Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003366.1 Hibiscus syriacus cultivar Beakdansim tig00007078_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: 64914
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:8512 original size:2 final size:2
Alignment explanation
Indices: 8505--8530 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
8495 CATTCTTTCG
8505 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
8531 AGCACTTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9112 original size:25 final size:25
Alignment explanation
Indices: 9084--9136 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
9074 TATTTTGAAT
*
9084 TCAAAGCAGCCCCTTAATTTGAAAA
1 TCAAACCAGCCCCTTAATTTGAAAA
* *
9109 TC-AACCATCCCCTTAGTTTGAAAA
1 TCAAACCAGCCCCTTAATTTGAAAA
9133 TCAA
1 TCAA
9137 CCGGCCTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 21 0.88
25 3 0.12
ACGTcount: A:0.38, C:0.26, G:0.09, T:0.26
Consensus pattern (25 bp):
TCAAACCAGCCCCTTAATTTGAAAA
Found at i:9120 original size:24 final size:24
Alignment explanation
Indices: 9093--9138 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
9083 TTCAAAGCAG
9093 CCCCTTAATTTGAAAATCAACCAT
1 CCCCTTAATTTGAAAATCAACCAT
*
9117 CCCCTTAGTTTGAAAATCAACC
1 CCCCTTAATTTGAAAATCAACC
9139 GGCCTTCTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.35, C:0.30, G:0.07, T:0.28
Consensus pattern (24 bp):
CCCCTTAATTTGAAAATCAACCAT
Found at i:10055 original size:21 final size:21
Alignment explanation
Indices: 10029--10069 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
10019 GTGAAGAATC
10029 CATCTTCTTCAGTCAAACTTA
1 CATCTTCTTCAGTCAAACTTA
10050 CATCTTCTTCAGTCAAACTT
1 CATCTTCTTCAGTCAAACTT
10070 GGGACTTTAA
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:0.27, C:0.29, G:0.05, T:0.39
Consensus pattern (21 bp):
CATCTTCTTCAGTCAAACTTA
Found at i:11451 original size:25 final size:25
Alignment explanation
Indices: 11410--11475 Score: 73
Period size: 24 Copynumber: 2.7 Consensus size: 25
11400 AAAACAACAA
* * * *
11410 CCTTATTTTG-AATTCAAAGCAGTC
1 CCTTAATTTGAAAATCAAACCAGCC
11434 CCTTAATTTGAAAATC-AACCAGCC
1 CCTTAATTTGAAAATCAAACCAGCC
*
11458 CCTTAGTTTGAAAATCAA
1 CCTTAATTTGAAAATCAA
11476 CCGGCCTTCT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
24 30 0.86
25 5 0.14
ACGTcount: A:0.35, C:0.23, G:0.11, T:0.32
Consensus pattern (25 bp):
CCTTAATTTGAAAATCAAACCAGCC
Found at i:18627 original size:14 final size:14
Alignment explanation
Indices: 18608--18693 Score: 90
Period size: 14 Copynumber: 6.4 Consensus size: 14
18598 TTGTGTAATC
18608 CGTTCATTTATGTT
1 CGTTCATTTATGTT
*
18622 CGTTCATTTAT-AT
1 CGTTCATTTATGTT
18635 C---CATTTATGTT
1 CGTTCATTTATGTT
*
18646 TGTTCATTTATGTT
1 CGTTCATTTATGTT
* *
18660 TGTTCATTTATTTT
1 CGTTCATTTATGTT
*
18674 CGTTCGTTTATGTT
1 CGTTCATTTATGTT
*
18688 CTTTCA
1 CGTTCA
18694 ACCCAATCTC
Statistics
Matches: 59, Mismatches: 9, Indels: 8
0.78 0.12 0.11
Matches are distributed among these distances:
10 7 0.12
11 1 0.02
13 2 0.03
14 49 0.83
ACGTcount: A:0.15, C:0.14, G:0.12, T:0.59
Consensus pattern (14 bp):
CGTTCATTTATGTT
Found at i:18687 original size:24 final size:24
Alignment explanation
Indices: 18609--18688 Score: 72
Period size: 24 Copynumber: 3.2 Consensus size: 24
18599 TGTGTAATCC
*
18609 GTTCATTTATGTTCGTTCATTTAT
1 GTTCATTTATTTTCGTTCATTTAT
* *
18633 ATCCATTTATGTTT-GTTCATTTATGTTT
1 GTTCATTTAT-TTTCGTTCATTTA----T
*
18661 GTTCATTTATTTTCGTTCGTTTAT
1 GTTCATTTATTTTCGTTCATTTAT
18685 GTTC
1 GTTC
18689 TTTCAACCCA
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
24 22 0.50
25 2 0.05
27 3 0.07
28 17 0.39
ACGTcount: A:0.15, C:0.12, G:0.12, T:0.60
Consensus pattern (24 bp):
GTTCATTTATTTTCGTTCATTTAT
Found at i:18896 original size:24 final size:24
Alignment explanation
Indices: 18869--18924 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
18859 ATTAGTTTAC
* *
18869 GTTCATTTATGATCGTCCGTTTGT
1 GTTCATTTACGATCGTCCATTTGT
* * *
18893 GTTCGTTTACGTTCGTTCATTTGT
1 GTTCATTTACGATCGTCCATTTGT
18917 GTTCATTT
1 GTTCATTT
18925 TTATTTTTCA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.11, C:0.16, G:0.20, T:0.54
Consensus pattern (24 bp):
GTTCATTTACGATCGTCCATTTGT
Found at i:20450 original size:20 final size:20
Alignment explanation
Indices: 20425--20517 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
