Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003193.1 Hibiscus syriacus cultivar Beakdansim tig00006718_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: 61676
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:2469 original size:22 final size:25
Alignment explanation
Indices: 2419--2472 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 25
2409 GTCTCTATTT
2419 TTTACCTTTTAATTGATGTTATAAA
1 TTTACCTTTTAATTGATGTTATAAA
*
2444 TTTACCTTTTAA-T-ATTTTA-AAA
1 TTTACCTTTTAATTGATGTTATAAA
2466 TTTACCT
1 TTTACCT
2473 AGATCACATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 10 0.36
23 5 0.18
24 1 0.04
25 12 0.43
ACGTcount: A:0.31, C:0.11, G:0.04, T:0.54
Consensus pattern (25 bp):
TTTACCTTTTAATTGATGTTATAAA
Found at i:3346 original size:20 final size:21
Alignment explanation
Indices: 3321--3413 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
3311 TTTTCCCAAT
*
3321 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
3341 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
3362 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
3382 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
3403 TCGCAATGCGA
1 TCGCAATGCGA
3414 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:3366 original size:41 final size:41
Alignment explanation
Indices: 3321--3413 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
3311 TTTTCCCAAT
3321 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
3362 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
3403 TCGCAATGCGA
1 TCGCAATGCGA
3414 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:3426 original size:41 final size:41
Alignment explanation
Indices: 3340--3474 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
3330 GAATAAGTAA
* *
3340 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
3381 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
3422 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
3463 TTCGCAACGCGA
1 ATCGCAACGCGA
3475 TACTGACTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:3427 original size:20 final size:20
Alignment explanation
Indices: 3402--3496 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
3392 AATTGGGAAA
*
3402 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
3422 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
3443 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
3463 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
3483 TTCGCAACGCGATA
1 ATCGCAACGCGATA
3497 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:3712 original size:22 final size:22
Alignment explanation
Indices: 3684--3727 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
3674 CACTCTCTCA
3684 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
3706 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
3728 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:4015 original size:20 final size:20
Alignment explanation
Indices: 3990--4027 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3980 CGATTCTCTC
3990 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
4010 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
4028 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:5364 original size:18 final size:18
Alignment explanation
Indices: 5343--5387 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
5333 TCCACTTCGG
*
5343 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
5361 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
5379 GAGCCATCA
1 GAGCCATCA
5388 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:5913 original size:19 final size:20
Alignment explanation
Indices: 5859--5925 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
5849 TAGTTTACTT
* *
5859 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
5879 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
5899 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
