Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002253.1 Hibiscus syriacus cultivar Beakdansim tig00004581_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: 59023
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:6920 original size:39 final size:39
Alignment explanation
Indices: 6877--6956 Score: 88
Period size: 39 Copynumber: 2.1 Consensus size: 39
6867 CTCAATTTGT
* * * *
6877 CTGAAGACGTCGTGCAATCGTGAAGTCTTTTTCATTTAC
1 CTGAAGACGCCATCCAATCGTGAAGTCTTCTTCATTTAC
* * * *
6916 CTGAATATGCCATCCAGTCGTGGAGTCTTCTTCATTTAC
1 CTGAAGACGCCATCCAATCGTGAAGTCTTCTTCATTTAC
6955 CT
1 CT
6957 TAATATGCCG
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.21, C:0.24, G:0.19, T:0.36
Consensus pattern (39 bp):
CTGAAGACGCCATCCAATCGTGAAGTCTTCTTCATTTAC
Found at i:6984 original size:39 final size:39
Alignment explanation
Indices: 6894--6984 Score: 110
Period size: 39 Copynumber: 2.3 Consensus size: 39
6884 CGTCGTGCAA
* *
6894 TCGTGAAGTCTTTTTCATTTACCTGAATATGCCATCCAG
1 TCGTGAAGTCTTCTTCATTTACCTGAATATGCCATCAAG
* * * *
6933 TCGTGGAGTCTTCTTCATTTACCTTAATATGCCGTGAAG
1 TCGTGAAGTCTTCTTCATTTACCTGAATATGCCATCAAG
* *
6972 TTGTGAAATCTTC
1 TCGTGAAGTCTTC
6985 ATATTTAGAA
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.22, C:0.21, G:0.18, T:0.40
Consensus pattern (39 bp):
TCGTGAAGTCTTCTTCATTTACCTGAATATGCCATCAAG
Found at i:7301 original size:18 final size:18
Alignment explanation
Indices: 7267--7301 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
7257 AAATACTGAC
*
7267 ATTATAATTAAATATTTT
1 ATTATAATTAAACATTTT
*
7285 ATTATAATTATACATTT
1 ATTATAATTAAACATTT
7302 CGTCTCTTAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTATAATTAAACATTTT
Found at i:7655 original size:27 final size:27
Alignment explanation
Indices: 7625--7682 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
7615 AAACTAATAA
7625 TATTTTTATATCT-TTAAAAATATATTT
1 TATTTTTATAT-TGTTAAAAATATATTT
**
7652 TATTTTTATATTGTTATTAATATATTT
1 TATTTTTATATTGTTAAAAATATATTT
7679 TATT
1 TATT
7683 ATTAACTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 1 0.04
27 27 0.96
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (27 bp):
TATTTTTATATTGTTAAAAATATATTT
Found at i:7661 original size:13 final size:13
Alignment explanation
Indices: 7643--7683 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
7633 TATCTTTAAA
7643 AATATATTTTATT
1 AATATATTTTATT
**
7656 TTTATATTGTTATT
1 AATATATT-TTATT
7670 AATATATTTTATT
1 AATATATTTTATT
7683 A
1 A
7684 TTAACTTAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (13 bp):
AATATATTTTATT
Found at i:7734 original size:26 final size:26
Alignment explanation
Indices: 7637--7739 Score: 75
Period size: 26 Copynumber: 3.8 Consensus size: 26
7627 TTTTTATATC
* *
7637 TTTAAAAATATATTTTATT-TTTATAT
1 TTTAAAAATATATATTATTATTT-TAA
** *
7663 TGTTATTAATATATTTTATTATTAACTTAA
1 T-TTAAAAATATATATTATTATT---TTAA
* * *
7693 TTTAAGACTATTTATTATTATTTTAA
1 TTTAAAAATATATATTATTATTTTAA
7719 TTTAAAAATATATATT-TTATT
1 TTTAAAAATATATATTATTATT
7740 CTTATCTTAG
Statistics
Matches: 61, Mismatches: 11, Indels: 11
0.73 0.13 0.13
Matches are distributed among these distances:
25 5 0.08