20415 TTTTCCCAAT
20425 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
20445 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
20465 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
20486 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
20507 TCGCAATGCGA
1 TCGCAATGCGA
20518 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:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:20467 original size:41 final size:41
Alignment explanation
Indices: 20422--20517 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
20412 CGATTTTCCC
20422 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
20463 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
20504 AAATCGCAATGCGA
1 AATTCGCAATGCGA
20518 TACTGACTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:20471 original size:21 final size:20
Alignment explanation
Indices: 20425--20517 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
20415 TTTTCCCAAT
*
20425 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
20445 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
20465 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
20486 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
20507 TCGCAATGCGA
1 TCGCAATGCGA
20518 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 29 0.50
21 29 0.50
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:20530 original size:41 final size:41
Alignment explanation
Indices: 20444--20578 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
20434 GAATAAGTAA
* * *
20444 ATCGCAACGCGAATTGGGAAATTCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
20485 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
20526 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
20567 TTCGCAACGCGA
1 ATCGCAACGCGA
20579 TACTGACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:20531 original size:20 final size:20
Alignment explanation
Indices: 20506--20600 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
20496 AATTGGGAAA
*
20506 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
20526 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
20547 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
20567 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
20587 TTCGCAACGCGATA
1 ATCGCAACGCGATA
20601 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:20816 original size:22 final size:22
Alignment explanation
Indices: 20788--20831 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
20778 CACTCTCTCA
20788 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
20810 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
20832 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:21115 original size:20 final size:20
Alignment explanation
Indices: 21090--21127 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
21080 CGATTCTCTC
21090 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
21110 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
21128 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:22467 original size:18 final size:18
Alignment explanation
Indices: 22446--22490 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
22436 TCCACTTCGG
*
22446 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
22464 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCCA
22482 GAGCCATCA
1 GAGCCATCA
22491 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:23017 original size:19 final size:20
Alignment explanation
Indices: 22963--23029 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
22953 TAGTTTACTT
* *
22963 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
22983 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
23003 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
23022 TCGCAACG
1 TCGCAACG
23030 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:23037 original size:14 final size:14
Alignment explanation
Indices: 23018--23075 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
23008 ATGCGAAATG
23018 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
23032 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
23048 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
23064 AAAATCGCAACG
1 AAAATCGCAACG
