Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000589.1 Hibiscus syriacus cultivar Beakdansim tig00001145_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: 60900
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:1666 original size:78 final size:78
Alignment explanation
Indices: 1535--1690 Score: 294
Period size: 78 Copynumber: 2.0 Consensus size: 78
1525 CCGGCAAGGG
*
1535 GCCTTTCCTGCTTATTTTAGCTGCTGGGTCTGCAACACTTGGTGTCTCGGTGGTCCTTCTCCCCT
1 GCCTTTCCTGCTTATTTTAGCTGCTGGGTCTGCAACACTTGGTGTCTCAGTGGTCCTTCTCCCCT
1600 CTGCAACAAAGTC
66 CTGCAACAAAGTC
1613 GCCTTTCCTGCTTATTTTAGCTGCTGGGTCTGCAACACTTGGTGTCTCAGTGGTCCTTCTCCCCT
1 GCCTTTCCTGCTTATTTTAGCTGCTGGGTCTGCAACACTTGGTGTCTCAGTGGTCCTTCTCCCCT
*
1678 CTGCAAGAAAGTC
66 CTGCAACAAAGTC
1691 AGGTCTTCCT
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 76 1.00
ACGTcount: A:0.13, C:0.30, G:0.22, T:0.35
Consensus pattern (78 bp):
GCCTTTCCTGCTTATTTTAGCTGCTGGGTCTGCAACACTTGGTGTCTCAGTGGTCCTTCTCCCCT
CTGCAACAAAGTC
Found at i:3557 original size:14 final size:16
Alignment explanation
Indices: 3533--3565 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
3523 CACGTGTCTT
3533 ATAATAAATATT-TAA
1 ATAATAAATATTATAA
3548 ATAA-AAATATTATAA
1 ATAATAAATATTATAA
3563 ATA
1 ATA
3566 GTTATCATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
ATAATAAATATTATAA
Found at i:5728 original size:16 final size:16
Alignment explanation
Indices: 5704--5752 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 16
5694 AATATTTTAA
5704 TTTTAATATAATATTC
1 TTTTAATATAATATTC
* *
5720 TTTTTATATATATAATC
1 TTTTAATATA-ATATTC
5737 TTTTAATTATAATATT
1 TTTTAA-TATAATATT
5753 TATTATGTCC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
16 9 0.33
17 14 0.52
18 4 0.15
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (16 bp):
TTTTAATATAATATTC
Found at i:6199 original size:15 final size:15
Alignment explanation
Indices: 6175--6217 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
6165 ACATCATTAA
*
6175 ATTAATTTATAAAAC
1 ATTAAATTATAAAAC
*
6190 ATTAAATTATAAAAT
1 ATTAAATTATAAAAC
*
6205 ACTAAATGTATAA
1 ATTAAAT-TATAA
6218 TTACAAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 19 0.79
16 5 0.21
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (15 bp):
ATTAAATTATAAAAC
Found at i:7191 original size:27 final size:27
Alignment explanation
Indices: 7161--7212 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
7151 CATATATAAT
7161 TTATAATATAATT-AATAATAAATAACC
1 TTATAAT-TAATTAAATAATAAATAACC
* *
7188 TTATAATTACTTAAATATTAAATAA
1 TTATAATTAATTAAATAATAAATAA
7213 TTGAATAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (27 bp):
TTATAATTAATTAAATAATAAATAACC
Found at i:9511 original size:18 final size:19
Alignment explanation
Indices: 9475--9513 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
9465 TTTAGATGTG
9475 TTTGATACATGATATAATTA
1 TTTGATACATGA-ATAATTA
9495 TTTGATACATG-ATAATTA
1 TTTGATACATGAATAATTA
