Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004787.1 Hibiscus syriacus cultivar Beakdansim tig00010792_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: 51213
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:5185 original size:20 final size:20
Alignment explanation
Indices: 5160--5221 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 20
5150 TGCGATTTAT
5160 GCGAATAAGTAAATCGCAAC
1 GCGAATAAGTAAATCGCAAC
** *
5180 GCGAAT---T-GGTCGCAAT
1 GCGAATAAGTAAATCGCAAC
5196 GCGAATAAGTAAATCGCAAC
1 GCGAATAAGTAAATCGCAAC
5216 GCGAAT
1 GCGAAT
5222 TGGGAAATCG
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
16 12 0.38
17 1 0.03
19 1 0.03
20 18 0.56
ACGTcount: A:0.39, C:0.19, G:0.24, T:0.18
Consensus pattern (20 bp):
GCGAATAAGTAAATCGCAAC
Found at i:5229 original size:20 final size:19
Alignment explanation
Indices: 5170--5239 Score: 65
Period size: 20 Copynumber: 3.7 Consensus size: 19
5160 GCGAATAAGT
5170 AAATCGCAACGCGAATTGG
1 AAATCGCAACGCGAATTGG
* * *
5189 ---TCGCAATGCGAATAAGT
1 AAATCGCAACGCGAAT-TGG
5206 AAATCGCAACGCGAATTGGG
1 AAATCGCAACGCGAATT-GG
*
5226 AAATCGCAATGCGA
1 AAATCGCAACGCGA
5240 TACTGACTAT
Statistics
Matches: 39, Mismatches: 7, Indels: 9
0.71 0.13 0.16
Matches are distributed among these distances:
16 12 0.31
17 1 0.03
20 26 0.67
ACGTcount: A:0.37, C:0.20, G:0.26, T:0.17
Consensus pattern (19 bp):
AAATCGCAACGCGAATTGG
Found at i:5251 original size:20 final size:20
Alignment explanation
Indices: 5228--5322 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
5218 GAATTGGGAA
*
5228 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
5248 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
5269 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
5289 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
5309 TTCGCAACGCGATA
1 ATCGCAACGCGATA
5323 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:5820 original size:20 final size:20
Alignment explanation
Indices: 5795--5832 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5785 CGATTCTCTC
5795 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
5815 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
5833 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:7169 original size:18 final size:18
Alignment explanation
Indices: 7148--7192 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
7138 TCCACTTCGG
*
7148 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
7166 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCCA
7184 GAGCCATCA
1 GAGCCATCA
7193 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:7737 original size:14 final size:14
Alignment explanation
Indices: 7718--7775 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
7708 ATGCGAAATG
*
7718 AAAATCTCAACGAC
1 AAAATCGCAACGAC
*
7732 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
7748 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
7764 AAAATCGCAACG
1 AAAATCGCAACG
7776 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.16, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:7761 original size:32 final size:33
Alignment explanation
Indices: 7702--7792 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
7692 GGAAATGGCT
* *
7702 ATCGCAATGCGAAATGAAAATCTCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
7735 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
7767 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
7793 TTGCGATAGC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 31 0.56
33 24 0.44
ACGTcount: A:0.47, C:0.23, G:0.18, T:0.12
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:7786 original size:19 final size:19
Alignment explanation
Indices: 7665--7792 Score: 73
Period size: 18 Copynumber: 7.3 Consensus size: 19
7655 TAGTTTACTT
* **
7665 TCGCAACACGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
***
7685 TCGCAACG-GAAATGGCTA
1 TCGCAACGCGAAATGAAAA
*
7703 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
* *
7722 TCTCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
7736 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
