Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000329.1 Hibiscus syriacus cultivar Beakdansim tig00000612_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: 110420
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:1816 original size:13 final size:13
Alignment explanation
Indices: 1784--1842 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
1774 AATACATATT
*
1784 ATGCATACTGTTA
1 ATGCATATTGTTA
* * *
1797 TTACATATTGCTA
1 ATGCATATTGTTA
*
1810 ATGCATAATGTTA
1 ATGCATATTGTTA
* *
1823 TTGCATATTGTTC
1 ATGCATATTGTTA
1836 ATGCATA
1 ATGCATA
1843 CAGTTGTTGG
Statistics
Matches: 34, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
13 34 1.00
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.42
Consensus pattern (13 bp):
ATGCATATTGTTA
Found at i:1821 original size:26 final size:26
Alignment explanation
Indices: 1784--1842 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 26
1774 AATACATATT
*
1784 ATGCATACTGTTATTACATATTGCTA
1 ATGCATAATGTTATTACATATTGCTA
* * *
1810 ATGCATAATGTTATTGCATATTGTTC
1 ATGCATAATGTTATTACATATTGCTA
1836 ATGCATA
1 ATGCATA
1843 CAGTTGTTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.42
Consensus pattern (26 bp):
ATGCATAATGTTATTACATATTGCTA
Found at i:3214 original size:26 final size:26
Alignment explanation
Indices: 3178--3227 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
3168 ACATACATTA
3178 CATCTTCAATTCTAACACAAGTCTTG
1 CATCTTCAATTCTAACACAAGTCTTG
*
3204 CATCTTCAATTCTAACACACGTCT
1 CATCTTCAATTCTAACACAAGTCT
3228 ATTAACCCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.30, C:0.30, G:0.06, T:0.34
Consensus pattern (26 bp):
CATCTTCAATTCTAACACAAGTCTTG
Found at i:3649 original size:17 final size:17
Alignment explanation
Indices: 3627--3659 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3617 GAAGCATTCT
3627 TCTTC-TTCTTCCTTCAC
1 TCTTCTTTCTT-CTTCAC
3644 TCTTCTTTCTTCTTCA
1 TCTTCTTTCTTCTTCA
3660 TTTTCCAGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.06, C:0.36, G:0.00, T:0.58
Consensus pattern (17 bp):
TCTTCTTTCTTCTTCAC
Found at i:10814 original size:33 final size:32
Alignment explanation
Indices: 10777--10844 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 32
10767 ATCGTCCTCC
* *
10777 GTTCTGGTTTGTGGAATATGGTTTACTAGCAAG
1 GTTCTGGTTTGTAGAATATGGTATA-TAGCAAG
*
10810 GTTCTGGTTTGTAGAATATGGTATATAGTAAG
1 GTTCTGGTTTGTAGAATATGGTATATAGCAAG
10842 GTT
1 GTT
10845 GCATCCTATG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 9 0.28
33 23 0.72
ACGTcount: A:0.24, C:0.06, G:0.29, T:0.41
Consensus pattern (32 bp):
GTTCTGGTTTGTAGAATATGGTATATAGCAAG
Found at i:20523 original size:60 final size:58
Alignment explanation
Indices: 20402--20562 Score: 170
Period size: 60 Copynumber: 2.8 Consensus size: 58
20392 TATAACCTTC
* * *
20402 CTTT-TAAATTGGTCCTTAAACTTTTAAATATTC---TTCATCCCTAAGCTATGACTCT
1 CTTTCTAAATTGGTCCTTAAACTTTT-AATATTCAATTTCATCCCTAAACTAAGACACT
* * *
20457 CATTCTAAATTAGTCCTTAAACTTTTAAGCATTCAAATTTCATCCCTAAACTAAGACACT
1 CTTTCTAAATTGGTCCTTAAACTTTTAA-TATTC-AATTTCATCCCTAAACTAAGACACT
*
20517 CTTTCTAAATTGGT-GTCTAAACTTTTGAATATTCCAATTTCATCCC
1 CTTTCTAAATTGGTCCT-TAAACTTTT-AATATT-CAATTTCATCCC
20563 CAAATTCATT
Statistics
Matches: 87, Mismatches: 10, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
55 5 0.06
56 24 0.28
59 1 0.01
60 54 0.62
61 3 0.03
ACGTcount: A:0.30, C:0.22, G:0.07, T:0.40
Consensus pattern (58 bp):
CTTTCTAAATTGGTCCTTAAACTTTTAATATTCAATTTCATCCCTAAACTAAGACACT
Found at i:22525 original size:27 final size:27
Alignment explanation
Indices: 22452--22518 Score: 116
Period size: 27 Copynumber: 2.5 Consensus size: 27