9513 T
1 T
9514 ATAAATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.42
20 11 0.58
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.46
Consensus pattern (19 bp):
TTTGATACATGAATAATTA
Found at i:11855 original size:17 final size:15
Alignment explanation
Indices: 11819--11859 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 15
11809 TTGTTAAAAT
*
11819 TGAATGGTTTAGCAC
1 TGAATGATTTAGCAC
11834 TGAATGATTTAGCAGTC
1 TGAATGATTTAGCA--C
11851 TGAATGATT
1 TGAATGATT
11860 AAGAGGCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.57
17 10 0.43
ACGTcount: A:0.29, C:0.10, G:0.24, T:0.37
Consensus pattern (15 bp):
TGAATGATTTAGCAC
Found at i:13820 original size:42 final size:43
Alignment explanation
Indices: 13673--14074 Score: 464
Period size: 42 Copynumber: 9.7 Consensus size: 43
13663 AATACTATAC
* * *
13673 TTTAGTGGCGTTTGT-ATA-AAAACGCCGCTAAAGA-ATCGTA-A
1 TTTAGTGGCGTTT-TAATACCAAACGCCGCTATAGACA-CGTACT
* * *
13714 TGTAGTGGCGTTTTTATA-CAAACGCCGCTATAAACTA-GTA-T
1 TTTAGTGGCGTTTTAATACCAAACGCCGCTATAGAC-ACGTACT
* *
13755 TTTAGTGGCGTTTTTATA-CAAACGCTGCTATAGACACGTACT
1 TTTAGTGGCGTTTTAATACCAAACGCCGCTATAGACACGTACT
* * *
13797 TTTA-TGGCGTTTTAATACCAAACGACGCTATAGACTCATAC-
1 TTTAGTGGCGTTTTAATACCAAACGCCGCTATAGACACGTACT
*
13838 TTTAGTGGCATTTT--TACACAAACGCCGCTATAGACACGTACT
1 TTTAGTGGCGTTTTAATAC-CAAACGCCGCTATAGACACGTACT
*
13880 TTT-GTGGCATTTTAATACCAAACGCCGCTATAGACACGTACT
1 TTTAGTGGCGTTTTAATACCAAACGCCGCTATAGACACGTACT
**
13922 TTT-GTGGCGTTTTAATACCAAACGCCGCTATAGATTCGTAC-
1 TTTAGTGGCGTTTTAATACCAAACGCCGCTATAGACACGTACT
13963 TTTAGTGGCGTTTT--TACACAAACGCCGCTATAGACACGTACT
1 TTTAGTGGCGTTTTAATAC-CAAACGCCGCTATAGACACGTACT
* * *
14005 TTT-GTGGCATTTTAATAACAAACGCCGCTATAGACTCGTAC-
1 TTTAGTGGCGTTTTAATACCAAACGCCGCTATAGACACGTACT
14046 TTTAGTGGCGTTTTAATACCAAACGCCGC
1 TTTAGTGGCGTTTTAATACCAAACGCCGC
14075 AATTGTCATA
Statistics
Matches: 317, Mismatches: 27, Indels: 33
0.84 0.07 0.09
Matches are distributed among these distances:
40 8 0.03
41 148 0.47
42 155 0.49
43 6 0.02
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.32
Consensus pattern (43 bp):
TTTAGTGGCGTTTTAATACCAAACGCCGCTATAGACACGTACT
Found at i:13852 original size:83 final size:83
Alignment explanation
Indices: 13669--14074 Score: 484
Period size: 83 Copynumber: 4.9 Consensus size: 83
13659 GCAAAATACT
* * * * * *
13669 ATACTTTAGTGGCGTTTGTATAAAAACGCCGCTAAAGA-ATCGTAATGTAGTGGCGTTTTTATA-
1 ATACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACA-CGTACTTTAGTGGCGTTTTAATAC
13732 CAAACGCCGCTATA-A-AC
65 CAAACGCCGCTATAGACAC
* *
13749 TAGTATTTTAGTGGCGTTTTTATACAAACGCTGCTATAGACACGTACTTTTA-TGGCGTTTTAAT
1 -A-TACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACACGTAC-TTTAGTGGCGTTTTAAT
* *
13813 ACCAAACGACGCTATAGACTC
63 ACCAAACGCCGCTATAGACAC
* * * *
13834 ATACTTTAGTGGCATTTTTACACAAACGCCGCTATAGACACGTACTTTTGTGGCATTTTAATACC
1 ATACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACACGTACTTTAGTGGCGTTTTAATACC