23076 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:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:23060 original size:32 final size:33
Alignment explanation
Indices: 23002--23092 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
22992 GGAAATGGCT
*
23002 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
23035 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
23067 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
23093 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.57
33 24 0.43
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:23086 original size:19 final size:19
Alignment explanation
Indices: 22963--23097 Score: 85
Period size: 19 Copynumber: 7.6 Consensus size: 19
22953 TAGTTTACTT
* **
22963 TCGCAACACGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
***
22983 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
23003 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
23022 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
23036 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
23054 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
23068 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
23087 TCGCAATGCGA
1 TCGCAACGCGA
23098 TTTGTGTTTC
Statistics
Matches: 92, Mismatches: 11, Indels: 25
0.72 0.09 0.20
Matches are distributed among these distances:
14 20 0.22
15 1 0.01
16 6 0.07
17 2 0.02
18 11 0.12
19 27 0.29
20 24 0.26
21 1 0.01
ACGTcount: A:0.43, C:0.24, G:0.21, T:0.13
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:23128 original size:14 final size:14
Alignment explanation
Indices: 23109--23166 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
23099 TTGTGTTTCG
23109 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
23123 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
23139 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
23155 CGTTGCGATTTT
1 CGTTGCGATTTT
23167 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:23143 original size:32 final size:33
Alignment explanation
Indices: 23104--23182 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
23094 GCGATTTGTG
23104 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
23136 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
23169 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
23183 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:23181 original size:19 final size:19
Alignment explanation
Indices: 23123--23240 Score: 95
Period size: 20 Copynumber: 6.4 Consensus size: 19
23113 GCGATTTTGT
23123 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
23141 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
23155 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
23174 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
**
23194 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
23213 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
23233 TGTTGCGA
1 CGTTGCGA
23241 AAGTAAACTA
Statistics
Matches: 81, Mismatches: 12, Indels: 12
0.77 0.11 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 11 0.14
19 26 0.32
20 29 0.36
ACGTcount: A:0.14, C:0.20, G:0.25, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:25131 original size:13 final size:13
Alignment explanation
Indices: 25084--25136 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
25074 TTGATTGTTT
25084 AATTGATTTGTAA
1 AATTGATTTGTAA
*
25097 AAGATGATTTGTAA
1 AA-TTGATTTGTAA
**
25111 ATATTGATTTGTTT
1 A-ATTGATTTGTAA
*
25125 AATTGATGTGTA
1 AATTGATTTGTA
25137 CATAATTTGT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
13 11 0.34
14 20 0.62
15 1 0.03
ACGTcount: A:0.34, C:0.00, G:0.19, T:0.47
Consensus pattern (13 bp):
AATTGATTTGTAA
Found at i:25248 original size:14 final size:15
Alignment explanation
Indices: 25229--25305 Score: 59
Period size: 14 Copynumber: 4.7 Consensus size: 15
25219 CGAAATGGCT
25229 ATCGCAA-CGAGAAA
1 ATCGCAAGCGAGAAA
*
25243 ATCGCAATGCGAAATGAA
1 ATCGCAA-GCGAGA--AA
25261 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCG--A-GAAA
25280 ATCGCAA-CGAGAAA
1 ATCGCAAGCGAGAAA
25294 ATCGCAATGCGA
1 ATCGCAA-GCGA
25306 TTTTCATTTC
Statistics
Matches: 52, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
14 18 0.35
15 1 0.02
16 7 0.13
17 2 0.04
18 13 0.25
19 9 0.17
20 1 0.02
21 1 0.02
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.13