26 18 0.30
27 16 0.26
28 2 0.03
29 16 0.26
30 3 0.05
31 1 0.02
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (26 bp):
TTTAAAAATATATATTATTATTTTAA
Found at i:7754 original size:31 final size:29
Alignment explanation
Indices: 7671--7766 Score: 99
Period size: 26 Copynumber: 3.3 Consensus size: 29
7661 ATTGTTATTA
* *
7671 ATATATTTTATTATTAACTTAATTT-AAG
1 ATATATTTTATTATTATCTTAATTTAAAT
* *
7699 A-CTA-TTTATTATTATTTTAATTTAAAAAT
1 ATATATTTTATTATTATCTTAATTT--AAAT
* *
7728 ATATATTTTATTCTTATCTTAGTTTAAAT
1 ATATATTTTATTATTATCTTAATTTAAAT
7757 ATATATTTTA
1 ATATATTTTA
7767 ATTTTTAAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 9
0.76 0.11 0.12
Matches are distributed among these distances:
26 17 0.31
27 2 0.04
28 1 0.02
29 17 0.31
30 2 0.04
31 16 0.29
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (29 bp):
ATATATTTTATTATTATCTTAATTTAAAT
Found at i:7935 original size:27 final size:28
Alignment explanation
Indices: 7888--7971 Score: 77
Period size: 27 Copynumber: 3.1 Consensus size: 28
7878 AATATATAAT
* * *
7888 TTTAAATTAA-TATAGTGATAAAACATC
1 TTTAAATTAAGTATAATAATAAAACATA
*
7915 TTTAAATTAAGT-TAATAATAAAATATA
1 TTTAAATTAAGTATAATAATAAAACATA
* *
7942 TTTAAAATTAAGTA-AA-AGTAAAATATA
1 TTT-AAATTAAGTATAATAATAAAACATA
7969 TTT
1 TTT
7972 TTAAAGATAT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
27 37 0.76
28 12 0.24
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.39
Consensus pattern (28 bp):
TTTAAATTAAGTATAATAATAAAACATA
Found at i:8282 original size:16 final size:17
Alignment explanation
Indices: 8261--8292 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
8251 AAATATGTTA
8261 AAAATAATAT-TAAATT
1 AAAATAATATGTAAATT
8277 AAAATAATATGTAAAT
1 AAAATAATATGTAAAT
8293 AACATAGACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (17 bp):
AAAATAATATGTAAATT
Found at i:13785 original size:40 final size:41
Alignment explanation
Indices: 13719--13807 Score: 101
Period size: 40 Copynumber: 2.2 Consensus size: 41
13709 TTTATATTGT
* * * *
13719 TAAAATATTTTTTTAATTATTAAAAATATAA-AACTTATTA
1 TAAAATATTATTTTAATCATTAAAAATATAATAAATAATTA
*
13759 TAAAATATTATTTTAA-CAGTTTAAAATATAATAAATAATTA
1 TAAAATATTATTTTAATCA-TTAAAAATATAATAAATAATTA
*
13800 TAAGATAT
1 TAAAATAT
13808 AAATATATTG
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
39 1 0.02
40 26 0.63
41 14 0.34
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (41 bp):
TAAAATATTATTTTAATCATTAAAAATATAATAAATAATTA
Found at i:17338 original size:17 final size:16
Alignment explanation
Indices: 17306--17358 Score: 54
Period size: 17 Copynumber: 3.3 Consensus size: 16
17296 TTTTATAATT
* *
17306 TTATGATGTGAAAATA
1 TTATTATGTTAAAATA
17322 TTATTATTGTTAAAATA
1 TTATTA-TGTTAAAATA
*
17339 TAATTAT-TTAAAATA
1 TTATTATGTTAAAATA
*
17354 ATATT
1 TTATT
17359 TAATTTTGAG
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
15 11 0.35
16 6 0.19
17 14 0.45
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (16 bp):
TTATTATGTTAAAATA
Found at i:18253 original size:27 final size:27
Alignment explanation
Indices: 18205--18258 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
18195 TATGAACGAA