7754 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
7768 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
7787 TCGCAA
1 TCGCAA
7793 TTGCGATAGC
Statistics
Matches: 84, Mismatches: 12, Indels: 25
0.69 0.10 0.21
Matches are distributed among these distances:
14 19 0.23
15 1 0.01
16 6 0.07
17 2 0.02
18 26 0.31
19 23 0.27
20 7 0.08
ACGTcount: A:0.45, C:0.23, G:0.19, T:0.13
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:7836 original size:19 final size:20
Alignment explanation
Indices: 7793--7838 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
7783 AAAATCGCAA
*
7793 TTGCGATAGCCATTTCCGTG
1 TTGCGATAGCCATTTCCGCG
*
7813 TTGCGATAGTCATTT-CGCG
1 TTGCGATAGCCATTTCCGCG
7832 TTGCGAT
1 TTGCGAT
7839 TTTAAGTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 10 0.42
20 14 0.58
ACGTcount: A:0.15, C:0.22, G:0.26, T:0.37
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGCG
Found at i:9861 original size:33 final size:35
Alignment explanation
Indices: 9816--9911 Score: 115
Period size: 37 Copynumber: 2.7 Consensus size: 35
9806 AAAACAGACT
* *** *
9816 ATCGCAACGCGAAATGGCTATCGCAA-CGAGA-AA
1 ATCGCAATGCGAAATGAAAATCGCAAGCGAAAGAA
9849 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 ATCGCAATGCGAAATGAAAATCGCAA-GCGAAA-GAA
9886 ATCGCAATGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
9912 TCGCAATGCG
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
33 22 0.41
35 4 0.07
37 28 0.52
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.15
Consensus pattern (35 bp):
ATCGCAATGCGAAATGAAAATCGCAAGCGAAAGAA
Found at i:9919 original size:18 final size:19
Alignment explanation
Indices: 9845--9912 Score: 129
Period size: 19 Copynumber: 3.6 Consensus size: 19
9835 ATCGCAACGA
9845 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
9864 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
9883 G-AAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
9901 GAAAATCGCAAT
1 GAAAATCGCAAT
9913 CGCAATGCGA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
18 18 0.38
19 30 0.62
ACGTcount: A:0.47, C:0.16, G:0.21, T:0.16
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:11024 original size:24 final size:24
Alignment explanation
Indices: 10997--11050 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
10987 GTATTCGAAA
* *
10997 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
11021 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
11045 TTTGAT
1 TTTGAT
11051 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:11240 original size:12 final size:12
Alignment explanation
Indices: 11223--11247 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
11213 ATATAATCCT
11223 GAAGAAGAAAAA
1 GAAGAAGAAAAA
11235 GAAGAAGAAAAA
1 GAAGAAGAAAAA
11247 G
1 G
11248 TCCCGAAGAA
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:13571 original size:33 final size:33
Alignment explanation
Indices: 13529--13655 Score: 175
Period size: 33 Copynumber: 3.8 Consensus size: 33
13519 GGAAATTACT
*
13529 ATCGCAATGCGAAATAAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* ***
13562 ATCGCAATGCAAAATGAAAATCGCAACTCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
13594 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
13628 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
13656 CGAATTTAAT
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
32 1 0.01
33 78 0.98
34 1 0.01
ACGTcount: A:0.44, C:0.20, G:0.20, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:13620 original size:19 final size:19
Alignment explanation
Indices: 13596--13659 Score: 66
Period size: 19 Copynumber: 3.6 Consensus size: 19
13586 AACTCTAATT
13596 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
**
13615 TCGCAA--CG--A-GGGAA
1 TCGCAATGCGAAATGAAAA
13629 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
*
13648 TCGCAACGCGAA
1 TCGCAATGCGAA
13660 TTTAATTTCG
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
14 9 0.26
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 20 0.57
ACGTcount: A:0.42, C:0.20, G:0.25, T:0.12
Consensus pattern (19 bp):
TCGCAATGCGAAATGAAAA
