAATTACGGGTTTCGATGTTTTT
* * * * *
110059 GGGATCAATACATT-TTATAAATGTATCGACACTTTGTTCGTGCACTTGGTTTGGAAATAAATTA
130 GGGATCGACAC-TTGTTATAAATGTATCGACACTTTTTTCGTGAACTTGGTTTGGAAATACATTA
*
110123 TGGACTAC
194 TGGACAAC
* *
110131 ATGTATCGACACGAATGAATAAAG
1 AAGTATCGACACAAATGAATAAAG
110155 CAAATTCATT
Statistics
Matches: 523, Mismatches: 86, Indels: 38
0.81 0.13 0.06
Matches are distributed among these distances:
197 3 0.01
198 94 0.18
199 72 0.14
200 85 0.16
201 101 0.19
202 3 0.01
204 93 0.18
205 70 0.13
206 2 0.00
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (201 bp):
AAGTATCGACACAAATGAATAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCGGT
AAATTTAAACCAGTTACATTGTAAAGTGACCTATTACATTATAATTACGGGTTTCGATGTTTTTG
GGATCGACACTTGTTATAAATGTATCGACACTTTTTTCGTGAACTTGGTTTGGAAATACATTATG
GACAAC
Found at i:112414 original size:183 final size:182
Alignment explanation
Indices: 111750--112399 Score: 858
Period size: 182 Copynumber: 3.6 Consensus size: 182
111740 ATTAAAGTAC
* * ** * * *
111750 CGACACTTTCAACATAACCGGTAGAGCTTTACCGGTTTTGTCATTTCGATACTGGTTTTGTCATA
1 CGACACTTTCAATATATCCGGTAGCTCTTTACCGGTTTTATCATTTCGAGACCGGTTTTGTCATA
* * * * *
111815 TTTTTACCTATTATATTGTTATTGATCGATACATTTTCATAAAGTATCGACACTTTATAAGCGCT
66 TTTTTACCTGTTATATTGCTATGGATCGATACATTTTTATAAAGTATCGACACTTTATAGGCGCT
* * *
111880 ATAACTTCTTCTCTTTTAAATTACGAAAGTGTCGATACTTATATTAATTTAT
131 ATAACTTCTTCTCTTTTAAATTTCAAAAGTGTCGATACTTATATTAATCTAT
* * * *
111932 CGACACTTTCAATATATCCGGTAGTTTTTTACCGATTTTATCATTTCGAGACCTGTTTTGTCATA
1 CGACACTTTCAATATATCCGGTAGCTCTTTACCGGTTTTATCATTTCGAGACCGGTTTTGTCATA
* * * *
111997 TTCTTACATGTTATATTGCTATGGATCGATACATTTGTATAAAGTATCAACACTTTATAGGCGCT
66 TTTTTACCTGTTATATTGCTATGGATCGATACATTTTTATAAAGTATCGACACTTTATAGGCGCT
112062 ATAACTTCTTCTCTTTTAAA-TTCAAAAAGTGTCGATACTTATATTAA-CGTAT
131 ATAACTTCTTCTCTTTTAAATTTC-AAAAGTGTCGATACTTATATTAATC-TAT
*
112114 CGACACTTTCAATATATCCGGTAGCTCTTTACCGGTTTTATCATTTCGTGACCGGTTTTGTCATA
1 CGACACTTTCAATATATCCGGTAGCTCTTTACCGGTTTTATCATTTCGAGACCGGTTTTGTCATA
* * * * * *
112179 CTTATACTTGTTATATTGTTATGGATCAATACGTTTTTATAAAGTATCGACACTTTATAGGCGCT
66 TTTTTACCTGTTATATTGCTATGGATCGATACATTTTTATAAAGTATCGACACTTTATAGGCGCT
* *
112244 ATTACTTCTTCTCTTTTAAATTTCAAAAGTGTCAATACTTAT-TTAAATCTAAT
131 ATAACTTCTTCTCTTTTAAATTTCAAAAGTGTCGATACTTATATT-AATCT-AT
* * * ** * * *
112297 CGATACTTTCGATATATCCAGTAGCGGTTTACCGGTTTTATCATAAT-GAAACCGGTTTTATCAT
1 CGACACTTTCAATATATCCGGTAGCTCTTTACCGGTTTTATCAT-TTCGAGACCGGTTTTGTCAT
*
112361 ATTTTTACCTGTTATATTGCTATGGAGCGATACATTTTT
65 ATTTTTACCTGTTATATTGCTATGGATCGATACATTTTT
112400 CATTTGTATC
Statistics
Matches: 407, Mismatches: 54, Indels: 13
0.86 0.11 0.03
Matches are distributed among these distances:
181 4 0.01
182 311 0.76
183 91 0.22
184 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.42
Consensus pattern (182 bp):
CGACACTTTCAATATATCCGGTAGCTCTTTACCGGTTTTATCATTTCGAGACCGGTTTTGTCATA
TTTTTACCTGTTATATTGCTATGGATCGATACATTTTTATAAAGTATCGACACTTTATAGGCGCT
ATAACTTCTTCTCTTTTAAATTTCAAAAGTGTCGATACTTATATTAATCTAT
Found at i:114223 original size:39 final size:38
Alignment explanation
Indices: 114149--114267 Score: 134
Period size: 39 Copynumber: 3.1 Consensus size: 38
114139 TTTAAAAAAT
* *