5918 TCGCAACG
1 TCGCAACG
5926 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:5933 original size:14 final size:14
Alignment explanation
Indices: 5914--5971 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
5904 ATGCGAAATG
5914 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
5928 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
5944 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
5960 AAAATCGCAACG
1 AAAATCGCAACG
5972 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:5956 original size:32 final size:33
Alignment explanation
Indices: 5898--5988 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
5888 GGAAATGGCT
5898 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
5931 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
5963 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
5989 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:6063 original size:19 final size:19
Alignment explanation
Indices: 6000--6122 Score: 96
Period size: 20 Copynumber: 6.7 Consensus size: 19
5990 GCGATTTGTG
6000 TTTCGCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTCA
6018 TTTCGCGTTGCGA-TTT--
1 TTTCGCGTTGCGATTTTCA
*
6034 TGT--CGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
* ***
6051 TTTCGCATTGCGATAGCCA
1 TTTCGCGTTGCGATTTTCA
* **
6070 TTTCCACGTTGCGATAGTCA
1 TTT-CGCGTTGCGATTTTCA
*
6090 TTTCGCGTTGCGATTTTAA
1 TTTCGCGTTGCGATTTTCA
*
6109 GTTTCGTGTTGCGA
1 -TTTCGCGTTGCGA
6123 AAGTAAACTA
Statistics
Matches: 84, Mismatches: 14, Indels: 12
0.76 0.13 0.11
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.02
17 2 0.02
18 16 0.19
19 25 0.30
20 28 0.33
ACGTcount: A:0.14, C:0.20, G:0.24, T:0.42
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:8100 original size:19 final size:19
Alignment explanation
Indices: 8078--8145 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
8068 ATCGCAACGA
8078 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
8097 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
8116 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
8130 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
8146 TTTTCATTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.24
15 1 0.02
16 2 0.04
17 2 0.04
19 30 0.65
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:8221 original size:20 final size:20
Alignment explanation
Indices: 8164--8221 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
8154 TCGCATTGCG
* * *
8164 ATTTTCTCGTTGCGATAACT
1 ATTTTCGCGTTGCGATAGCC
8184 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
8204 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
8222 TCAAATGATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.17, C:0.21, G:0.22, T:0.40
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:9330 original size:24 final size:24
Alignment explanation
Indices: 9279--9332 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
9269 GTATTCGAAA
* * *
9279 TTTGATCTTGGTCAATACCCGTAC
1 TTTGATATTGGTCAATACACGGAC
*
9303 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
9327 TTTGAT
1 TTTGAT
9333 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:9524 original size:12 final size:12
Alignment explanation
Indices: 9507--9531 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9497 ATATAATCCT
9507 GAAGAAGAAAAA
1 GAAGAAGAAAAA
9519 GAAGAAGAAAAA
1 GAAGAAGAAAAA
9531 G
1 G
9532 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:11867 original size:33 final size:33
Alignment explanation
Indices: 11821--11914 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
11811 GGAAATTACT
*
11821 ATCGCAATACGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
11854 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
11887 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
11915 CGAATTTAAT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:11917 original size:19 final size:19