13899 AAACGCCGCTATAGACAC
66 AAACGCCGCTATAGACAC
* * * **
13917 GTACTTTTGTGGCGTTTTAATACCAAACGCCGCTATAGATTCGTACTTTAGTGGCGTTTT--TAC
1 ATACTTTAGTGGCGTTTTTATA-CAAACGCCGCTATAGACACGTACTTTAGTGGCGTTTTAATAC
13980 ACAAACGCCGCTATAGACAC
65 -CAAACGCCGCTATAGACAC
* * * * *
14000 GTACTTTTGTGGCATTTTAATAACAAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTAATAC
1 ATACTTTAGTGGCGTTTTTAT-ACAAACGCCGCTATAGACACGTACTTTAGTGGCGTTTTAATAC
14065 CAAACGCCGC
65 CAAACGCCGC
14075 AATTGTCATA
Statistics
Matches: 284, Mismatches: 29, Indels: 21
0.85 0.09 0.06
Matches are distributed among these distances:
81 1 0.00
82 54 0.19
83 179 0.63
84 46 0.16
85 4 0.01
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (83 bp):
ATACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACACGTACTTTAGTGGCGTTTTAATACC
AAACGCCGCTATAGACAC
Found at i:14071 original size:125 final size:125
Alignment explanation
Indices: 13670--14074 Score: 579
Period size: 125 Copynumber: 3.3 Consensus size: 125
13660 CAAAATACTA
* * * * *
13670 TACTTTAGTGGCGTTTGT-ATA-AAAACGCCGCTAAAGAATCGTAATGTAGTGGCGTTTTTATAC
1 TACTTTAGTGGCGTTT-TAATACCAAACGCCGCTATAGAATCGTACTTTAGTGGCGTTTTTACAC
* * * *
13733 AAACGCCGCTATAAACTA-GTA-TTTTAGTGGCGTTTTTAT-ACAAACGCTGCTATAGACACG
65 AAACGCCGCTATAGAC-ACGTACTTTT-GTGGCATTTTAATAACAAACGCCGCTATAGACACG
* * * *
13793 TACTTTTA-TGGCGTTTTAATACCAAACGACGCTATAGACTCATACTTTAGTGGCATTTTTACAC
1 TAC-TTTAGTGGCGTTTTAATACCAAACGCCGCTATAGAATCGTACTTTAGTGGCGTTTTTACAC
*
13857 AAACGCCGCTATAGACACGTACTTTTGTGGCATTTTAATACCAAACGCCGCTATAGACACG
65 AAACGCCGCTATAGACACGTACTTTTGTGGCATTTTAATAACAAACGCCGCTATAGACACG
* *
13918 TACTTTTGTGGCGTTTTAATACCAAACGCCGCTATAGATTCGTACTTTAGTGGCGTTTTTACACA
1 TACTTTAGTGGCGTTTTAATACCAAACGCCGCTATAGAATCGTACTTTAGTGGCGTTTTTACACA
*
13983 AACGCCGCTATAGACACGTACTTTTGTGGCATTTTAATAACAAACGCCGCTATAGACTCG
66 AACGCCGCTATAGACACGTACTTTTGTGGCATTTTAATAACAAACGCCGCTATAGACACG
14043 TACTTTAGTGGCGTTTTAATACCAAACGCCGC
1 TACTTTAGTGGCGTTTTAATACCAAACGCCGC
14075 AATTGTCATA
Statistics
Matches: 253, Mismatches: 22, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
122 1 0.00
123 15 0.06
124 69 0.27
125 168 0.66
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.32
Consensus pattern (125 bp):
TACTTTAGTGGCGTTTTAATACCAAACGCCGCTATAGAATCGTACTTTAGTGGCGTTTTTACACA
AACGCCGCTATAGACACGTACTTTTGTGGCATTTTAATAACAAACGCCGCTATAGACACG
Found at i:16251 original size:21 final size:21
Alignment explanation
Indices: 16227--16285 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
16217 TGATTTATTA
**
16227 TTATGGATTTCATTTTTCTTG
1 TTATGGATTTCAAGTTTCTTG
* *
16248 TTATGGATTTTAAGTTTGTTG
1 TTATGGATTTCAAGTTTCTTG
*
16269 TTATGGATGTCAAGTTT
1 TTATGGATTTCAAGTTT
16286 ATTGGAAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.19, C:0.05, G:0.20, T:0.56
Consensus pattern (21 bp):
TTATGGATTTCAAGTTTCTTG
Found at i:16485 original size:43 final size:42
Alignment explanation
Indices: 16438--16662 Score: 290