Consensus pattern (15 bp):
ATCGCAAGCGAGAAA
Found at i:25261 original size:19 final size:19
Alignment explanation
Indices: 25239--25305 Score: 92
Period size: 18 Copynumber: 3.8 Consensus size: 19
25229 ATCGCAACGA
25239 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
25258 G-AAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
25276 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
25290 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
25306 TTTTCATTTC
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
14 11 0.25
15 1 0.02
16 2 0.05
17 2 0.05
18 18 0.41
19 10 0.23
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:25381 original size:20 final size:20
Alignment explanation
Indices: 25331--25381 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
25321 GCGATATTCT
* *
25331 CGTTGCGATAACCATTTTCG
1 CGTTGCGATAGCCATTTTCA
25351 CGTTGCGATAGCCATTTTCA
1 CGTTGCGATAGCCATTTTCA
25371 CGTTGCGATAG
1 CGTTGCGATAG
25382 TCAAATGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGCCATTTTCA
Found at i:25766 original size:14 final size:14
Alignment explanation
Indices: 25747--25782 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
25737 ATTGTTTAAT
25747 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
25761 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
25775 TGATTTGT
1 TGATTTGT
25783 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:25929 original size:19 final size:19
Alignment explanation
Indices: 25899--25966 Score: 76
Period size: 19 Copynumber: 3.8 Consensus size: 19
25889 ATCGCAACGA
*
25899 GAAAAGCGCAATGCGAAAAT
1 GAAAATCGCAATGCG-AAAT
25919 G-AAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
25937 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
25951 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
25967 TTTTCATTTC
Statistics
Matches: 43, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
14 11 0.26
15 1 0.02
16 2 0.05
17 2 0.05
18 5 0.12
19 21 0.49
20 1 0.02
ACGTcount: A:0.47, C:0.18, G:0.24, T:0.12
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:26042 original size:20 final size:20
Alignment explanation
Indices: 25992--26042 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
25982 GCGATATTCT
* *
25992 CGTTGCGATAACCATTTTCG
1 CGTTGCGATAGCCATTTTCA
26012 CGTTGCGATAGCCATTTTCA
1 CGTTGCGATAGCCATTTTCA
26032 CGTTGCGATAG
1 CGTTGCGATAG
26043 TCAAATGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGCCATTTTCA
Found at i:27155 original size:24 final size:24
Alignment explanation
Indices: 27104--27157 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
27094 GTATTCGAAA
* * **
27104 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACAAAC
*
27128 TTTGATATTGGTCAATACACAAAT
1 TTTGATATTGGTCAATACACAAAC
27152 TTTGAT
1 TTTGAT
27158 GATGTTTCAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACAAAC
Found at i:29666 original size:19 final size:19
Alignment explanation
Indices: 29644--29741 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
29634 GGAAATTACT
29644 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
29663 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
29677 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
29696 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
29710 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
29729 ATCGCAACGCGAA
1 ATCGCAATGCGAA
29742 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:0.44, C:0.19, G:0.24, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:29686 original size:33 final size:33
Alignment explanation
Indices: 29644--29737 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
29634 GGAAATTACT
29644 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
29677 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
29710 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
29738 CGAATTTAAT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:29759 original size:19 final size:20
Alignment explanation
Indices: 29737--29779 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
29727 AAATCGCAAC
29737 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
29756 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
29776 GCGA
1 GCGA