22442 GATGAAGAAG
* *
22452 TTATAAGAAATTAAAGAAAACGGGTTT
1 TTATATGAAATTAAAGAAAACGAGTTT
22479 TTATATGAAATTAAAGAAAACGAGTTT
1 TTATATGAAATTAAAGAAAACGAGTTT
22506 TTATATGAAATTA
1 TTATATGAAATTA
22519 TGGAAAAGAG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.48, C:0.03, G:0.15, T:0.34
Consensus pattern (27 bp):
TTATATGAAATTAAAGAAAACGAGTTT
Found at i:25122 original size:2 final size:2
Alignment explanation
Indices: 25115--25139 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
25105 TATGATAGCT
25115 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 T
25140 TATGAACAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:26684 original size:106 final size:106
Alignment explanation
Indices: 26563--26773 Score: 386
Period size: 106 Copynumber: 2.0 Consensus size: 106
26553 TTCATATCTC
26563 TTTCCGTGTTGTAATGTTATTTAATAAAATAAATATAATTTAAAATTGTAAAATATATTTATAAT
1 TTTCCGTGTTGTAATGTTATTTAATAAAATAAATATAATTTAAAATTGTAAAATATATTTATAAT
* ** *
26628 GTTATTTTAAAAAATTATATCTTAGAATTAAGTATTTATAG
66 ATTATTTTAAAAAACGATATCTTAGAATAAAGTATTTATAG
26669 TTTCCGTGTTGTAATGTTATTTAATAAAATAAATATAATTTAAAATTGTAAAATATATTTATAAT
1 TTTCCGTGTTGTAATGTTATTTAATAAAATAAATATAATTTAAAATTGTAAAATATATTTATAAT
26734 ATTATTTTAAAAAACGATATCTTAGAATAAAGTATTTATA
66 ATTATTTTAAAAAACGATATCTTAGAATAAAGTATTTATA
26774 AGAGCATAAA
Statistics
Matches: 101, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
106 101 1.00
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (106 bp):
TTTCCGTGTTGTAATGTTATTTAATAAAATAAATATAATTTAAAATTGTAAAATATATTTATAAT
ATTATTTTAAAAAACGATATCTTAGAATAAAGTATTTATAG
Found at i:35415 original size:21 final size:21
Alignment explanation
Indices: 35300--35415 Score: 60
Period size: 21 Copynumber: 5.6 Consensus size: 21
35290 GCGAAATAAA
**
35300 AATCGCAACGCGA-TCCCCAG
1 AATCGCAACGCGATTTTCCAG
** * *
35320 AATCGCAAATC-AGTTTCCAA
1 AATCGCAACGCGATTTTCCAG
* *
35340 AATCGCAACGCGATTCTT-GAC
1 AATCGCAACGCGATT-TTCCAG
* ** *
35361 AATCGCAATGCGATAGTACA-
1 AATCGCAACGCGATTTTCCAG
**
35381 AATTCGCATTGCGATTTTCCAG
1 AA-TCGCAACGCGATTTTCCAG
35403 AATCGCAACGCGA
1 AATCGCAACGCGA
35416 ATATGAAAAT
Statistics
Matches: 70, Mismatches: 20, Indels: 11
0.69 0.20 0.11
Matches are distributed among these distances:
19 1 0.01
20 25 0.36
21 40 0.57
22 4 0.06
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.22
Consensus pattern (21 bp):
AATCGCAACGCGATTTTCCAG
Found at i:35497 original size:20 final size:20
Alignment explanation
Indices: 35403--35575 Score: 215
Period size: 20 Copynumber: 8.6 Consensus size: 20
35393 GATTTTCCAG
* ** *
35403 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
35423 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
35443 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
35463 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
35483 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
35503 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
35523 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
35543 AATCGCAACGAC-AATCCGTAA
1 AATCGCAACG-CGTATCCGT-A
35564 AATCGCAACGCG
1 AATCGCAACGCG
35576 ATTTTTAAAG
Statistics
Matches: 134, Mismatches: 14, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
19 1 0.01
20 119 0.89
21 14 0.10
ACGTcount: A:0.35, C:0.28, G:0.19, T:0.18
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:35994 original size:33 final size:33
Alignment explanation
Indices: 35955--36025 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
35945 TTCACTTAGA
*
35955 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTATCTCGTTGCGAT
* *
35988 TTTCATTTCGCGTTGCTATTATCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTATCTCGTTGCGAT
36021 TTTCA
1 TTTCA
36026 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.13, C:0.23, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTATCTCGTTGCGAT
Found at i:36198 original size:21 final size:21
Alignment explanation
Indices: 36172--36236 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
36162 CGCGTTGCGA
36172 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
36193 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
36213 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
36234 TTC
1 TTC
36237 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:36233 original size:20 final size:20
Alignment explanation
Indices: 36171--36234 Score: 92
Period size: 20 Copynumber: 3.1 Consensus size: 20
36161 TCGCGTTGCG
36171 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
***
36191 ATTTCTCTCGTTGCGACAGTC
1 A-TTCTCTCGTTGCGATTTTC
36212 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
36232 ATT
1 ATT
36235 TCAACCAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 20 0.54
21 17 0.46
ACGTcount: A:0.12, C:0.25, G:0.16, T:0.47
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:38080 original size:93 final size:93
Alignment explanation
Indices: 37921--38236 Score: 614
Period size: 93 Copynumber: 3.4 Consensus size: 93
37911 TAGATTGCTT
* *
37921 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAATTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
37986 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
38014 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
38079 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
38107 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
38172 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
38200 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
38237 AATACCCTGA
Statistics
Matches: 221, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 221 1.00
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:38390 original size:14 final size:14
Alignment explanation
Indices: 38369--38427 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
38359 ACGCGAAATG
38369 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
38383 AGAATCGCAACGCGAAACC
1 AAAATCGCAA--CG--A-C
38402 AAAATCGCAACGAC
1 AAAATCGCAACGAC
38416 AAAATCGCAACG
1 AAAATCGCAACG
38428 CGAAACCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.47, C:0.29, G:0.17, T:0.07
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:38394 original size:33 final size:33
Alignment explanation
Indices: 38350--38443 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
38340 CACGAAACTT
**
38350 AAAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAAATCGCAACGCGAAACCAAAATCGCAACGAC
*
38383 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 AAAATCGCAACGCGAAACCAAAATCGCAACGAC
38416 AAAATCGCAACGCGAAACCAAAATCGCA
1 AAAATCGCAACGCGAAACCAAAATCGCA
38444 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.48, C:0.28, G:0.17, T:0.07
Consensus pattern (33 bp):
AAAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:38439 original size:19 final size:19
Alignment explanation
Indices: 38334--38443 Score: 96
Period size: 19 Copynumber: 6.3 Consensus size: 19
38324 TAGTTTACTT
* *
38334 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
**
38354 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
38373 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
38387 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
38406 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAACCAAAA
38420 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