Period size: 43 Copynumber: 5.3 Consensus size: 42
16428 ACCAGATCTT
* *
16438 TTGCGGTGTTTGTGGGAAAAACGCCGCTAAATATCAAGACCTA
1 TTGCGGCGTTTGT-GGAAAAACGCCGCTAAATATCAACACCTA
16481 TTGCGGCGTTTGTGGACAAAACGCCGCTAAATATCAACACCTA
1 TTGCGGCGTTTGTGGA-AAAACGCCGCTAAATATCAACACCTA
*
16524 TTGCGGCGTTTGTGGAAAAAACGCCGCTAAATCTCAACACCTA
1 TTGCGGCGTTTGTGG-AAAAACGCCGCTAAATATCAACACCTA
* * *
16567 TTGCGGCATTTGTTGGAAAAA-GCCACCAAATATCAACACCTA
1 TTGCGGCGTTTG-TGGAAAAACGCCGCTAAATATCAACACCTA
** * ***
16609 TTGCGGCGTTTGTCCAACAAACGCCGCTATATATCGTTACCTA
1 TTGCGGCGTTTGTGGAA-AAACGCCGCTAAATATCAACACCTA
16652 TTGCGGCGTTT
1 TTGCGGCGTTT
16663 TTGTTACCAA
Statistics
Matches: 161, Mismatches: 16, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
41 3 0.02
42 35 0.22
43 119 0.74
44 4 0.02
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.26
Consensus pattern (42 bp):
TTGCGGCGTTTGTGGAAAAACGCCGCTAAATATCAACACCTA
Found at i:16617 original size:85 final size:86
Alignment explanation
Indices: 16438--16658 Score: 293
Period size: 85 Copynumber: 2.6 Consensus size: 86
16428 ACCAGATCTT
* * * *
16438 TTGCGGTGTTTGTGGGAAAAACGCCGCTAAATATCAAGACCTATTGCGGCGTTTGTGGACAAAAC
1 TTGCGGCGTTTGTGGAAAAAACGCCGCTAAATATCAACACCTATTGCGGCATTTGTGGACAAAAC
* *
16503 GCCGCTAAATATCAACACCTA
66 GCCACCAAATATCAACACCTA
*
16524 TTGCGGCGTTTGTGGAAAAAACGCCGCTAAATCTCAACACCTATTGCGGCATTTGTTGGA-AAAA
1 TTGCGGCGTTTGTGGAAAAAACGCCGCTAAATATCAACACCTATTGCGGCATTTG-TGGACAAAA
16588 -GCCACCAAATATCAACACCTA
65 CGCCACCAAATATCAACACCTA
** * * ***
16609 TTGCGGCGTTTGTCCAACAAACGCCGCTATATATCGTTACCTATTGCGGC
1 TTGCGGCGTTTGTGGAAAAAACGCCGCTAAATATCAACACCTATTGCGGC
16659 GTTTTTGTTA
Statistics
Matches: 119, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
85 61 0.51
86 54 0.45
87 4 0.03
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.25
Consensus pattern (86 bp):
TTGCGGCGTTTGTGGAAAAAACGCCGCTAAATATCAACACCTATTGCGGCATTTGTGGACAAAAC
GCCACCAAATATCAACACCTA
Found at i:17478 original size:18 final size:18
Alignment explanation
Indices: 17457--17496 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
17447 CCGAAGGAGG
17457 TGAACGACAGAAGAAGGA
1 TGAACGACAGAAGAAGGA
* *
17475 TGAACGACCGAAGGAGGA
1 TGAACGACAGAAGAAGGA
17493 TGAA
1 TGAA
17497 TCGATTGCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.12, G:0.35, T:0.07
Consensus pattern (18 bp):
TGAACGACAGAAGAAGGA
Found at i:22493 original size:60 final size:60
Alignment explanation
Indices: 22424--22538 Score: 176
Period size: 60 Copynumber: 1.9 Consensus size: 60
22414 GACGATATAC
** *
22424 CAAAATAAAACAAAAAATAAACATTAGATATGATTTTTCAACAAATGAAAGTTTAGGTAT
1 CAAAATAAAACAAAAAATAAACATTAGATATGATTTTAAAACAAATAAAAGTTTAGGTAT
* * *
22484 CAAAATAAAATAAAAAATAAATATTAGATATGATTTTAAAATAAATAAAAGTTTA
1 CAAAATAAAACAAAAAATAAACATTAGATATGATTTTAAAACAAATAAAAGTTTA
22539 TGTAGTAAAC
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 49 1.00
ACGTcount: A:0.57, C:0.05, G:0.08, T:0.30
Consensus pattern (60 bp):