114149 AATTTATAAGGTTAAGATGAAATAATTTAAGAAATTAAG
1 AATTTAGAATGTT-AGATGAAATAATTTAAGAAATTAAG
* *
114188 AGTTTAGAATGTTATGATGGAATAATTTAAGAAATT-AG
1 AATTTAGAATGTTA-GATGAAATAATTTAAGAAATTAAG
* *
114226 TAATTTATAATGTTAGACTGAAATAATTTGAG-AATTAAG
1 -AATTTAGAATGTTAGA-TGAAATAATTTAAGAAATTAAG
114265 AAT
1 AAT
114268 ACAAATTTTA
Statistics
Matches: 68, Mismatches: 8, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
38 12 0.18
39 56 0.82
ACGTcount: A:0.46, C:0.01, G:0.17, T:0.36
Consensus pattern (38 bp):
AATTTAGAATGTTAGATGAAATAATTTAAGAAATTAAG
Found at i:116762 original size:23 final size:23
Alignment explanation
Indices: 116736--116804 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
116726 CACCACAGCT
*
116736 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* *
116759 CGTAGAATTGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
*
116782 CGTAGAAATGCACCGTAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
116805 TATAAGATGT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:118868 original size:16 final size:16
Alignment explanation
Indices: 118847--118877 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
118837 GATTTATGCG
118847 ATATATGAAAATGAAA
1 ATATATGAAAATGAAA
*
118863 ATATATGAATATGAA
1 ATATATGAAAATGAA
118878 GAGTTATAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.13, T:0.29
Consensus pattern (16 bp):
ATATATGAAAATGAAA
Found at i:119910 original size:23 final size:23
Alignment explanation
Indices: 119884--119938 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
119874 ATGGCACTTC
119884 GGTGCATTTCTACGCGGCACTAA
1 GGTGCATTTCTACGCGGCACTAA
* * **
119907 GGTGCAATTCTACGTGGCACTTC
1 GGTGCATTTCTACGCGGCACTAA
119930 GGTGCATTT
1 GGTGCATTT
119939 ATATGAGTTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.18, C:0.24, G:0.27, T:0.31
Consensus pattern (23 bp):
GGTGCATTTCTACGCGGCACTAA
Found at i:124844 original size:38 final size:38
Alignment explanation
Indices: 124792--124866 Score: 114
Period size: 38 Copynumber: 2.0 Consensus size: 38
124782 AGCAGCAGTT
* *
124792 ACATCACATTAGTAACATGGAAAACTACTAGATCTGTA
1 ACATCACATGAGTAACATGGAAAACTACTAAATCTGTA
* *
124830 ACATCACATGAGTAACATGGACAACTATTAAATCTGT
1 ACATCACATGAGTAACATGGAAAACTACTAAATCTGT
124867 GCCATCCTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.27
Consensus pattern (38 bp):
ACATCACATGAGTAACATGGAAAACTACTAAATCTGTA
Found at i:130249 original size:21 final size:23
Alignment explanation
Indices: 130198--130249 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 23
130188 CATCATTCAA
*
130198 TAAATTTTTATATCGTATATTATT
1 TAAATTTTTAAATC-TATATTATT
**
130222 TCTATTTTTAAAT-TA-ATTATT
1 TAAATTTTTAAATCTATATTATT
130243 TAAATTT
1 TAAATTT
130250 AATTTATTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
21 11 0.48
22 2 0.09
24 10 0.43
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.60
Consensus pattern (23 bp):
TAAATTTTTAAATCTATATTATT
Found at i:130438 original size:15 final size:15
Alignment explanation
Indices: 130394--130444 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
130384 TAATTTGAGA
130394 TTATAAATAATAAAT
1 TTATAAATAATAAAT
* *
130409 ATTA-AGAT-TTAAAT
1 -TTATAAATAATAAAT
130423 TTATAAATAATAAAT
1 TTATAAATAATAAAT