Found at i:13636 original size:66 final size:66
Alignment explanation
Indices: 13530--13654 Score: 223
Period size: 66 Copynumber: 1.9 Consensus size: 66
13520 GAAATTACTA
13530 TCGCAATGCGAAATAAAAATCGCAACGAGAGAATCGCAATGCAAAATGAAAATCGCAACTCTAAT
1 TCGCAATGCGAAATAAAAATCGCAACGAGAGAATCGCAATGCAAAATGAAAATCGCAACTCTAAT
13595 T
66 T
* * *
13596 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAAC
1 TCGCAATGCGAAATAAAAATCGCAACGAGAGAATCGCAATGCAAAATGAAAATCGCAAC
13655 GCGAATTTAA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 56 1.00
ACGTcount: A:0.44, C:0.20, G:0.20, T:0.16
Consensus pattern (66 bp):
TCGCAATGCGAAATAAAAATCGCAACGAGAGAATCGCAATGCAAAATGAAAATCGCAACTCTAAT
T
Found at i:13729 original size:19 final size:18
Alignment explanation
Indices: 13659--13730 Score: 71
Period size: 19 Copynumber: 4.1 Consensus size: 18
13649 CGCAACGCGA
*
13659 ATTTAATTTCGCGTTGCG
1 ATTTCATTTCGCGTTGCG
13677 ATTTCATTTTCGCGTTGCG
1 ATTTCA-TTTCGCGTTGCG
*
13696 A-TTC---TCTCGTTGCG
1 ATTTCATTTCGCGTTGCG
*
13710 ATTTTCATTTCGCATTGCG
1 A-TTTCATTTCGCGTTGCG
13729 AT
1 AT
13731 AGTACTTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
14 10 0.23
16 3 0.07
18 9 0.20
19 22 0.50
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.46
Consensus pattern (18 bp):
ATTTCATTTCGCGTTGCG
Found at i:13856 original size:14 final size:14
Alignment explanation
Indices: 13837--13873 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
13827 CATCAATTAA
13837 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
13851 ACAAATCACCTTTT
1 ACAAATCAACATTT
13865 ACAAATCAA
1 ACAAATCAA
13874 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:17331 original size:20 final size:19
Alignment explanation
Indices: 17300--17479 Score: 121
Period size: 19 Copynumber: 9.8 Consensus size: 19
17290 TCTTTTGGTT
17300 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
17319 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
17340 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
17359 G--A-G--AATCGCAACGCA
1 GAAATGAAAATCGCAACG-A
**
17374 -AAATGACTATCG---CGA
1 GAAATGAAAATCGCAACGA
** * *
17389 -CCA-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGA
*
17406 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGA
* *
17426 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
*
17445 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
17464 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
17480 TGCGATTTTG
Statistics
Matches: 131, Mismatches: 16, Indels: 28
0.75 0.09 0.16
Matches are distributed among these distances:
14 16 0.12
15 3 0.02
16 4 0.03
17 4 0.03
18 1 0.01
19 54 0.41
20 47 0.36
21 2 0.02
ACGTcount: A:0.45, C:0.22, G:0.21, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:17383 original size:33 final size:33
Alignment explanation
Indices: 17325--17423 Score: 135
Period size: 33 Copynumber: 3.0 Consensus size: 33
17315 ACGAGATAAT
*
17325 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
* *
17359 GAGAATCGCAACGCAAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
17392 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
17424 GCGAAATAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
33 43 0.75
34 14 0.25
ACGTcount: A:0.40, C:0.26, G:0.22, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:17417 original size:19 final size:19
Alignment explanation
Indices: 17395--17484 Score: 153
Period size: 19 Copynumber: 4.7 Consensus size: 19
17385 GCGACCAGAC
17395 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
17414 AATCGCAACCGCGAAATAAA
1 AATCGCAA-CGCGAAATGAA
17434 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
17453 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
17472 AATCGCAATGCGA
1 AATCGCAACGCGA
17485 TTTTGGTTTC
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
19 49 0.73
20 18 0.27
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:17427 original size:39 final size:38
Alignment explanation
Indices: 17395--17484 Score: 153
Period size: 39 Copynumber: 2.3 Consensus size: 38
17385 GCGACCAGAC
17395 AATCGCAACGCGAAATGAAAATCGCAACCGCGAAATAAA