38439 TCGCA
1 TCGCA
38444 TTGCGATTTT
Statistics
Matches: 74, Mismatches: 6, Indels: 21
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.27
15 2 0.03
16 4 0.05
17 4 0.05
18 2 0.03
19 30 0.41
20 12 0.16
ACGTcount: A:0.46, C:0.28, G:0.16, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:38485 original size:20 final size:19
Alignment explanation
Indices: 38439--38488 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
38429 GAAACCAAAA
* *
38439 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTAATT
38458 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTAA-TT
*
38478 TCGTGTTGCGA
1 TCGCGTTGCGA
38489 AAGTAAACTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.14, C:0.18, G:0.24, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTAATT
Found at i:38946 original size:44 final size:44
Alignment explanation
Indices: 38883--38968 Score: 118
Period size: 44 Copynumber: 2.0 Consensus size: 44
38873 GCCCGACTCG
* * *
38883 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCC
* * *
38927 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
38969 ACTGTCATCA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.21, C:0.41, G:0.16, T:0.22
Consensus pattern (44 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCC
Found at i:40430 original size:14 final size:14
Alignment explanation
Indices: 40411--40446 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
40401 ATTGTTTAAT
40411 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
40425 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
40439 TGATTTGT
1 TGATTTGT
40447 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:40565 original size:19 final size:19
Alignment explanation
Indices: 40537--40624 Score: 114
Period size: 19 Copynumber: 4.8 Consensus size: 19
40527 GCATTATGTT
40537 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAATGC
*
40556 GAAATAAAAATCGCAA--C
1 GAAATGAAAATCGCAATGC
*
40573 G--A-GAGAATCGCAATGC
1 GAAATGAAAATCGCAATGC
40589 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAATGC
40608 GGAAATGAAAATCGCAA
1 -GAAATGAAAATCGCAA
40625 CGAGAGAATC
Statistics
Matches: 59, Mismatches: 4, Indels: 11
0.80 0.05 0.15
Matches are distributed among these distances:
14 9 0.15
15 1 0.02
16 2 0.03
17 2 0.03
18 1 0.02
19 28 0.47
20 16 0.27
ACGTcount: A:0.49, C:0.16, G:0.22, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAATGC
Found at i:40656 original size:53 final size:53
Alignment explanation
Indices: 40537--40643 Score: 198
Period size: 53 Copynumber: 2.0 Consensus size: 53
40527 GCATTATGTT
40537 GAAATGAAAATCGCAATGC-GAAATAAAAATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAATGCGGAAATAAAAATCGCAACGAGAGAATCGCAATGC
*
40589 GAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAATGCGGAAATAAAAATCGCAACGAGAGAATCGCAATGC
40642 GA
1 GA
40644 TTTTCATTTC
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
52 19 0.36
53 34 0.64
ACGTcount: A:0.47, C:0.17, G:0.23, T:0.13
Consensus pattern (53 bp):
GAAATGAAAATCGCAATGCGGAAATAAAAATCGCAACGAGAGAATCGCAATGC
Found at i:40720 original size:72 final size:69
Alignment explanation
Indices: 40634--40927 Score: 280
Period size: 72 Copynumber: 4.2 Consensus size: 69
40624 ACGAGAGAAT
*
40634 CGCAATGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATT
1 CGCATTGCGATTTTC-TTTCG--TTGCGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATT
40699 TTCATTT-
62 TTCATTTC
* * * * *
40706 CGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCATTGCGA
1 CGCATTGCGATTTTC-TTTCG--TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCGTTGCGA
40768 TTTTCATTTC
60 TTTTCATTTC
* *
40778 CGCATTGCGA--TTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGAT
1 CGCATTGCGATTTTCTTTCGTTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGAT
40841 TTTCATTTC
61 TTTCATTTC
* * *
40850 CGCATTGCGATTTTC-TT-GTTGGGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTGTAA
1 CGCATTGCGATTTTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
40913 TTTC
66 TTTC
**
40917 CGTGTTGCGAT
1 CGCATTGCGAT
40928 AGTCAAATGC
Statistics
Matches: 188, Mismatches: 20, Indels: 33
0.78 0.08 0.14
Matches are distributed among these distances:
65 9 0.05
66 3 0.02
67 31 0.16
68 2 0.01
69 8 0.04
70 8 0.04
71 18 0.10
72 95 0.51
73 7 0.04
74 7 0.04
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.45
Consensus pattern (69 bp):
CGCATTGCGATTTTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
TTTC
Found at i:40759 original size:105 final size:109
Alignment explanation
Indices: 40639--40908 Score: 434
Period size: 105 Copynumber: 2.6 Consensus size: 109
40629 AGAATCGCAA
40639 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
40704 TTCGCATTGCGATTTTCATTTCGCATTGCGA-TTC-TCT-CG-T
66 TTCGCATTGCGATTTTCATTTCGCATTGCGATTTCATCTCCGAT
40744 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
*
40809 TTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCAT
66 TTCGCATTGCGATTTTCATTTCGCATTGCGA-TTTCATCTCCG-AT
*
40855 TGCGATTTTC--TT-G--TTGGGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATT
40909 GTAATTTCCG
Statistics
Matches: 157, Mismatches: 2, Indels: 12
0.92 0.01 0.07
Matches are distributed among these distances:
105 122 0.78
106 14 0.09
107 3 0.02
108 3 0.02
109 4 0.03
111 11 0.07
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.46
Consensus pattern (109 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
TTCGCATTGCGATTTTCATTTCGCATTGCGATTTCATCTCCGAT
Found at i:40923 original size:53 final size:52
Alignment explanation
Indices: 40639--40908 Score: 415
Period size: 53 Copynumber: 5.1 Consensus size: 52
40629 AGAATCGCAA
40639 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
40692 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
40744 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
*
40797 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCT-CG--T
*
40855 TGCGATTTTC--TT-G--TTGGGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
40902 TGCGATT
1 TGCGATT
40909 GTAATTTCCG
Statistics
Matches: 207, Mismatches: 3, Indels: 20
0.90 0.01 0.09
Matches are distributed among these distances:
47 8 0.04
49 2 0.01
50 2 0.01
51 3 0.01
52 62 0.30
53 109 0.53
54 3 0.01
55 3 0.01
56 4 0.02
58 11 0.05
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.46
Consensus pattern (52 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:43413 original size:24 final size:24
Alignment explanation
Indices: 43379--43425 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
43369 CTGAAACATC
43379 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
43403 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
43426 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:44146 original size:20 final size:20
Alignment explanation
Indices: 44118--44326 Score: 222
Period size: 20 Copynumber: 10.4 Consensus size: 20
44108 AAATTTCAGT
* * *
44118 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
44138 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
44158 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
44178 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
44198 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