* * * *
18205 TATAGAATTTTATATTAAAAATGAATT
1 TATAAAATTTTAAAATAAAAATAAATT
*
18232 TATAAAATTTTAAAATACAAATAAATT
1 TATAAAATTTTAAAATAAAAATAAATT
18259 AGAAAATATA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.41
Consensus pattern (27 bp):
TATAAAATTTTAAAATAAAAATAAATT
Found at i:19483 original size:79 final size:80
Alignment explanation
Indices: 19400--19552 Score: 204
Period size: 80 Copynumber: 1.9 Consensus size: 80
19390 AACATCTTTT
* *
19400 AGGTAACGTCCAATATTAAAATTT-TCGGTAG-AAAAATTAATGTTTT-ATTTAACGCTTTACCG
1 AGGTAACGTCCAATATTAAAATTTAT-GGTAGAAAAAAATAATGTTTTAAGTT-ACGCTTTACCG
*
19462 GAAATGTTAAACATTTC
64 GAAATATTAAACATTTC
* * * *
19479 AGGTAGCGTCCAATATTAACATTTATGGTAGAAAAAAATAATGTTTTAAGTTGCGCTTTATCGGA
1 AGGTAACGTCCAATATTAAAATTTATGGTAGAAAAAAATAATGTTTTAAGTTACGCTTTACCGGA
19544 AATATTAAA
66 AATATTAAA
19553 AAAAATATTA
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
79 27 0.42
80 34 0.53
81 3 0.05
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (80 bp):
AGGTAACGTCCAATATTAAAATTTATGGTAGAAAAAAATAATGTTTTAAGTTACGCTTTACCGGA
AATATTAAACATTTC
Found at i:24575 original size:5 final size:5
Alignment explanation
Indices: 24565--24605 Score: 73
Period size: 5 Copynumber: 8.2 Consensus size: 5
24555 AATTTATATG
*
24565 CTATA CTATA CTATA TTATA CTATA CTATA CTATA CTATA C
1 CTATA CTATA CTATA CTATA CTATA CTATA CTATA CTATA C
24606 ATTTCATCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.39, C:0.20, G:0.00, T:0.41
Consensus pattern (5 bp):
CTATA
Found at i:24646 original size:2 final size:2
Alignment explanation
Indices: 24639--24678 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
24629 TTATATTCTC
24639 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24679 GTTTATAATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26544 original size:23 final size:22
Alignment explanation
Indices: 26508--26551 Score: 79
Period size: 23 Copynumber: 2.0 Consensus size: 22
26498 CTCACATCTA
26508 AATAAAAATTATTGAATGATTT
1 AATAAAAATTATTGAATGATTT
26530 AATAAAATATTATTGAATGATT
1 AATAAAA-ATTATTGAATGATT
26552 CAACATTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (22 bp):
AATAAAAATTATTGAATGATTT
Found at i:28597 original size:22 final size:20
Alignment explanation
Indices: 28558--28597 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
28548 TTGAATCTTG
*
28558 ATAATTTTAAAAATAAAAAA
1 ATAATTTTAAAAAGAAAAAA
28578 ATAATTTTTCAAAAAGAAAA
1 ATAA-TTTT-AAAAAGAAAA
28598 TATAAACAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 4 0.24
22 9 0.53
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (20 bp):
ATAATTTTAAAAAGAAAAAA
Found at i:30626 original size:18 final size:18
Alignment explanation
Indices: 30603--30653 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
30593 AAATTAATAC
30603 AATAAAATATAATAAAAT
1 AATAAAATATAATAAAAT
*
30621 AATAAACTAT--T-AAAT
1 AATAAAATATAATAAAAT
*
30636 AATTATAATATAATAAAA
1 AA-TAAAATATAATAAAA
30654 AATTAGCTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 7
0.72 0.08 0.19
Matches are distributed among these distances:
15 6 0.23
16 7 0.27
18 10 0.38
19 3 0.12
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (18 bp):