1 AATCGCAACGCGAAATGAAAATCGCAA-CGCGAAATAAA
*
17434 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
*
17472 AATCGCAATGCGA
1 AATCGCAACGCGA
17485 TTTTGGTTTC
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 22 0.45
39 27 0.55
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (38 bp):
AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
Found at i:17513 original size:19 final size:19
Alignment explanation
Indices: 17480--17560 Score: 64
Period size: 19 Copynumber: 4.5 Consensus size: 19
17470 AAAATCGCAA
**
17480 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
17499 TGCGATTTTTATTTCGTGT
1 TGCGATTTTTATTTCGCGT
*
17518 TGCGA---TTA--TCTCGT
1 TGCGATTTTTATTTCGCGT
**
17532 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
17552 TGCGATTTT
1 TGCGATTTT
17561 CATTCTCGAA
Statistics
Matches: 48, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
14 9 0.19
16 3 0.06
17 3 0.06
19 22 0.46
20 11 0.23
ACGTcount: A:0.11, C:0.16, G:0.25, T:0.48
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:18144 original size:41 final size:41
Alignment explanation
Indices: 18092--18169 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
18082 CGAAAGTCAG
* * *
18092 TATCGCGTTGCGAAAGTAAGTAACTCGTTGCGATTTTTTAT
1 TATCGCATTGCGAAAGTAAGTAACGCATTGCGATTTTTTAT
* * *
18133 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTAACGCATTGCGATTTT
18170 CCCAATTCGC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.38
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTAACGCATTGCGATTTTTTAT
Found at i:18166 original size:20 final size:20
Alignment explanation
Indices: 18073--18166 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
18063 CGCTATGTAA
*
18073 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* *
18093 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTCAGT
* * ** * *
18113 AACTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTCAGT
*
18134 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
18154 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
18167 TTTCCCAATT
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 46 0.79
21 12 0.21
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:18185 original size:41 final size:41
Alignment explanation
Indices: 18155--18250 Score: 138
Period size: 41 Copynumber: 2.3 Consensus size: 41
18145 ATAGTCAGTA
* * *
18155 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
* * *
18196 TCGCATTGCGAATTTCCCAATTCGCGTTACGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
18237 TCGCATTGCGAATT
1 TCGCATTGCGAATT
18251 GGGAAAATCG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.20, C:0.24, G:0.17, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
Found at i:18199 original size:20 final size:20
Alignment explanation
Indices: 18155--18247 Score: 87
Period size: 20 Copynumber: 4.5 Consensus size: 20
18145 ATAGTCAGTA
* **
18155 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
18176 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
18196 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
* *
18217 TCGCGTTACGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
18237 TCGCATTGCGA
1 TCGCATTGCGA
18248 ATTGGGAAAA
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 31 0.55
21 25 0.45
ACGTcount: A:0.19, C:0.25, G:0.17, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:21219 original size:30 final size:30
Alignment explanation
Indices: 21183--21319 Score: 157
Period size: 30 Copynumber: 4.5 Consensus size: 30
21173 TTATTGGTAC
* *
21183 CCAAATAAGCTCTTAAACTAGAACTAGTAG
1 CCAAATAAGCCCTTAAACTATAACTAGTAG
* * * *
21213 CCAAATAAGCCCTTAATCTTTAACTTGTAT
1 CCAAATAAGCCCTTAAACTATAACTAGTAG
21243 CCAAATAAGCCCTTAAACTATAACTAGTAG
1 CCAAATAAGCCCTTAAACTATAACTAGTAG
* * * * *
21273 CCAAAGAAGCCTCTCTAATCTTTAACTTGTAT
1 CCAAATAAGCC-CT-TAAACTATAACTAGTAG
21305 CCAAATAAGCCCTTA
1 CCAAATAAGCCCTTA
21320 GCCTTTAAGT
Statistics
Matches: 89, Mismatches: 16, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
30 62 0.70
31 4 0.04
32 23 0.26
ACGTcount: A:0.38, C:0.24, G:0.09, T:0.28
Consensus pattern (30 bp):