29780 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:29764 original size:14 final size:14
Alignment explanation
Indices: 29765--29798 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
29755 TGCGATTTTC
29765 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
29779 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
29793 ATTTTC
1 ATTTTC
29799 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:29939 original size:14 final size:14
Alignment explanation
Indices: 29920--29956 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
29910 CATCAATTAA
29920 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
29934 ACAAATCACCTTTT
1 ACAAATCAACTTTT
29948 ACAAATCAA
1 ACAAATCAA
29957 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:31381 original size:21 final size:21
Alignment explanation
Indices: 31315--31381 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
31305 GTGAATCGGG
*
31315 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
31335 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
31357 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
31378 CTCT
1 CTCT
31382 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:31400 original size:42 final size:41
Alignment explanation
Indices: 31315--31437 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
31305 GTGAATCGGG
* * * * *
31315 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
31357 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
31399 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
31438 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:33521 original size:33 final size:33
Alignment explanation
Indices: 33464--33562 Score: 135
Period size: 33 Copynumber: 3.0 Consensus size: 33
33454 ACGAGATAAT
* *
33464 GAGAATCACAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
33498 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
33531 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
33563 GCGAAATTAA
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
33 45 0.78
34 13 0.22
ACGTcount: A:0.40, C:0.26, G:0.22, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:33556 original size:19 final size:19
Alignment explanation
Indices: 33439--33604 Score: 109
Period size: 20 Copynumber: 9.1 Consensus size: 19
33429 TCTTTTGGTT
*
33439 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
* *
33458 GATAATGAGAATCACAACGC
1 GA-AATGAAAATCGCAACGC
**
33478 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
33496 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
33512 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
33530 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
33545 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
33565 GAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
33584 GAAACCAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
33603 GA
1 GA
33605 TTTTGGTTTC
Statistics
Matches: 116, Mismatches: 18, Indels: 26
0.73 0.11 0.16
Matches are distributed among these distances:
14 19 0.16
15 3 0.03
16 2 0.02
17 1 0.01
18 4 0.03
19 42 0.36
20 43 0.37
21 2 0.02
ACGTcount: A:0.43, C:0.23, G:0.21, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:34207 original size:20 final size:20
Alignment explanation
Indices: 34179--34230 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
34169 CGCTAAGTAA
* *
34179 ATCGCGTTGCGCAAGTCAGT
1 ATCGCGTTGCGAAAGTAAGT
*
34199 ATCGTGTTGCGAAAGTAAGT
1 ATCGCGTTGCGAAAGTAAGT
*
34219 ATCTCGTTGCGA
1 ATCGCGTTGCGA
34231 TTTTCAGATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.29
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTAAGT
Found at i:34533 original size:33 final size:33
Alignment explanation
Indices: 34491--34557 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
34481 TCTCGAGTCC
34491 TTGTTTTGATCATTTAAATCTTGAATATGAATA
1 TTGTTTTGATCATTTAAATCTTGAATATGAATA
*
34524 TTGTTTTGATCATTTAAATTTTGAATATGAATA
1 TTGTTTTGATCATTTAAATCTTGAATATGAATA
34557 T
1 T
34558 GAATTTTATA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.33, C:0.04, G:0.12, T:0.51
Consensus pattern (33 bp):
TTGTTTTGATCATTTAAATCTTGAATATGAATA
Found at i:38504 original size:14 final size:15
Alignment explanation
Indices: 38485--38518 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
38475 ACCATCCGAG
38485 AGATTAGA-GTTTTT
1 AGATTAGACGTTTTT