AATAAAATATAATAAAAT
Found at i:31576 original size:29 final size:29
Alignment explanation
Indices: 31541--31637 Score: 176
Period size: 29 Copynumber: 3.3 Consensus size: 29
31531 TTAAATTTCA
*
31541 ACTTTCACAATATGTTCAATTTAGTCCCT
1 ACTTTCACAATGTGTTCAATTTAGTCCCT
31570 ACTTTCACAATGTGTTCAATTTAGTCCCT
1 ACTTTCACAATGTGTTCAATTTAGTCCCT
*
31599 ACTTTCACAATGTGTTCAATTTAATCCCT
1 ACTTTCACAATGTGTTCAATTTAGTCCCT
31628 ACTTTCACAA
1 ACTTTCACAA
31638 ATATTTAAAA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 66 1.00
ACGTcount: A:0.28, C:0.25, G:0.07, T:0.40
Consensus pattern (29 bp):
ACTTTCACAATGTGTTCAATTTAGTCCCT
Found at i:33283 original size:21 final size:21
Alignment explanation
Indices: 33257--33455 Score: 189
Period size: 21 Copynumber: 9.6 Consensus size: 21
33247 GTTTTCAGAT
*
33257 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
33278 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
*
33299 TCGCAATGCGAA-TAT-GTA-AA
1 TCGCAATGCGAACT-TCG-ACTA
* *
33319 TCGTAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTCGACTA
*
33340 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
*
33361 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
* *
33382 TCGCAATGCGAACTTGGGCTA
1 TCGCAATGCGAACTTCGACTA
*
33403 TCGCAATGCGAA-TAT-GTA-AA
1 TCGCAATGCGAACT-TCG-ACTA
*
33423 TCGCAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTCGACTA
33444 TCGCAATGCGAA
1 TCGCAATGCGAA
33456 TATGTAAATC
Statistics
Matches: 149, Mismatches: 18, Indels: 23
0.78 0.09 0.12
Matches are distributed among these distances:
20 33 0.22
21 116 0.78
ACGTcount: A:0.31, C:0.24, G:0.23, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:33376 original size:104 final size:104
Alignment explanation
Indices: 33257--33455 Score: 380
Period size: 104 Copynumber: 1.9 Consensus size: 104
33247 GTTTTCAGAT
33257 TCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCG
1 TCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCG
*
33322 TAATGCGATAGTCGACTATCGCAATGCGAACTTGGACTA
66 CAATGCGATAGTCGACTATCGCAATGCGAACTTGGACTA
*
33361 TCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGGCTATCGCAATGCGAATATGTAAATCG
1 TCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCG
33426 CAATGCGATAGTCGACTATCGCAATGCGAA
66 CAATGCGATAGTCGACTATCGCAATGCGAA
33456 TATGTAAATC
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
104 93 1.00
ACGTcount: A:0.31, C:0.24, G:0.23, T:0.23
Consensus pattern (104 bp):
TCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCG
CAATGCGATAGTCGACTATCGCAATGCGAACTTGGACTA
Found at i:33426 original size:62 final size:63
Alignment explanation
Indices: 33257--33455 Score: 178
Period size: 62 Copynumber: 3.2 Consensus size: 63
33247 GTTTTCAGAT
* * * * * *
33257 TCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATA-T-GTA-AA
1 TCGCAATGCGAACTTGGGCTATCGCAATGCGAACTTGGACAATCGCAACGCG-ATAGTCG-ACTA
* * * * * *
33319 TCGTAATGCGATA-GTCGACTATCGCAATGCGAACTTGGACTATCGCAACGCGA-ACTTCGACTA
1 TCGCAATGCGA-ACTTGGGCTATCGCAATGCGAACTTGGACAATCGCAACGCGATA-GTCGACTA
* *
33382 TCGCAATGCGAACTTGGGCTATCGCAATGCGAA-TATGTA-AATCGCAATGCGATAGTCGACTA