Alignment explanation
Indices: 11821--11918 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
11811 GGAAATTACT
*
11821 ATCGCAATACGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
11840 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
11854 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
11873 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
11887 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
11906 ATCGCAACGCGAA
1 ATCGCAATGCGAA
11919 TTTAATTTCG
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 19 0.31
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 31 0.50
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:11936 original size:19 final size:20
Alignment explanation
Indices: 11914--11956 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
11904 AAATCGCAAC
11914 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
11933 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
11953 GCGA
1 GCGA
11957 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:11941 original size:14 final size:14
Alignment explanation
Indices: 11942--11975 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
11932 TGCGATTTTC
11942 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
11956 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
11970 ATTTTC
1 ATTTTC
11976 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:12116 original size:14 final size:14
Alignment explanation
Indices: 12097--12133 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
12087 CATCAATTAA
12097 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
12111 ACAAATCACCTTTT
1 ACAAATCAACTTTT
12125 ACAAATCAA
1 ACAAATCAA
12134 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:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:13557 original size:21 final size:21
Alignment explanation
Indices: 13491--13557 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
13481 GTGAATCGGG
*
13491 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
13511 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
13533 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
13554 CTCT
1 CTCT
13558 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:13576 original size:42 final size:41
Alignment explanation
Indices: 13491--13613 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
13481 GTGAATCGGG
* * * * *
13491 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
13533 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
13575 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
13614 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:15695 original size:33 final size:33
Alignment explanation
Indices: 15638--15736 Score: 135
Period size: 33 Copynumber: 3.0 Consensus size: 33
15628 ACGAGATAAT
*
15638 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
15672 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* * **
15705 GACAATTGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
15737 GCGAAATAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
33 44 0.76
34 14 0.24
ACGTcount: A:0.39, C:0.25, G:0.23, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:15734 original size:19 final size:19
Alignment explanation
Indices: 15613--15797 Score: 156
Period size: 19 Copynumber: 10.1 Consensus size: 19
15603 TCTTTTGGTT
* *
15613 GAAATGAGAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
15632 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
15652 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
15670 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
15686 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
* *
15704 ---A-GACAATTGCAACGC
1 GAAATGAAAATCGCAACGC
15719 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
15739 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