44218 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
44238 GTTGCTATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
44258 GTTGCTATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
44278 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
44298 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
44318 GTTGCGATT
1 GTTGCGATT
44327 CTTGAAAATC
Statistics
Matches: 167, Mismatches: 20, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
20 166 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:44379 original size:21 final size:20
Alignment explanation
Indices: 44294--44391 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
44284 ATTTATGTGT
* *
44294 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCAAAA
*
44314 TCGCGTTGCGATTCTTGAAAA
1 TCGCGTTGCGATT-TTCAAAA
** **
44335 TCGCAATGCGAATTTGT-ACTA
1 TCGCGTTGCG-ATTT-TCAAAA
*
44356 TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTTCAA-AA
44377 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
44392 GGAAACTGAT
Statistics
Matches: 62, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
19 1 0.02
20 18 0.29
21 39 0.63
22 4 0.06
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCAAAA
Found at i:44387 original size:42 final size:43
Alignment explanation
Indices: 44294--44392 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
44284 ATTTATGTGT
* *
44294 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTCTTGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTTCAAAA
**
44335 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATT-TTCAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTCTTCAA-AA
*
44377 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
44393 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 12 0.26
42 32 0.68
43 3 0.06
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTTCAAAA
Found at i:52293 original size:51 final size:51
Alignment explanation
Indices: 52222--52318 Score: 158
Period size: 51 Copynumber: 1.9 Consensus size: 51
52212 GGTCAAAGGA
*
52222 TGACGAAGACGATGATGATAAGAAGTCAAGATATAGAAAAAAGAAAGACAG
1 TGACGAAGACGATGACGATAAGAAGTCAAGATATAGAAAAAAGAAAGACAG
* * *
52273 TGACGAAGATGATGACGATAAGAAGTCGAGATATAGGAAAAAGAAA
1 TGACGAAGACGATGACGATAAGAAGTCAAGATATAGAAAAAAGAAA
52319 AATAATGATG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 42 1.00
ACGTcount: A:0.52, C:0.07, G:0.27, T:0.14
Consensus pattern (51 bp):
TGACGAAGACGATGACGATAAGAAGTCAAGATATAGAAAAAAGAAAGACAG
Found at i:52335 original size:57 final size:51
Alignment explanation
Indices: 52222--52374 Score: 153
Period size: 51 Copynumber: 2.9 Consensus size: 51
52212 GGTCAAAGGA
* * * *
52222 TGACGAAGACGATGATGATAAGAAGTCAAGATATAGAAAAAAGAAAGACAG
1 TGACGAAGATGATGATGATAAGAAGTCGAGATATAGAAAAAAGAAAAAAAG
* *
52273 TGACGAAGATGATGACGATAAGAAGTCGAGATATAGGAAAAAGAAAAATAATG
1 TGACGAAGATGATGATGATAAGAAGTCGAGATATAGAAAAAAGAAAAA-AA-G
* * * * *
52326 ATGACGACGATGATAACGATGACAAGAAGTCGAGAAATCGTAAAAAGAA
1 -TGACGAAGATGAT---GATGATAAGAAGTCGAGATATAGAAAAAAGAA
52375 GAATGATTAC
Statistics
Matches: 84, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
51 43 0.51
52 1 0.01
53 1 0.01
54 12 0.14
57 27 0.32
ACGTcount: A:0.51, C:0.08, G:0.25, T:0.15
Consensus pattern (51 bp):
TGACGAAGATGATGATGATAAGAAGTCGAGATATAGAAAAAAGAAAAAAAG
Found at i:52338 original size:51 final size:51
Alignment explanation
Indices: 52221--52338 Score: 155
Period size: 51 Copynumber: 2.3 Consensus size: 51
52211 AGGTCAAAGG
* *
52221 ATGACGAAGACGATGATGATAAGAAGTCAAGATATAGAAAAAAGAAAGACA
1 ATGACGAAGACGATGACGATAAGAAGTCAAGATATAGAAAAAAGAAAAACA
* * * * *
52272 GTGACGAAGATGATGACGATAAGAAGTCGAGATATAGGAAAAAGAAAAATA