1 TCGCAATGCGAACTTGGGCTATCGCAATGCGAACT-TGGACAATCGCAACGCGATAGTCGACTA
33444 TCGCAATGCGAA
1 TCGCAATGCGAA
33456 TATGTAAATC
Statistics
Matches: 116, Mismatches: 13, Indels: 16
0.80 0.09 0.11
Matches are distributed among these distances:
60 1 0.01
61 1 0.01
62 80 0.69
63 34 0.29
ACGTcount: A:0.31, C:0.24, G:0.23, T:0.23
Consensus pattern (63 bp):
TCGCAATGCGAACTTGGGCTATCGCAATGCGAACTTGGACAATCGCAACGCGATAGTCGACTA
Found at i:33426 original size:83 final size:82
Alignment explanation
Indices: 33257--33455 Score: 226
Period size: 83 Copynumber: 2.4 Consensus size: 82
33247 GTTTTCAGAT
* * *
33257 TCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCG
1 TCGCAATGCGAACTTCGACTATCGCAATGCGAACTTCGACTATCGCAATGCGAATATGGAAATCG
* *
33322 TAATGCGATAGTCGACTA
66 CAATGCGATAGTC-ACAA
* * **
33340 TCGCAATGCGAACTTGGACTATCGCAACGCGAACTTCGACTATCGCAATGCGAACT-TGGGCTAT
1 TCGCAATGCGAACTTCGACTATCGCAATGCGAACTTCGACTATCGCAATGCGAA-TAT-GGAAAT
33404 CGCAATGCGAATATGT-A-AA
64 CGCAATGCG-ATA-GTCACAA
*
33423 TCGCAATGCGATA-GTCGACTATCGCAATGCGAA
1 TCGCAATGCGA-ACTTCGACTATCGCAATGCGAA
33456 TATGTAAATC
Statistics
Matches: 99, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
83 80 0.81
84 14 0.14
85 3 0.03
86 2 0.02
ACGTcount: A:0.31, C:0.24, G:0.23, T:0.23
Consensus pattern (82 bp):
TCGCAATGCGAACTTCGACTATCGCAATGCGAACTTCGACTATCGCAATGCGAATATGGAAATCG
CAATGCGATAGTCACAA
Found at i:33427 original size:20 final size:20
Alignment explanation
Indices: 33402--33474 Score: 96
Period size: 20 Copynumber: 3.6 Consensus size: 20
33392 AACTTGGGCT
33402 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
*
33422 ATCGCAATGCG-ATA-GTCGACT
1 ATCGCAATGCGAATATGT--A-A
33443 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
33463 ATCGCAATGCGA
1 ATCGCAATGCGA
33475 TAGTCGAAGT
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
18 2 0.04
19 3 0.07
20 24 0.52
21 12 0.26
22 3 0.07
23 2 0.04
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:33445 original size:41 final size:41
Alignment explanation
Indices: 33400--33481 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
33390 CGAACTTGGG
33400 CTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGA
1 CTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGA
33441 CTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGA
1 CTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGA
33482 AGTTCGCGAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (41 bp):
CTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGA
Found at i:34267 original size:21 final size:21
Alignment explanation
Indices: 34241--34393 Score: 81
Period size: 21 Copynumber: 7.4 Consensus size: 21
34231 TATTTGGACT
*
34241 ATCGCAACGAATTTGGAATGA
1 ATCGCAACGAACTTGGAATGA
* **
34262 ATCGCAACGCGAACTTCGCCT--
1 ATCGCAA--CGAACTTGGAATGA
*
34283 ATTGCAACGAA-TTGGAATGA
1 ATCGCAACGAACTTGGAATGA
* **
34303 ATCGCAACGCGAACTTCGCCT--
1 ATCGCAA--CGAACTTGGAATGA
*
34324 ATCGCAACG-ATTTGGAATGA
1 ATCGCAACGAACTTGGAATGA
* *
34344 ATCGCAACGCAAACTTCGACT--
1 ATCGCAACG--AACTTGGAATGA
*
34365 ATCGCAACG-ATTTGGAATGA
1 ATCGCAACGAACTTGGAATGA
34385 ATCGCAACG
1 ATCGCAACG
34394 CGAACTTCGC
Statistics