CAAAATAAAACAAAAAATAAACATTAGATATGATTTTAAAACAAATAAAAGTTTAGGTAT
Found at i:40631 original size:83 final size:83
Alignment explanation
Indices: 40492--40678 Score: 338
Period size: 83 Copynumber: 2.3 Consensus size: 83
40482 GAGATTTTGA
40492 AGATTGTATTAGGGTTGAAATGTTCCAATAAGATAGGTTTCTTTTGAGTATAAACTCTAACAATT
1 AGATTGTATTAGGGTTGAAATGTTCCAATAAGATAGGTTTCTTTTGAGTATAAACTCTAACAATT
40557 ATAAGAGAGAATACAAGG
66 ATAAGAGAGAATACAAGG
* * *
40575 AGATTGTATCAGGGTTGAAATGTTCTAATAAGATAGGTTTCTTTTGAGTATAAACTCTAACAGTT
1 AGATTGTATTAGGGTTGAAATGTTCCAATAAGATAGGTTTCTTTTGAGTATAAACTCTAACAATT
40640 ATAAGAGAGAATACAAGG
66 ATAAGAGAGAATACAAGG
*
40658 AGATTGTCTTAGGGTTGAAAT
1 AGATTGTATTAGGGTTGAAAT
40679 CATTTAATGA
Statistics
Matches: 99, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
83 99 1.00
ACGTcount: A:0.37, C:0.08, G:0.22, T:0.33
Consensus pattern (83 bp):
AGATTGTATTAGGGTTGAAATGTTCCAATAAGATAGGTTTCTTTTGAGTATAAACTCTAACAATT
ATAAGAGAGAATACAAGG
Found at i:40806 original size:29 final size:29
Alignment explanation
Indices: 40768--40904 Score: 113
Period size: 29 Copynumber: 4.7 Consensus size: 29
40758 TAAGTTAAGA
40768 TAATAATAAGAATAAAATATATTTTTAATT
1 TAAT-ATAAGAATAAAATATATTTTTAATT
40798 TAATATAAGAATAAAATATATTTTT-A--
1 TAATATAAGAATAAAATATATTTTTAATT
* *
40824 TAAGAATAA-AATATTATATATATTTTTAATT
1 TAA-TATAAGAATA--AAATATATTTTTAATT
* * *
40855 TAAAATAAGAGTGAAATATATATTCTTATATT
1 TAATATAAGAAT-AAA-ATATATTTTTA-ATT
* *
40887 AAAT-TAATAATAAAATAT
1 TAATATAAGAATAAAATAT
40905 TTAAATATAT
Statistics
Matches: 88, Mismatches: 9, Indels: 21
0.75 0.08 0.18
Matches are distributed among these distances:
26 7 0.08
27 4 0.05
28 12 0.14
29 26 0.30
30 13 0.15
31 20 0.23
32 6 0.07
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.42
Consensus pattern (29 bp):
TAATATAAGAATAAAATATATTTTTAATT
Found at i:41033 original size:29 final size:29
Alignment explanation
Indices: 40996--41078 Score: 98
Period size: 29 Copynumber: 2.8 Consensus size: 29
40986 AATAAAAACA
40996 AAATATATTTAATAAATTAAGACAAAAATT
1 AAATATATTTAATAAATTAAGACAAAAA-T
* *
41026 AAA-ATATTTAATAAGTTAAAACAAAAAT
1 AAATATATTTAATAAATTAAGACAAAAAT
*
41054 AAATATAATTTTAA-AATTTAAGACA
1 AAATAT-A-TTTAATAAATTAAGACA
41079 TATAACATAT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
28 4 0.09
29 24 0.52
30 13 0.28
31 5 0.11
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.33
Consensus pattern (29 bp):
AAATATATTTAATAAATTAAGACAAAAAT
Found at i:41768 original size:22 final size:21
Alignment explanation
Indices: 41725--41778 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
41715 CCCTTTATAT
*
41725 ATTATTTTT-TTAATTAAATA
1 ATTATTTTTATTAATAAAATA
41745 ATTATTTTTATTGAATAAAATA
1 ATTATTTTTATT-AATAAAATA
*
41767 A-TATTCTTATTA
1 ATTATTTTTATTA
41779 TTTTGGGTCG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 10 0.33
21 11 0.37
22 9 0.30
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (21 bp):
ATTATTTTTATTAATAAAATA