1 ATGACGAAGACGATGACGATAAGAAGTCAAGATATAGAAAAAAGAAAAACA
* *
52323 ATGATGACGACGATGA
1 ATGACGAAGACGATGA
52339 TAACGATGAC
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
51 56 1.00
ACGTcount: A:0.51, C:0.08, G:0.26, T:0.15
Consensus pattern (51 bp):
ATGACGAAGACGATGACGATAAGAAGTCAAGATATAGAAAAAAGAAAAACA
Found at i:54621 original size:18 final size:18
Alignment explanation
Indices: 54598--54661 Score: 119
Period size: 18 Copynumber: 3.6 Consensus size: 18
54588 CAGTGAGTTT
54598 ATGAGCATCAGGCAAAGG
1 ATGAGCATCAGGCAAAGG
*
54616 ATGAGCATCAGACAAAGG
1 ATGAGCATCAGGCAAAGG
54634 ATGAGCATCAGGCAAAGG
1 ATGAGCATCAGGCAAAGG
54652 ATGAGCATCA
1 ATGAGCATCA
54662 TCCGGATTGA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.41, C:0.17, G:0.30, T:0.12
Consensus pattern (18 bp):
ATGAGCATCAGGCAAAGG
Found at i:69146 original size:24 final size:26
Alignment explanation
Indices: 69119--69177 Score: 68
Period size: 29 Copynumber: 2.2 Consensus size: 26
69109 TCCTACATGG
*
69119 TTAATTT-A-CTTCACTGTAATTTGT
1 TTAATTTCATCTTCAATGTAATTTGT
69143 TTAATTGCTTCATCTTCAATGTAATTTGT
1 TTAA-T--TTCATCTTCAATGTAATTTGT
69172 TTAATT
1 TTAATT
69178 GTTTATATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
24 4 0.14
25 1 0.03
26 1 0.03
27 2 0.07
28 2 0.07
29 19 0.66
ACGTcount: A:0.25, C:0.12, G:0.08, T:0.54
Consensus pattern (26 bp):
TTAATTTCATCTTCAATGTAATTTGT
Found at i:69335 original size:20 final size:20
Alignment explanation
Indices: 69275--69337 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 20
69265 ACTTGTTATT
69275 TTGTTAAGGTAATCTGTTTAA
1 TTGTT-AGGTAATCTGTTTAA
** *
69296 TTGTTTATCTATAATATGTTTAA
1 TTG-TTA--GGTAATCTGTTTAA
69319 TTGTTAGGTAATCTGTTTA
1 TTGTTAGGTAATCTGTTTA
69338 GAATTTAGAT
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
20 10 0.30
21 4 0.12
22 5 0.15
23 14 0.42
ACGTcount: A:0.27, C:0.05, G:0.16, T:0.52
Consensus pattern (20 bp):
TTGTTAGGTAATCTGTTTAA
Found at i:72982 original size:33 final size:33
Alignment explanation
Indices: 72940--73023 Score: 141
Period size: 33 Copynumber: 2.5 Consensus size: 33
72930 TTAATGAGCA
*
72940 CATGCATCTATGGGTGTCCATCCATGTCTCTAT
1 CATGCATCTATGGGTATCCATCCATGTCTCTAT
*
72973 CATGCATCTATAGGTATCCATCCATGTCTCTAT
1 CATGCATCTATGGGTATCCATCCATGTCTCTAT
*
73006 CATGTATCTATGGGTATC
1 CATGCATCTATGGGTATC
73024 TTGCACTGCC
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.37
Consensus pattern (33 bp):
CATGCATCTATGGGTATCCATCCATGTCTCTAT
Found at i:78395 original size:15 final size:15
Alignment explanation
Indices: 78375--78403 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
78365 AATCAATTCG
78375 GATTTGAATTTTATT
1 GATTTGAATTTTATT
78390 GATTTGAATTTTAT
1 GATTTGAATTTTAT
78404 CAAACAAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.59
Consensus pattern (15 bp):
GATTTGAATTTTATT
Found at i:78879 original size:2 final size:2
Alignment explanation
Indices: 78872--78927 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
78862 TGGAATTATG
78872 AT 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 AT
78914 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
78928 GTTGTAATGG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:81898 original size:15 final size:15
Alignment explanation
Indices: 81878--81906 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
81868 TGTTTGCTCG
81878 GTAACCTGCCCATAC
1 GTAACCTGCCCATAC
81893 GTAACCTGCCCATA
1 GTAACCTGCCCATA
81907 GCGTCTTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.38, G:0.14, T:0.21
Consensus pattern (15 bp):
GTAACCTGCCCATAC
Found at i:82458 original size:60 final size:60
Alignment explanation