Matches: 96, Mismatches: 22, Indels: 29
0.65 0.15 0.20
Matches are distributed among these distances:
18 15 0.16
19 6 0.06
20 24 0.25
21 29 0.30
22 4 0.04
23 18 0.19
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.22
Consensus pattern (21 bp):
ATCGCAACGAACTTGGAATGA
Found at i:34303 original size:41 final size:41
Alignment explanation
Indices: 34239--34452 Score: 320
Period size: 41 Copynumber: 5.2 Consensus size: 41
34229 AATATTTGGA
34239 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
1 CTATCGCAACGAA-TTGGAATGAATCGCAACGCGAACTTCGC
*
34281 CTATTGCAACGAATTGGAATGAATCGCAACGCGAACTTCGC
1 CTATCGCAACGAATTGGAATGAATCGCAACGCGAACTTCGC
* * *
34322 CTATCGCAACGATTTGGAATGAATCGCAACGCAAACTTCGA
1 CTATCGCAACGAATTGGAATGAATCGCAACGCGAACTTCGC
*
34363 CTATCGCAACGATTTGGAATGAATCGCAACGCGAACTTCGC
1 CTATCGCAACGAATTGGAATGAATCGCAACGCGAACTTCGC
* * * * *
34404 CTATTGCAACGAATTTGAAATAAATCGCAATGCGAACTTCGA
1 CTATCGCAACGAA-TTGGAATGAATCGCAACGCGAACTTCGC
34446 CTATCGC
1 CTATCGC
34453 GTTGCGAATA
Statistics
Matches: 157, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
41 115 0.73
42 42 0.27
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (41 bp):
CTATCGCAACGAATTGGAATGAATCGCAACGCGAACTTCGC
Found at i:36115 original size:22 final size:22
Alignment explanation
Indices: 36062--36120 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 22
36052 TTAGATAGTA
36062 TAATGATTAAAATATTTTTATAATT
1 TAAT-ATTAAAATA--TTTATAATT
** *
36087 TTTTATTCAAATATTTATAATT
1 TAATATTAAAATATTTATAATT
36109 TAATATTAAAAT
1 TAATATTAAAAT
36121 TAATTTTTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
22 18 0.64
24 8 0.29
25 2 0.07
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (22 bp):
TAATATTAAAATATTTATAATT
Found at i:41051 original size:21 final size:21
Alignment explanation
Indices: 41025--41065 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
41015 AAATAAATTC
41025 TAAATTTTCAAATTTCTTTTT
1 TAAATTTTCAAATTTCTTTTT
41046 TAAATTTTCAAATTTCTTTT
1 TAAATTTTCAAATTTCTTTT
41066 GAAATTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.61
Consensus pattern (21 bp):
TAAATTTTCAAATTTCTTTTT
Found at i:45133 original size:9 final size:9
Alignment explanation
Indices: 45119--45144 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
45109 TAAGTAACAT
45119 ATTAAATAA
1 ATTAAATAA
45128 ATTAAATAA
1 ATTAAATAA
45137 ATTAAATA
1 ATTAAATA
45145 TAAAATATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (9 bp):
ATTAAATAA
Found at i:45145 original size:25 final size:25
Alignment explanation
Indices: 45097--45151 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
45087 TTATATCTGC
45097 AAAA-AAATTAAATAAGTAACATAT
1 AAAATAAATTAAATAAGTAACATAT
* *
45121 TAAATAAATTAAATAAATTAA-ATAT
1 AAAATAAATTAAAT-AAGTAACATAT
45146 AAAATA
1 AAAATA
45152 TTAAAAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
24 3 0.12
25 18 0.69
26 5 0.19
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (25 bp):
AAAATAAATTAAATAAGTAACATAT
Found at i:45926 original size:35 final size:35
Alignment explanation
Indices: 45885--46031 Score: 186
Period size: 35 Copynumber: 4.2 Consensus size: 35