*
38499 AGATTATACGTTTTT
1 AGATTAGACGTTTTT
38514 AGATT
1 AGATT
38519 TCCAGGGTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.29, C:0.03, G:0.18, T:0.50
Consensus pattern (15 bp):
AGATTAGACGTTTTT
Found at i:40886 original size:13 final size:13
Alignment explanation
Indices: 40849--40888 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
40839 TCGATATTGA
40849 AAAATAAATA-TT
1 AAAATAAATATTT
*
40861 AAAATAATTTATTT
1 AAAATAA-ATATTT
40875 AAAATAAATATTT
1 AAAATAAATATTT
40888 A
1 A
40889 TTTATTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 7 0.29
13 8 0.33
14 9 0.38
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAATAAATATTT
Found at i:41447 original size:16 final size:16
Alignment explanation
Indices: 41426--41463 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
41416 ACCGTTGGCT
*
41426 GAGGCGGTTGGAGGCA
1 GAGGCGGCTGGAGGCA
41442 GAGGCGGCTGGAGGCA
1 GAGGCGGCTGGAGGCA
41458 GAGGCG
1 GAGGCG
41464 ACTAGGGTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.58, T:0.08
Consensus pattern (16 bp):
GAGGCGGCTGGAGGCA
Found at i:41589 original size:3 final size:3
Alignment explanation
Indices: 41581--41700 Score: 141
Period size: 3 Copynumber: 40.0 Consensus size: 3
41571 TATATATATT
* *
41581 TAA TAA TAA TAA TAA TAA TAA TAT TTA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * * *
41629 TAT TTA TAG TAA TAA TAA TAA TAA TAA TAT TTA TAG TAA TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
41677 TAA TAA TTA TAA TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
41701 ATCAATATGG
Statistics
Matches: 95, Mismatches: 22, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 95 1.00
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:41612 original size:27 final size:27
Alignment explanation
Indices: 41581--41700 Score: 186
Period size: 27 Copynumber: 4.3 Consensus size: 27
41571 TATATATATT
41581 TAATAATAATAATAATAATAATATTTA
1 TAATAATAATAATAATAATAATATTTA
41608 TAATAATAATAATAATAATAATATTTA
1 TAATAATAATAATAATAATAATATTTA
*
41635 TAGTAATAATAATAATAATAATATTTA
1 TAATAATAATAATAATAATAATATTTA
* *
41662 TAGTAATTATAATAATAATAATTATAATTA
1 TAATAATAATAATAATAATAA-TAT--TTA
41692 TAATAATAA
1 TAATAATAA
41701 ATCAATATGG
Statistics
Matches: 86, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
27 73 0.85
28 3 0.03
30 10 0.12
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (27 bp):
TAATAATAATAATAATAATAATATTTA
Found at i:42484 original size:16 final size:17
Alignment explanation
Indices: 42463--42499 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
42453 AATCAAGGTC
*
42463 TAAAAACATAA-AATTT
1 TAAAAACATAACAACTT
42479 TAAAAACATAACAACTT
1 TAAAAACATAACAACTT
42496 TAAA
1 TAAA
42500 CATTAAATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.62, C:0.11, G:0.00, T:0.27
Consensus pattern (17 bp):
TAAAAACATAACAACTT
Found at i:43323 original size:34 final size:33
Alignment explanation
Indices: 43243--43325 Score: 82
Period size: 33 Copynumber: 2.5 Consensus size: 33
43233 CTTAATTTTA
* *
43243 AAAATATATATTATTTTTTTATTAATTAAGTTAAT
1 AAAATATATA-TATTTTTTAATTAATAAAG-TAAT
43278 AATAA-AT-TATATTTTTTAAGTTAATAAAAG-AAT
1 AA-AATATATATATTTTTTAA-TTAAT-AAAGTAAT
43311 AAAATATATATATTT
1 AAAATATATATATTT
43326 GAGGTTAAGG
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
32 2 0.05
33 16 0.39
34 14 0.34
35 7 0.17
36 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (33 bp):
AAAATATATATATTTTTTAATTAATAAAGTAAT
Found at i:43363 original size:23 final size:25
Alignment explanation
Indices: 43314--43364 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
43304 AAAGAATAAA
* *
43314 ATATATATATTTGAGGTTAAGGTAT
1 ATATAGATATTTGAAGTTAAGGTAT
*
43339 ATATAGATATTTGAAGTTAAGATAT
1 ATATAGATATTTGAAGTTAAGGTAT
43364 A
1 A
43365 ACAAATATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (25 bp):
ATATAGATATTTGAAGTTAAGGTAT
Found at i:43400 original size:25 final size:23
Alignment explanation
Indices: 43362--43435 Score: 78
Period size: 24 Copynumber: 3.0 Consensus size: 23
43352 AAGTTAAGAT
43362 ATAACAAATATATTTTTAAAGTTA
1 ATAA-AAATATATTTTTAAAGTTA
*
43386 ATAAAAGTATATATTTTTTAAGTTAA
1 ATAAAA--ATATATTTTTAAAGTT-A
*
43412 GATAAAAA-ATATTTTTAAAATTA
1 -ATAAAAATATATTTTTAAAGTTA
43435 A
1 A
43436 AATCAAAATA
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