Indices: 82335--82466 Score: 144
Period size: 59 Copynumber: 2.2 Consensus size: 60
82325 AAATATTCGT
* * * * * *
82335 TTTGTAACTTTTAATAGTCGAGGGACTCGACAAAGCAACTATATATAGTCGGAGGACCGC
1 TTTGTAACTTTTAATACTCGAGGGACTCAACAAAACAACTATATATAATCAGAGAACCGC
* * *
82395 TTTGTAACTTTTAATACTCG-GGGACTCAATAAAACAA-TATCTTATAATCAGAGAACCATC
1 TTTGTAACTTTTAATACTCGAGGGACTCAACAAAACAACTAT-ATATAATCAGAGAACC-GC
82455 TTTGT-ACTTTTA
1 TTTGTAACTTTTA
82467 CTCTAATTTT
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
58 3 0.05
59 33 0.54
60 25 0.41
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (60 bp):
TTTGTAACTTTTAATACTCGAGGGACTCAACAAAACAACTATATATAATCAGAGAACCGC
Found at i:96166 original size:22 final size:22
Alignment explanation
Indices: 96112--96175 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
96102 AAGAATAAAC
* *
96112 ACGTGTCACAAAGACATAGAAAA
1 ACGTGTCATAAAGACA-AAAAAA
** *
96135 ATATGCCATAAAGACAAAAAAA
1 ACGTGTCATAAAGACAAAAAAA
*
96157 ACGTGTCATAAAGATAAAA
1 ACGTGTCATAAAGACAAAA
96176 TTATTCTTAT
Statistics
Matches: 32, Mismatches: 9, Indels: 1
0.76 0.21 0.02
Matches are distributed among these distances:
22 20 0.62
23 12 0.38
ACGTcount: A:0.56, C:0.14, G:0.14, T:0.16
Consensus pattern (22 bp):
ACGTGTCATAAAGACAAAAAAA
Found at i:97860 original size:21 final size:21
Alignment explanation
Indices: 97836--97875 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
97826 CAATACTCGG
97836 GTCTAATATGTGAATAAAGTT
1 GTCTAATATGTGAATAAAGTT
*
97857 GTCTACTATGTGAATAAAG
1 GTCTAATATGTGAATAAAG
97876 GGATGTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.35
Consensus pattern (21 bp):
GTCTAATATGTGAATAAAGTT
Found at i:102724 original size:3 final size:3
Alignment explanation
Indices: 102718--102779 Score: 70
Period size: 3 Copynumber: 20.0 Consensus size: 3
102708 TCATTTAAAT
** * *
102718 TTA TTA TTA TTA AAA TTA TTA TTA TTA GTA TTA TTA TTA TAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
102766 TATA TTA TTTA TTA
1 T-TA TTA -TTA TTA
102780 AATATTACAA
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
3 43 0.88
4 6 0.12
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:102730 original size:15 final size:15
Alignment explanation
Indices: 102712--102757 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
102702 TTTTTTTCAT
102712 TTAAATTTATTATTA
1 TTAAATTTATTATTA
*
102727 TTAAAATTATTATTA
1 TTAAATTTATTATTA
*
102742 TT-AGTATTATTATTA
1 TTAAAT-TTATTATTA
102757 T
1 T
102758 AATTATTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
14 1 0.04
15 26 0.96
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (15 bp):
TTAAATTTATTATTA
Found at i:104913 original size:20 final size:21
Alignment explanation
Indices: 104890--104941 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
104880 AGAAATTAAA
104890 AATTCATTTATTT-AATTTTT
1 AATTCATTTATTTAAATTTTT
* *
104910 AATTCTTTTCTTTCAAATTTTT
1 AATTCATTTATTT-AAATTTTT
104932 -ATT-ATTTATT
1 AATTCATTTATT
104942 ATTTTTATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 16 0.62
21 3 0.12
22 7 0.27
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (21 bp):
AATTCATTTATTTAAATTTTT
Found at i:109570 original size:17 final size:18
Alignment explanation
Indices: 109540--109581 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
109530 TCCAGCAAAG
* *
109540 AAAAAAATAGAAA-GAAA
1 AAAAAAACAAAAAGGAAA
109557 AAAAAAACAAAAAGGAAA
1 AAAAAAACAAAAAGGAAA
109575 AAGAAAA
1 AA-AAAA
109582 GGAAAATTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 11 0.52
18 6 0.29
19 4 0.19
ACGTcount: A:0.83, C:0.02, G:0.12, T:0.02
Consensus pattern (18 bp):
AAAAAAACAAAAAGGAAA
Done.