45875 AAAACATTCC
* *
45885 TCAATTTCATTTTAAACCCCAAATTCCAAAGCAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAGTAAT
*
45920 TCAATTTCATTCTAAACCCTAAATTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAGTAAT
* *
45955 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAGTAAT
* * * * * * *
45990 TTAATTACATTATAAAACCCAAATTCTAAAATATT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAGTAAT
46025 TCAATTT
1 TCAATTT
46032 AAGGAGGAAT
Statistics
Matches: 99, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 99 1.00
ACGTcount: A:0.42, C:0.21, G:0.01, T:0.35
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAGTAAT
Found at i:49417 original size:37 final size:37
Alignment explanation
Indices: 49376--49451 Score: 134
Period size: 37 Copynumber: 2.1 Consensus size: 37
49366 GATGAGCTCA
* *
49376 AATCTCAGAAGATCTATGGAAGATGATAAACAGATCT
1 AATCTCAGAAGATCCATGGAAAATGATAAACAGATCT
49413 AATCTCAGAAGATCCATGGAAAATGATAAACAGATCT
1 AATCTCAGAAGATCCATGGAAAATGATAAACAGATCT
49450 AA
1 AA
49452 CTTAACTTAC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.46, C:0.14, G:0.17, T:0.22
Consensus pattern (37 bp):
AATCTCAGAAGATCCATGGAAAATGATAAACAGATCT
Found at i:56417 original size:23 final size:23
Alignment explanation
Indices: 56391--56445 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
56381 TTTTAGTAAC
* *
56391 TTTATCTTTGTGACACACGTTCT
1 TTTATCTTTATGACACACGTTCA
*
56414 TTTATCTTTATGACACACTTTCA
1 TTTATCTTTATGACACACGTTCA
*
56437 TCTATCTTT
1 TTTATCTTT
56446 TGGTATATGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.20, C:0.22, G:0.07, T:0.51
Consensus pattern (23 bp):
TTTATCTTTATGACACACGTTCA
Found at i:58333 original size:35 final size:34
Alignment explanation
Indices: 58242--58334 Score: 100
Period size: 35 Copynumber: 2.7 Consensus size: 34
58232 AAAACTTATG
*
58242 ATTATAATTTGAATATTAACTATAATATATATAT
1 ATTATAATTTGAATATTAATTATAATATATATAT
** *
58276 ATCTAT-ATTTTTATCGTTAATTAT-ATATAATATAT
1 AT-TATAATTTGAAT-ATTAATTATAATAT-ATATAT
58311 ATTATAATTTGAATATTAAATTAT
1 ATTATAATTTGAATATT-AATTAT
58335 TTTTAATGAT
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
34 17 0.36
35 30 0.64
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (34 bp):
ATTATAATTTGAATATTAATTATAATATATATAT
Found at i:58776 original size:14 final size:13
Alignment explanation
Indices: 58759--58797 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
58749 TAATATTCAA
58759 ATTATAATATATGT
1 ATTATAATATAT-T
*
58773 ATTATATTATATT
1 ATTATAATATATT
*
58786 ATGATAATATAT
1 ATTATAATATAT
58798 ATATATTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (13 bp):
ATTATAATATATT
Found at i:58787 original size:24 final size:25
Alignment explanation
Indices: 58759--58815 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 25
58749 TAATATTCAA
*
58759 ATTATAATATATGTAT-TATATTAT
1 ATTATAATATATATATATATATTAT
*
58783 ATTATGATA-ATATATATATATTAT
1 ATTATAATATATATATATATATTAT
*
58807 AGT-TAATAT
1 ATTATAATAT
58816 TCAAATTATA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
23 9 0.33
24 18 0.67
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (25 bp):
ATTATAATATATATATATATATTAT
Done.