130438 TTATAAA
1 TTATAAA
130445 AATGAACAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
13 3 0.10
14 8 0.28
15 15 0.52
16 3 0.10
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (15 bp):
TTATAAATAATAAAT
Found at i:142833 original size:16 final size:17
Alignment explanation
Indices: 142812--142849 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
142802 TTCTGTGTTA
* *
142812 TGTTTGTATG-TATCCT
1 TGTTTGGATGTTAGCCT
142828 TGTTTGGATGTTAGCCT
1 TGTTTGGATGTTAGCCT
142845 TGTTT
1 TGTTT
142850 TTTTGTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.11, C:0.11, G:0.24, T:0.55
Consensus pattern (17 bp):
TGTTTGGATGTTAGCCT
Found at i:143276 original size:38 final size:38
Alignment explanation
Indices: 143192--143308 Score: 186
Period size: 38 Copynumber: 3.1 Consensus size: 38
143182 ATCCTTATTC
143192 TTATTGAATAAAAGTAATATTTTTTATAAATATATTTT
1 TTATTGAATAAAAGTAATATTTTTTATAAATATATTTT
*
143230 TT-TGGAATAAAAGTAATATTTTTT-TAAA-ATAATTTT
1 TTATTGAATAAAAGTAATATTTTTTATAAATAT-ATTTT
143266 TTCATTGAATAAAAGTAATATTTTTTATAAATATATTTT
1 TT-ATTGAATAAAAGTAATATTTTTTATAAATATATTTT
143305 TTAT
1 TTAT
143309 CTCAGAACTA
Statistics
Matches: 72, Mismatches: 2, Indels: 10
0.86 0.02 0.12
Matches are distributed among these distances:
35 2 0.03
36 11 0.15
37 21 0.29
38 25 0.35
39 11 0.15
40 2 0.03
ACGTcount: A:0.41, C:0.01, G:0.06, T:0.52
Consensus pattern (38 bp):
TTATTGAATAAAAGTAATATTTTTTATAAATATATTTT
Found at i:153119 original size:30 final size:30
Alignment explanation
Indices: 153060--153119 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
153050 ACTATATCTT
* *
153060 TTATGAGAATAATATTTATTTAATAATTAA
1 TTATGAGAATAATATTTATTAAAAAATTAA
*
153090 TTATGAGAATTATATTTA-TAAAAACATTAA
1 TTATGAGAATAATATTTATTAAAAA-ATTAA
153120 CATTCTATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 4 0.15
30 22 0.85
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (30 bp):
TTATGAGAATAATATTTATTAAAAAATTAA
Found at i:153364 original size:16 final size:15
Alignment explanation
Indices: 153342--153385 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
153332 ATGATTCATA
153342 ATTAAATAATTGAT-
1 ATTAAATAATTGATG
*
153356 ATTTTAAATAATTCATG
1 A--TTAAATAATTGATG
153373 ATTAAATAATTGA
1 ATTAAATAATTGA
153386 CAATAATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
14 1 0.04
15 11 0.44
16 12 0.48
17 1 0.04
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (15 bp):
ATTAAATAATTGATG
Found at i:153379 original size:15 final size:14
Alignment explanation
Indices: 153335--153383 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 14
153325 TGTTTACATG
153335 ATTCATAATTAAATA
1 ATTCAT-ATTAAATA
*
153350 ATTGATATTTTAAATA
1 ATTCATA--TTAAATA
153366 ATTCATGATTAAATA
1 ATTCAT-ATTAAATA
153381 ATT
1 ATT
153384 GACAATAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
14 1 0.03
15 15 0.52
16 12 0.41
17 1 0.03
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (14 bp):
ATTCATATTAAATA
Found at i:156662 original size:60 final size:59
Alignment explanation
Indices: 156578--156708 Score: 147
Period size: 60 Copynumber: 2.2 Consensus size: 59
156568 ATCATATGTT
* * * * * *
156578 CCTAAATTATAAATCTTAATTTAAATTGGCCCATAAACTTTTAAATATT-TCAATTTCATC