15758 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
15777 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
15796 GA
1 GA
15798 TTTTGGTTTC
Statistics
Matches: 137, Mismatches: 16, Indels: 26
0.77 0.09 0.15
Matches are distributed among these distances:
14 18 0.13
15 3 0.02
16 2 0.01
17 1 0.01
18 4 0.03
19 61 0.45
20 46 0.34
21 2 0.01
ACGTcount: A:0.43, C:0.22, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:15755 original size:39 final size:38
Alignment explanation
Indices: 15712--15797 Score: 145
Period size: 39 Copynumber: 2.2 Consensus size: 38
15702 CCAGACAATT
15712 GCAACGCGAAATGAAAATCGCAACCGCGAAATAAAAATC
1 GCAACGCGAAATGAAAATCGCAA-CGCGAAATAAAAATC
*
15751 GCAACGCGAAATGAAAATCGCAACGCGAAATGAAAATC
1 GCAACGCGAAATGAAAATCGCAACGCGAAATAAAAATC
*
15789 GCAATGCGA
1 GCAACGCGA
15798 TTTTGGTTTC
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 22 0.49
39 23 0.51
ACGTcount: A:0.47, C:0.22, G:0.21, T:0.10
Consensus pattern (38 bp):
GCAACGCGAAATGAAAATCGCAACGCGAAATAAAAATC
Found at i:15826 original size:19 final size:19
Alignment explanation
Indices: 15793--15859 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
15783 AAAATCGCAA
**
15793 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
15812 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
** *
15831 TGCGATAGTTATTTCCGTGT
1 TGCGATTTTTATTT-CGCGT
15851 TGCGATTTT
1 TGCGATTTT
15860 CATTCTCGAA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 29 0.73
20 11 0.28
ACGTcount: A:0.10, C:0.15, G:0.25, T:0.49
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:16397 original size:20 final size:20
Alignment explanation
Indices: 16372--16423 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
16362 CGCTATGTAA
* *
16372 ATCGCGTTGTGAAAGTCAGT
1 ATCGCGTTGCGAAAGTAAGT
16392 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGAAAGTAAGT
*
16412 ATCTCGTTGCGA
1 ATCGCGTTGCGA
16424 TTTTTTATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTAAGT
Found at i:16478 original size:20 final size:20
Alignment explanation
Indices: 16434--16526 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
16424 TTTTTTATTA
* **
16434 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
16455 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
16475 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
16496 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
16516 TCGCATTGCGA
1 TCGCATTGCGA
16527 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:16479 original size:41 final size:41
Alignment explanation
Indices: 16416--16526 Score: 188
Period size: 41 Copynumber: 2.7 Consensus size: 41
16406 GTAAGTATCT
*
16416 CGTTGCGATTT-TTTATTATCGCATTGCGATTTTCCCAATTCG
1 CGTTGCGATTTACTTA-T-TCGCATTGCGATTTTCCCAATTCG
16458 CGTTGCGATTTACTTATTCGCATTGCGATTTTCCCAATTCG
1 CGTTGCGATTTACTTATTCGCATTGCGATTTTCCCAATTCG
16499 CGTTGCGATTTACTTATTCGCATTGCGA
1 CGTTGCGATTTACTTATTCGCATTGCGA
16527 ATTGGGAAAA
Statistics
Matches: 67, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
41 52 0.78
42 12 0.18
43 3 0.04
ACGTcount: A:0.17, C:0.23, G:0.18, T:0.42
Consensus pattern (41 bp):
CGTTGCGATTTACTTATTCGCATTGCGATTTTCCCAATTCG
Found at i:17724 original size:14 final size:14
Alignment explanation
Indices: 17702--17754 Score: 61
Period size: 14 Copynumber: 3.7 Consensus size: 14
17692 AAAACCTAAG
*
17702 TTAGAGTTTAGAGT
1 TTAGGGTTTAGAGT
*
17716 TTAGGGTTTAGAGG
1 TTAGGGTTTAGAGT
* *
17730 TTATGGTGTTATAGT
1 TTAGGGT-TTAGAGT
17745 TTAGGGTTTA
1 TTAGGGTTTA
17755 TAATTGGCTT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
14 21 0.66
15 11 0.34
ACGTcount: A:0.23, C:0.00, G:0.32, T:0.45
Consensus pattern (14 bp):
TTAGGGTTTAGAGT
Found at i:28860 original size:28 final size:28
Alignment explanation
Indices: 28813--28922 Score: 102
Period size: 28 Copynumber: 3.9 Consensus size: 28
28803 GCAAATATCC