Found at i:45414 original size:21 final size:20
Alignment explanation
Indices: 45388--45437 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
45378 AATTTTTTAA
*
45388 TTTTTTTGTATTTATGATACG
1 TTTTTTTAT-TTTATGATACG
*
45409 TTTTTTTATTTTTTGATACG
1 TTTTTTTATTTTATGATACG
45429 TTTTTTTAT
1 TTTTTTTAT
45438 ATGTTTTCGA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 19 0.70
21 8 0.30
ACGTcount: A:0.16, C:0.04, G:0.10, T:0.70
Consensus pattern (20 bp):
TTTTTTTATTTTATGATACG
Found at i:45434 original size:22 final size:22
Alignment explanation
Indices: 45388--45444 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 22
45378 AATTTTTTAA
* *
45388 TTTTTTTGTA-TTTATGATACG
1 TTTTTTTATATTTTTTGATACG
45409 -TTTTTT-TATTTTTTGATACG
1 TTTTTTTATATTTTTTGATACG
*
45429 TTTTTTTATATGTTTT
1 TTTTTTTATATTTTTT
45445 CGATTATCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 2 0.06
20 16 0.52
21 6 0.19
22 7 0.23
ACGTcount: A:0.16, C:0.04, G:0.11, T:0.70
Consensus pattern (22 bp):
TTTTTTTATATTTTTTGATACG
Found at i:48584 original size:189 final size:188
Alignment explanation
Indices: 48265--48633 Score: 639
Period size: 189 Copynumber: 2.0 Consensus size: 188
48255 GGGTTATCCT
48265 AAGTAAAGACATCATTTCATCTTTCATGACTGGGACTTTACTTCCATAGGGCTACTTTCCAAATT
1 AAGTAAAGACATCATTTCATCTTTCATGACTGGGACTTTACTTCCATAGGGCTACTTTCCAAATT
* * * *
48330 GCACTTATCATTTTTCATTGGACTTGAAGATCTCAAAAGCATTTCAGTGTGCCACTTGGGAGGTG
66 GCACCTATCATTTTTCATTGGACTTGAAGATCTCAAAAGCAGTTCAGTGTGCAACTCGGGAGGTG
* *
48395 ATGCTTTGTCCGGAATAAAGGACTCATTTCTTGTTTCCTGCTCTAGAAGCTTTACACC
131 ATGCTTTGTCCGGAATAAAGGACTCAATTCTTGTTTCCTGCTCTAAAAGCTTTACACC
* *
48453 AAGTAAAGACATCATTTCATCTTTCATTACTGGGACTTTACTTCCATAGGGGCTACTTTCCATAT
1 AAGTAAAGACATCATTTCATCTTTCATGACTGGGACTTTACTTCCATA-GGGCTACTTTCCAAAT
*
48518 TGCCCCTATCATTTTTCATTGGACTTGAAGATCTCAAAAGCAGTTCAGTGTGCAACTCGGGAGGT
65 TGCACCTATCATTTTTCATTGGACTTGAAGATCTCAAAAGCAGTTCAGTGTGCAACTCGGGAGGT
*
48583 GATGCTTTGTCCGGAATAAAGGGCTCAATTCTTGTTTCCTGCTCTAAAAGC
130 GATGCTTTGTCCGGAATAAAGGACTCAATTCTTGTTTCCTGCTCTAAAAGC
48634 CTGCAAAATC
Statistics
Matches: 170, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
188 47 0.28
189 123 0.72
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.34
Consensus pattern (188 bp):
AAGTAAAGACATCATTTCATCTTTCATGACTGGGACTTTACTTCCATAGGGCTACTTTCCAAATT
GCACCTATCATTTTTCATTGGACTTGAAGATCTCAAAAGCAGTTCAGTGTGCAACTCGGGAGGTG
ATGCTTTGTCCGGAATAAAGGACTCAATTCTTGTTTCCTGCTCTAAAAGCTTTACACC
Found at i:60405 original size:24 final size:24
Alignment explanation
Indices: 60378--60423 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
60368 TGTTAGGAGG
60378 ATAAA-TCACTAAAATTGTAAGGGA
1 ATAAACTCA-TAAAATTGTAAGGGA
* *
60402 ATAAACTTATAAAATTTTAAGG
1 ATAAACTCATAAAATTGTAAGG
60424 ATGAAAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 17 0.89
25 2 0.11
ACGTcount: A:0.50, C:0.07, G:0.13, T:0.30
Consensus pattern (24 bp):
ATAAACTCATAAAATTGTAAGGGA
Done.