1 CCTAAATTATGATTCTCATTTTAAATTAGCCCATAAAC-TTTAAACATTCT-AATTTCATC
* * * *
156638 CTTAAATTATGATTCTCATTTTAAATTAGTCCTTAAACTTTGAACATTCTAATTTCATC
1 CCTAAATTATGATTCTCATTTTAAATTAGCCCATAAACTTTAAACATTCTAATTTCATC
156697 CCTAAATTATGA
1 CCTAAATTATGA
156709 CCATCTTTCT
Statistics
Matches: 59, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
59 28 0.47
60 31 0.53
ACGTcount: A:0.36, C:0.17, G:0.05, T:0.43
Consensus pattern (59 bp):
CCTAAATTATGATTCTCATTTTAAATTAGCCCATAAACTTTAAACATTCTAATTTCATC
Found at i:156707 original size:59 final size:59
Alignment explanation
Indices: 156628--156755 Score: 163
Period size: 59 Copynumber: 2.2 Consensus size: 59
156618 TTAAATATTT
* * *
156628 CAATTTCATCCTTAAATTATGATTC-TCATTT-TAAATTAGTCCTTAAACTTTGAA-CATTC
1 CAATTTCATCCCTAAATTATGA-CCATC-TTTCTAAATTAGTCCTCAAACTTTGAATC-TTC
* *
156687 TAATTTCATCCCTAAATTATGACCATCTTTCTAAATTGGTCCTCAAACTTTGAATCTTC
1 CAATTTCATCCCTAAATTATGACCATCTTTCTAAATTAGTCCTCAAACTTTGAATCTTC
156746 CAATTTCATC
1 CAATTTCATC
156756 ACCAGATTCA
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
58 4 0.07
59 55 0.92
60 1 0.02
ACGTcount: A:0.30, C:0.22, G:0.05, T:0.42
Consensus pattern (59 bp):
CAATTTCATCCCTAAATTATGACCATCTTTCTAAATTAGTCCTCAAACTTTGAATCTTC
Found at i:157040 original size:60 final size:60
Alignment explanation
Indices: 156914--157041 Score: 134
Period size: 60 Copynumber: 2.1 Consensus size: 60
156904 TGAATGTTTG
* * * *** * *
156914 AAAAGTCTGGGGACCAATTTAGAATGAAGTTCATAGTTTGGGGATGAAATTGAAATTTTC
1 AAAAGTTTGAGGACCAATCTAGAATGAAGTTCATAGTTTACAGATGAAACTGAAAATTTC
* *
156974 ACAAGTTTGAGGACTAATCTAGAATGATAG-TCATAGTTTACAGATGAAACTGAAACATTT-
1 AAAAGTTTGAGGACCAATCTAGAATGA-AGTTCATAGTTTACAGATGAAACTGAAA-ATTTC
157034 AAAAGTTT
1 AAAAGTTT
157042 ATGGATCAAT
Statistics
Matches: 55, Mismatches: 11, Indels: 4
0.79 0.16 0.06
Matches are distributed among these distances:
60 50 0.91
61 5 0.09
ACGTcount: A:0.38, C:0.09, G:0.21, T:0.31
Consensus pattern (60 bp):
AAAAGTTTGAGGACCAATCTAGAATGAAGTTCATAGTTTACAGATGAAACTGAAAATTTC
Found at i:160211 original size:72 final size:72
Alignment explanation
Indices: 160094--160236 Score: 250
Period size: 72 Copynumber: 2.0 Consensus size: 72
160084 TCCGACAACA
* *
160094 GTGGTGGAGGTTAGTGACGATAATAGACTTTGGGATTATGGATTTGGGCTTAGGGAATTTAGGGG
1 GTGGTGGAGGTTAGTGACGATAATAAACTTTGGGATTATGGATTTGGGCTTAGGAAATTTAGGGG
160159 TTTAATC
66 TTTAATC
* *
160166 GTGGTGGAGGTTAGTGACGATAATAAATTTTGGGATTATGGATTTGGGCTTATGAAATTTAGGGG
1 GTGGTGGAGGTTAGTGACGATAATAAACTTTGGGATTATGGATTTGGGCTTAGGAAATTTAGGGG
160231 TTTAAT
66 TTTAAT
160237 GTTTAGGGAG
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 67 1.00
ACGTcount: A:0.25, C:0.04, G:0.34, T:0.36
Consensus pattern (72 bp):
GTGGTGGAGGTTAGTGACGATAATAAACTTTGGGATTATGGATTTGGGCTTAGGAAATTTAGGGG
TTTAATC
Found at i:164129 original size:15 final size:15
Alignment explanation
Indices: 164109--164139 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
164099 TTCAGAAACG
164109 TTCTTTCAAATATAC
1 TTCTTTCAAATATAC
164124 TTCTTTCAAATATAC
1 TTCTTTCAAATATAC
164139 T
1 T
164140 ATAAAGTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.19, G:0.00, T:0.48
Consensus pattern (15 bp):
TTCTTTCAAATATAC
Done.