28813 GTAATTGCTCAAATCTGAATTCTCTAAT
1 GTAATTGCTCAAATCTGAATTCTCTAAT
* *
28841 GTATTTGCTCAAA-CTCGAATAT-TTTAAT
1 GTAATTGCTCAAATCT-GAAT-TCTCTAAT
* * *
28869 GCAATTGTTCAAATCTGAA-TCTTCTAAC
1 GTAATTGCTCAAATCTGAATTC-TCTAAT
*
28897 GTAATTGCTTAAA-CTTGAATTCTCTA
1 GTAATTGCTCAAATC-TGAATTCTCTA
28923 GTGAAAATAT
Statistics
Matches: 65, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
26 1 0.02
27 3 0.05
28 56 0.86
29 5 0.08
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.40
Consensus pattern (28 bp):
GTAATTGCTCAAATCTGAATTCTCTAAT
Found at i:29451 original size:15 final size:15
Alignment explanation
Indices: 29433--29488 Score: 51
Period size: 15 Copynumber: 3.6 Consensus size: 15
29423 TAACCGGTTT
29433 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
* *
29448 CGGTTTTTTTAAAAATC
1 CGG--TTTTAAAAAAAC
29465 C-GTTTATAAAAAAAC
1 CGGTTT-TAAAAAAAC
*
29480 CGATTTTAA
1 CGGTTTTAA
29489 TATTATTAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 8
0.71 0.11 0.18
Matches are distributed among these distances:
14 3 0.09
15 14 0.44
16 4 0.12
17 11 0.34
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.36
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:29469 original size:16 final size:17
Alignment explanation
Indices: 29436--29486 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
29426 CCGGTTTCGG
29436 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
* *
29453 TTTTTAAAAATCC-G-T
1 TTTTAAAAAAACCGGTT
* *
29468 TTATAAAAAAACCGATT
1 TTTTAAAAAAACCGGTT
29485 TT
1 TT
29487 AATATTATTA
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
15 11 0.42
16 1 0.04
17 14 0.54
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.39
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:29566 original size:32 final size:33
Alignment explanation
Indices: 29530--29638 Score: 161
Period size: 33 Copynumber: 3.4 Consensus size: 33
29520 ACAAAGTTTA
* *
29530 CGAT-AATTGAAATATTTAAATACTTCCAAGTT
1 CGATAAATTGAAATACTTAAAAACTTCCAAGTT
*
29562 CGATAAATTAAAATACTTAAAAACTTCCAAGTT
1 CGATAAATTGAAATACTTAAAAACTTCCAAGTT
*
29595 CGATAAATTCAAATACTTAAAAACTT-CAAGTT
1 CGATAAATTGAAATACTTAAAAACTTCCAAGTT
29627 CGAT-AATTGAAA
1 CGATAAATTGAAA
29639 CAAAGTTTAC
Statistics
Matches: 71, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
31 7 0.10
32 14 0.20
33 50 0.70
ACGTcount: A:0.46, C:0.14, G:0.08, T:0.32
Consensus pattern (33 bp):
CGATAAATTGAAATACTTAAAAACTTCCAAGTT
Found at i:29651 original size:21 final size:21
Alignment explanation
Indices: 29627--29668 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
29617 ACTTCAAGTT
*
29627 CGATAATTGAAACAAAGTTTA
1 CGATAATTAAAACAAAGTTTA
*
29648 CGATAATTAAAATAAAGTTTA
1 CGATAATTAAAACAAAGTTTA
29669 AAAATAAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.31
Consensus pattern (21 bp):
CGATAATTAAAACAAAGTTTA
Found at i:32023 original size:13 final size:14
Alignment explanation
Indices: 32001--32035 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
31991 TTTTATCCTG
32001 TAAAAAAACCGG-T
1 TAAAAAAACCGGTT
*
32014 TAAAATAACCGGTT
1 TAAAAAAACCGGTT
32028 TAAAAAAA
1 TAAAAAAA
32036 TCCGATCCGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.57, C:0.11, G:0.11, T:0.20
Consensus pattern (14 bp):
TAAAAAAACCGGTT
Found at i:32061 original size:14 final size:14
Alignment explanation
Indices: 32002--32061 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 14
31992 TTTATCCTGT
32002 AAAAAAACCGGTT-
1 AAAAAAACCGGTTA
*
32015 AAAATAACCGGTTTA
1 AAAAAAACCGG-TTA
32030 AAAAAATCCGATCCGGTTA
1 AAAAAA----A-CCGGTTA
32049 AAAAAAACCGGTT
1 AAAAAAACCGGTT
32062 TTTCCCAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 13
0.72 0.04 0.25
Matches are distributed among these distances:
13 10 0.26
14 8 0.21
15 6 0.16
19 10 0.26
20 4 0.11
ACGTcount: A:0.48, C:0.17, G:0.15, T:0.20
Consensus pattern (14 bp):
AAAAAAACCGGTTA
Found at i:33361 original size:30 final size:27