CCAAATAAGCCCTTAAACTATAACTAGTAG
Found at i:21248 original size:60 final size:62
Alignment explanation
Indices: 21183--21319 Score: 233
Period size: 60 Copynumber: 2.2 Consensus size: 62
21173 TTATTGGTAC
* *
21183 CCAAATAAGCTCTTAAACTAGAACTAGTAGCCAAATAAGCC-CT-TAATCTTTAACTTGTAT
1 CCAAATAAGCCCTTAAACTAGAACTAGTAGCCAAAGAAGCCTCTCTAATCTTTAACTTGTAT
*
21243 CCAAATAAGCCCTTAAACTATAACTAGTAGCCAAAGAAGCCTCTCTAATCTTTAACTTGTAT
1 CCAAATAAGCCCTTAAACTAGAACTAGTAGCCAAAGAAGCCTCTCTAATCTTTAACTTGTAT
21305 CCAAATAAGCCCTTA
1 CCAAATAAGCCCTTA
21320 GCCTTTAAGT
Statistics
Matches: 72, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
60 38 0.53
61 2 0.03
62 32 0.44
ACGTcount: A:0.38, C:0.24, G:0.09, T:0.28
Consensus pattern (62 bp):
CCAAATAAGCCCTTAAACTAGAACTAGTAGCCAAAGAAGCCTCTCTAATCTTTAACTTGTAT
Found at i:31022 original size:43 final size:43
Alignment explanation
Indices: 30847--31069 Score: 258
Period size: 43 Copynumber: 5.2 Consensus size: 43
30837 GGCTTCAATT
* * * *
30847 TTTTTTCATTCTCACTTTTTACCTTTATAATTAAGACCTCTAA
1 TTTTTTCAATCTCACTCTTTACCTTTATAATTGAGGCCTCTAA
* * * * *
30890 TTTTGTTCAGTCTCACT-TTCTACCTTTCTAATTGATGCAT-TAG
1 TTTT-TTCAATCTCACTCTT-TACCTTTATAATTGAGGCCTCTAA
* *
30933 TTTTTTTAATCTCACTTTTTACC-TTATAA-TGAGGCCTCTAA
1 TTTTTTCAATCTCACTCTTTACCTTTATAATTGAGGCCTCTAA
*
30974 TTTTTTCAATCTCACTCTTTACCTTTATAATTGAGGTCTCTAA
1 TTTTTTCAATCTCACTCTTTACCTTTATAATTGAGGCCTCTAA
* *
31017 TTTTTTCAATCTCAC-CTTTTACCTTTATAATTGAGGCCCCCAA
1 TTTTTTCAATCTCACTC-TTTACCTTTATAATTGAGGCCTCTAA
31060 TTTTTTCAAT
1 TTTTTTCAAT
31070 TCCATAAAAT
Statistics
Matches: 154, Mismatches: 19, Indels: 14
0.82 0.10 0.07
Matches are distributed among these distances:
40 6 0.04
41 28 0.18
42 21 0.14
43 73 0.47
44 26 0.17
ACGTcount: A:0.23, C:0.22, G:0.07, T:0.49
Consensus pattern (43 bp):
TTTTTTCAATCTCACTCTTTACCTTTATAATTGAGGCCTCTAA
Found at i:33326 original size:22 final size:22
Alignment explanation
Indices: 33301--33357 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
33291 ATATACAAGC
33301 TACAAAGTGAACCTACAGATGA
1 TACAAAGTGAACCTACAGATGA
*
33323 TACAAAGTGAACCTACAGATGG
1 TACAAAGTGAACCTACAGATGA
*
33345 GACAAAGTGAACC
1 TACAAAGTGAACC
33358 CACAAAGTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.44, C:0.19, G:0.21, T:0.16
Consensus pattern (22 bp):
TACAAAGTGAACCTACAGATGA
Found at i:35420 original size:169 final size:169
Alignment explanation
Indices: 35135--35467 Score: 596
Period size: 169 Copynumber: 2.0 Consensus size: 169
35125 TGTTTCGAGG
*
35135 CCAATATCCTTTGCTGTGAAGTTGAAATTGACTCTGAAACTGGAAGTTGTTTGTTGACAGCCAGC
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAACTGGAAGTTGTTTGTTGACAGCCAGC
* *
35200 GGCCCCTTCGTTGTGAAGTTGAACCTGTGCTGTCTTAAACTGGGGAATTTTGTTGACAACCAGCG
66 GGCCCCTTCGTTGTGAAGTTGAACCTGTGATGTCTTAAACTGGGAAATTTTGTTGACAACCAGCG
35265 GCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGT
131 GCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGT
* *
35304 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTG-AATTGGGAAGTTGTTTGTTGACAGCCAG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAACT-GGAAGTTGTTTGTTGACAGCCAG
*
35368 CGGCCCCTTCGTTGTGAAGTTGAACTTGTGATGTCTTAAACTGGGAAATTTTGTTGACAACCAGC
65 CGGCCCCTTCGTTGTGAAGTTGAACCTGTGATGTCTTAAACTGGGAAATTTTGTTGACAACCAGC
35433 GGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
130 GGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
35468 GATACTGGGA
Statistics
Matches: 157, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
168 3 0.02
169 154 0.98
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (169 bp):
CCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAACTGGAAGTTGTTTGTTGACAGCCAGC
GGCCCCTTCGTTGTGAAGTTGAACCTGTGATGTCTTAAACTGGGAAATTTTGTTGACAACCAGCG
GCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGT
Found at i:35435 original size:64 final size:65
Alignment explanation
Indices: 35343--35533 Score: 312
Period size: 64 Copynumber: 2.9 Consensus size: 65
35333 GGCTCTGAAT
* * *
35343 TGGGAAGTTGTTTGTTGACAGCCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGATGTCTTAAA
1 TGGGAAATT-TTTGTTGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTAAA
35408 C
65 C
* *
35409 TGGGAAA-TTTTGTTGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGATAC
1 TGGGAAATTTTTGTTGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTAAAC
*
35473 TGGGAAATTTTTGTTAACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
1 TGGGAAATTTTTGTTGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
35534 GAATTCCAAT
Statistics
Matches: 117, Mismatches: 7, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
64 59 0.50
65 52 0.44
66 6 0.05
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.35
Consensus pattern (65 bp):
TGGGAAATTTTTGTTGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTAAAC
Found at i:35520 original size:65 final size:64
Alignment explanation
Indices: 35311--35532 Score: 308
Period size: 64 Copynumber: 3.5 Consensus size: 64
35301 AGTCCAATAT
* * * * * *
35311 CCTTCGCTGTGAAGTTGAAATTG-G--CTCTGAATTGGGAAGTTGTTTGTTGACAGCCAGCGGCC
1 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGAACTGGGAAATT-TTTGTTGACAACCAGCGGCC
* *
35373 CCTTCGTTGTGAAGTTGAACTTGTGATGTCTTAAACTGGGAAA-TTTTGTTGACAACCAGCGGCC
1 CCTTCGTTGTGAAGTTGAACTTGTGTTGTC-TGAACTGGGAAATTTTTGTTGACAACCAGCGGCC
*
35437 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGATACTGGGAAATTTTTGTTAACAACCAGCGGCC
1 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGA-ACTGGGAAATTTTTGTTGACAACCAGCGGCC
35502 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
1 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
35533 TGAATTCCAA
Statistics
Matches: 144, Mismatches: 10, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
62 21 0.15
63 3 0.02
64 57 0.40
65 54 0.38
66 9 0.06
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.35
Consensus pattern (64 bp):
CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGAACTGGGAAATTTTTGTTGACAACCAGCGGCC
Found at i:36957 original size:22 final size:22
Alignment explanation
Indices: 36931--36979 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
36921 TTGTGTTTGG
* *
36931 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGACATTGGATGC
36953 TCAAAGGTTTGACATTGGATGC
1 TCAAAGGTTTGACATTGGATGC
36975 TCAAA
1 TCAAA
36980 AGATTGATGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (22 bp):
TCAAAGGTTTGACATTGGATGC
Found at i:36986 original size:22 final size:22
Alignment explanation
Indices: 36943--36986 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
36933 AAAGGTTTGG
* * *
36943 CATTTGATGCTCAAAGGTTTGA
1 CATTGGATGCTCAAAAGATTGA
36965 CATTGGATGCTCAAAAGATTGA
1 CATTGGATGCTCAAAAGATTGA
36987 TGGGGTAGCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.32
Consensus pattern (22 bp):
CATTGGATGCTCAAAAGATTGA
Found at i:37619 original size:21 final size:22
Alignment explanation
Indices: 37579--37620 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
37569 TGCATGTGCT
* *
37579 TTTTTGTCTCTTTTTTTTTTGA
1 TTTTTGTCTCTTTCTATTTTGA
37601 TTTTTGT-TCTTTCTATTTTG
1 TTTTTGTCTCTTTCTATTTTG
37621 TTTCCTTCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.05, C:0.10, G:0.10, T:0.76
Consensus pattern (22 bp):
TTTTTGTCTCTTTCTATTTTGA
Found at i:37621 original size:14 final size:14
Alignment explanation
Indices: 37601--37648 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
37591 TTTTTTTTGA
37601 TTTTTG-TTCTTTC
1 TTTTTGCTTCTTTC
* *
37614 TATTTTGTTTCCTTC
1 T-TTTTGCTTCTTTC
37629 TTTTTGCTTCTTTTC
1 TTTTTGCTTC-TTTC
37644 TTTTT
1 TTTTT
37649 TTGATTTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 1 0.03
14 13 0.45
15 15 0.52
ACGTcount: A:0.02, C:0.17, G:0.06, T:0.75
Consensus pattern (14 bp):
TTTTTGCTTCTTTC
Found at i:38837 original size:20 final size:21
Alignment explanation
Indices: 38807--38854 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
38797 GAAATACTTA
*
38807 AAAAATG--AAATGTATATGC
1 AAAAATGCAAAATGTAAATGC
38826 -AAAATGCAAAATGTAAATGC
1 AAAAATGCAAAATGTAAATGC
38846 AAAAATGCA
1 AAAAATGCA
38855 TGAAATATTC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 6 0.24
20 11 0.44
21 8 0.32
ACGTcount: A:0.56, C:0.08, G:0.15, T:0.21
Consensus pattern (21 bp):
AAAAATGCAAAATGTAAATGC
Done.