22 1 0.02
23 3 0.07
24 16 0.37
25 16 0.37
26 1 0.02
27 6 0.14
ACGTcount: A:0.51, C:0.01, G:0.05, T:0.42
Consensus pattern (23 bp):
ATAAAAATATATTTTTAAAGTTA
Found at i:43501 original size:32 final size:30
Alignment explanation
Indices: 43440--43501 Score: 72
Period size: 32 Copynumber: 2.0 Consensus size: 30
43430 AATTAAAATC
43440 AAAATAAAAATATATTTAATAAATTGGATAG
1 AAAATAAAAATATATTT-ATAAATTGGATAG
*
43471 AAAATAAATTATATATTT-TAAACTTCGGATA
1 AAAATAAA-AATATATTTATAAA-TT-GGATA
43502 TGAATTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
30 4 0.15
31 10 0.37
32 13 0.48
ACGTcount: A:0.53, C:0.03, G:0.08, T:0.35
Consensus pattern (30 bp):
AAAATAAAAATATATTTATAAATTGGATAG
Found at i:45074 original size:2 final size:2
Alignment explanation
Indices: 45069--45112 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
45059 TATGAGTAAG
45069 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
45111 TC
1 TC
45113 CTAGAATTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:49851 original size:152 final size:153
Alignment explanation
Indices: 49680--49990 Score: 597
Period size: 155 Copynumber: 2.0 Consensus size: 153
49670 AAAACTGCTA
49680 AAATCCCACACATTTTTATTACAGTAATCAACACTCAAAAAGACTCTCTTTTCT-GAAGAAGAAG
1 AAATCCCACACATTTTTATTACAGTAATCAACACTCAAAAAGACTCTCTTTTCTAGAAGAAGAAG
49744 AAGAAAAGCCGCTAAGAAAGCGGTAACTATTACAGGGAAACTAAAACAGAGGGAAAACAGGGGAA
66 AAGAAAAGCCGCTAAGAAAGCGGTAACTATTACAGGGAAACTAAAACAGAGGGAAAACAGGGGAA
49809 GGTAACACGTTTGCTGTGTTTTG
131 GGTAACACGTTTGCTGTGTTTTG
49832 AAATCCCACACATTTTTATTACAGTAATCAACACTCAAAAAGACTCTCTTTTCTGAAGAAGAAGA
1 AAATCCCACACATTTTTATTACAGTAATCAACACTCAAAAAGACTCTCTTTTCT--AGAAGAAGA
49897 AGAAGAAAAGCCGCTAAGAAAGCGGTAACTATTACAGGGAAACTAAAACAGAGGGAAAACAGGGG
64 AGAAGAAAAGCCGCTAAGAAAGCGGTAACTATTACAGGGAAACTAAAACAGAGGGAAAACAGGGG
49962 AAGGTAACACGTTTGCTGTGTTTTG
129 AAGGTAACACGTTTGCTGTGTTTTG
49987 AAAT
1 AAAT
49991 ACCGTCGAAG
Statistics
Matches: 156, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
152 54 0.35
155 102 0.65
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (153 bp):
AAATCCCACACATTTTTATTACAGTAATCAACACTCAAAAAGACTCTCTTTTCTAGAAGAAGAAG
AAGAAAAGCCGCTAAGAAAGCGGTAACTATTACAGGGAAACTAAAACAGAGGGAAAACAGGGGAA
GGTAACACGTTTGCTGTGTTTTG
Found at i:51475 original size:19 final size:19
Alignment explanation
Indices: 51451--51497 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
51441 AGAGTTATTT
51451 AAAATCAAAAAACCAAAGG
1 AAAATCAAAAAACCAAAGG
51470 AAAATCAAAAAACCAAAGG
1 AAAATCAAAAAACCAAAGG
51489 AAAATCAAA
1 AAAATCAAA
51498 GATGTAGTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.70, C:0.15, G:0.09, T:0.06
Consensus pattern (19 bp):
AAAATCAAAAAACCAAAGG
Found at i:55171 original size:20 final size:21
Alignment explanation
Indices: 55146--55187 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
55136 ATGGTAAAAA
*
55146 TACCTAAAACA-TATTATTTT
1 TACCTAAAACATTAATATTTT
55166 TACCTAAAACATTAATATTTT
1 TACCTAAAACATTAATATTTT
55187 T
1 T
55188 TAACAATTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.40, C:0.14, G:0.00, T:0.45
Consensus pattern (21 bp):
TACCTAAAACATTAATATTTT
Found at i:57203 original size:28 final size:29
Alignment explanation
Indices: 57138--57203 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 29
57128 TGATTTTAAG
57138 TTAGGGA-G-ACTTAAACTTATAAAAATT
1 TTAGGGACGAACTTAAACTTATAAAAATT
* * *
57165 TCAGGGGCGAACTTGAACTTAT-AAAATT
1 TTAGGGACGAACTTAAACTTATAAAAATT
57193 TTAGGGACGAA
1 TTAGGGACGAA
57204 AACATATTTC
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
27 5 0.16
28 16 0.50
29 11 0.34
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.29
Consensus pattern (29 bp):
TTAGGGACGAACTTAAACTTATAAAAATT
Found at i:59280 original size:38 final size:37
Alignment explanation
Indices: 59230--59311 Score: 148
Period size: 38 Copynumber: 2.2 Consensus size: 37
59220 GAAGAGTTTG
59230 ATTAA-CTCTGGCATGAATTGGTTGAATAAGCATCGA
1 ATTAATCTCTGGCATGAATTGGTTGAATAAGCATCGA
59266 ATTAATCTCTTGGCATGAATTGGTTGAATAAGCATCGA
1 ATTAATCTC-TGGCATGAATTGGTTGAATAAGCATCGA
59304 ATTAATCT
1 ATTAATCT
59312 AGATTATGAC
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
36 5 0.11
37 3 0.07
38 36 0.82
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.34
Consensus pattern (37 bp):
ATTAATCTCTGGCATGAATTGGTTGAATAAGCATCGA
Done.