Alignment explanation
Indices: 33311--33404 Score: 82
Period size: 28 Copynumber: 3.3 Consensus size: 27
33301 TGAATATCTA
*
33311 AAATATTTT-TAGTTAAAATAAGTACCT
1 AAATATTTTATA-TCAAAATAAGTACCT
* * *
33338 AAAGTTATTTTTTGATCAGAATAAGTACTT
1 AAA--TATTTTAT-ATCAAAATAAGTACCT
*
33368 CAAATATTTTATATCAAAATAGGTACCT
1 -AAATATTTTATATCAAAATAAGTACCT
33396 AAACTATTT
1 AAA-TATTT
33405 AAACTTTTTC
Statistics
Matches: 54, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
27 6 0.11
28 18 0.33
29 13 0.24
30 13 0.24
31 4 0.07
ACGTcount: A:0.41, C:0.10, G:0.09, T:0.40
Consensus pattern (27 bp):
AAATATTTTATATCAAAATAAGTACCT
Found at i:37853 original size:16 final size:16
Alignment explanation
Indices: 37832--37876 Score: 90
Period size: 16 Copynumber: 2.8 Consensus size: 16
37822 TAATAAATAA
37832 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
37848 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
37864 ACGAACATAAACG
1 ACGAACATAAACG
37877 TTGGAGACCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.56, C:0.24, G:0.13, T:0.07
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:38969 original size:14 final size:14
Alignment explanation
Indices: 38952--38993 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
38942 GATTGGGTTA
*
38952 AACATAAATGAACG
1 AACATAAACGAACG
*
38966 AACATAACCGAACG
1 AACATAAACGAACG
38980 AACATAAACGAACG
1 AACATAAACGAACG
38994 TTCACGAACG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.55, C:0.21, G:0.14, T:0.10
Consensus pattern (14 bp):
AACATAAACGAACG
Found at i:40598 original size:32 final size:32
Alignment explanation
Indices: 40557--40634 Score: 147
Period size: 32 Copynumber: 2.4 Consensus size: 32
40547 ATCAAATAAG
*
40557 GGTGGAGGAAATATATTTATCTAGTTAAGTCA
1 GGTGAAGGAAATATATTTATCTAGTTAAGTCA
40589 GGTGAAGGAAATATATTTATCTAGTTAAGTCA
1 GGTGAAGGAAATATATTTATCTAGTTAAGTCA
40621 GGTGAAGGAAATAT
1 GGTGAAGGAAATAT
40635 GTTTTTAAGG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.37, C:0.05, G:0.26, T:0.32
Consensus pattern (32 bp):
GGTGAAGGAAATATATTTATCTAGTTAAGTCA
Found at i:48746 original size:98 final size:98
Alignment explanation
Indices: 48631--49607 Score: 1545
Period size: 98 Copynumber: 10.0 Consensus size: 98
48621 ATTCTTCGTG
* * * * * *
48631 AAAGAAAGAAAAAGATAGTGTGAAAGAAAAGATTGTTCTTCGTGAGAATGAAAAGATAGAAACTA
1 AAAGAAAGAAAAAGATAGTGTGGAAGAGAAGATTGTTCTTGGTGAGAGTGAGAAGATAGAAACCA
* *
48696 TACCCGAATCAACTCAAAAGCTACACCCGAACT
66 TACCCGAATCAGCTCAAAAACTACACCCGAACT
* *
48729 AAAGAAAGAAAAAGATAGTGTGGAAGAGAAGATTGCTCTTGGTGAGAGTGAGAAGATAGAAATCA
1 AAAGAAAGAAAAAGATAGTGTGGAAGAGAAGATTGTTCTTGGTGAGAGTGAGAAGATAGAAACCA
* *
48794 TATCCAAATCAGCT-AAAAACTACACCCG----
66 TACCCGAATCAGCTCAAAAACTACACCCGAACT
* * *
48822 -AAGAAAGAAAAAAATAGTGTGGAAGAGAAGATTGTTCTTGGTGAGAGTGATAAGATATAAACCA
1 AAAGAAAGAAAAAGATAGTGTGGAAGAGAAGATTGTTCTTGGTGAGAGTGAGAAGATAGAAACCA
* * *
48886 TACTCGAATCAACTCAAAAACTACACCCGAATT
66 TACCCGAATCAGCTCAAAAACTACACCCGAACT
*
48919 AAAGAAAGAAAAAGATAGTGCGGAAGAGAAGATTGTTCTTGGTGAGAGTGAGAAGATAGAAACCA
1 AAAGAAAGAAAAAGATAGTGTGGAAGAGAAGATTGTTCTTGGTGAGAGTGAGAAGATAGAAACCA
* *
48984 TATCCGAATCAGCTTAAAAACTACACCCGAACT
66 TACCCGAATCAGCTCAAAAACTACACCCGAACT
* * *
49017 AAAGAAAGAAAAAGATAGTGCGGAAGAGAAGATTGATCTTGGTGATAGTGAGAAGATAGAAACCA
1 AAAGAAAGAAAAAGATAGTGTGGAAGAGAAGATTGTTCTTGGTGAGAGTGAGAAGATAGAAACCA
*
49082 TACCCGAATCAGCTCAAAAACTACACCTGAACT
66 TACCCGAATCAGCTCAAAAACTACACCCGAACT
49115 AAAGAAAGAAAAAGATAGTGTGGAAGAGAAGATTGTTCTTGGTGAGAGTGAGAAGATAGAAACCA
1 AAAGAAAGAAAAAGATAGTGTGGAAGAGAAGATTGTTCTTGGTGAGAGTGAGAAGATAGAAACCA
*
49180 TACCCGAATTAGCTCAAAAACTACACCCGAACT
66 TACCCGAATCAGCTCAAAAACTACACCCGAACT
* *
49213 AAAGAAAGAAAAAGATAGTGTGGAAGAGAAGTTTGTTCTTGGTGAGAGTGAGAAGATATAAACCA
1 AAAGAAAGAAAAAGATAGTGTGGAAGAGAAGATTGTTCTTGGTGAGAGTGAGAAGATAGAAACCA
*
49278 TACCTGAATCAGCTCAAAAACTACACCCGAACT
66 TACCCGAATCAGCTCAAAAACTACACCCGAACT
* * *
49311 AAAGAAAGAAAAATATAGTGCGGAAGAGAATATTG-TCTTTGGTGAGAGTGAGAAGATAGAAACC
1 AAAGAAAGAAAAAGATAGTGTGGAAGAGAAGATTGTTC-TTGGTGAGAGTGAGAAGATAGAAACC
*
49375 ATACCCGAATCAACTCAAAAACTACACCCGAACT
65 ATACCCGAATCAGCTCAAAAACTACACCCGAACT
*
49409 AAAGAAAGAAAAAGATAGTGTGAAAGAGAAGATTGTTCTTGGTGAGAGTGAGAAGATAGAAACCA
1 AAAGAAAGAAAAAGATAGTGTGGAAGAGAAGATTGTTCTTGGTGAGAGTGAGAAGATAGAAACCA
*
49474 TACCCGAATCAGCTCAAAAACTACACTCGAACT
66 TACCCGAATCAGCTCAAAAACTACACCCGAACT
49507 AAAGAAAGAAAAAGATAGTGTGGAAGAGAAGATTGTTCTTGGTGAGAAGTGAGAAGATAGAAACC
1 AAAGAAAGAAAAAGATAGTGTGGAAGAGAAGATTGTTCTTGGTGAG-AGTGAGAAGATAGAAACC
* * *
49572 ATACCCAAATCAACTCAAAAAATACACCCGAACT
65 ATACCCGAATCAGCTCAAAAACTACACCCGAACT
49606 AA
1 AA
49608 TCTAACCGTT
Statistics
Matches: 808, Mismatches: 62, Indels: 17
0.91 0.07 0.02
Matches are distributed among these distances:
92 69 0.09
93 14 0.02
97 15 0.02
98 658 0.81
99 52 0.06
ACGTcount: A:0.45, C:0.14, G:0.22, T:0.19
Consensus pattern (98 bp):
AAAGAAAGAAAAAGATAGTGTGGAAGAGAAGATTGTTCTTGGTGAGAGTGAGAAGATAGAAACCA
TACCCGAATCAGCTCAAAAACTACACCCGAACT
Found at i:50759 original size:2 final size:2
Alignment explanation
Indices: 50754--50833 Score: 151
Period size: 2 Copynumber: 39.5 Consensus size: 2
50744 CCTTGTGTGC
50754 TA TA TA TA TA TA TA TA TA TA TA TA TA TCA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA
50797 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
50834 GTTTTAAATA
Statistics
Matches: 77, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 75 0.97
3 2 0.03
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:58621 original size:13 final size:13
Alignment explanation
Indices: 58603--58629 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
58593 AAAAGATAAT
58603 TAAATTTATTAAA
1 TAAATTTATTAAA
58616 TAAATTTATTAAA
1 TAAATTTATTAAA
58629 T
1 T
58630 TTATTCCTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TAAATTTATTAAA
Found at i:59077 original size:13 final size:13
Alignment explanation
Indices: 59059--59114 Score: 50
Period size: 13 Copynumber: 4.6 Consensus size: 13
59049 GTGTCATATT
59059 GTACATGTTAAAA
1 GTACATGTTAAAA
*
59072 GTACATG-TAGAA
1 GTACATGTTAAAA
*
59084 GTATCATATT----
1 GTA-CATGTTAAAA
59094 GTACATGTTAAAA
1 GTACATGTTAAAA
59107 GTACATGT
1 GTACATGT
59115 ATCACATTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 12
0.69 0.06 0.24
Matches are distributed among these distances:
9 5 0.15
10 3 0.09
12 7 0.21
13 18 0.53
14 1 0.03
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.34
Consensus pattern (13 bp):
GTACATGTTAAAA
Found at i:59091 original size:35 final size:35
Alignment explanation
Indices: 59043--59115 Score: 137
Period size: 35 Copynumber: 2.1 Consensus size: 35
59033 TTTTATCAAA
*
59043 GTAGAAGTGTCATATTGTACATGTTAAAAGTACAT
1 GTAGAAGTATCATATTGTACATGTTAAAAGTACAT
59078 GTAGAAGTATCATATTGTACATGTTAAAAGTACAT
1 GTAGAAGTATCATATTGTACATGTTAAAAGTACAT
59113 GTA
1 GTA
59116 TCACATTGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.34
Consensus pattern (35 bp):
GTAGAAGTATCATATTGTACATGTTAAAAGTACAT
Found at i:59128 original size:29 final size:31
Alignment explanation
Indices: 59084--59146 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 31
59074 ACATGTAGAA
* *
59084 GTATCATATTGTACA-TGT-TAAAAGTACAT
1 GTATCACATTGAACATTGTCTAAAAGTACAT
* *
59113 GTATCACATTGAACATTGTCTCAAAGTATAT
1 GTATCACATTGAACATTGTCTAAAAGTACAT
59144 GTA
1 GTA
59147 CCAAATATGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 13 0.46
30 3 0.11
31 12 0.43
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.37
Consensus pattern (31 bp):
GTATCACATTGAACATTGTCTAAAAGTACAT
Found at i:61119 original size:2 final size:2
Alignment explanation
Indices: 61114--61143 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
61104 ACGAGGGATC
61114 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
61144 AACACACACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.