Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001378.1 Hibiscus syriacus cultivar Beakdansim tig00002690_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: 42918
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1729 original size:29 final size:28
Alignment explanation
Indices: 1696--1815 Score: 93
Period size: 29 Copynumber: 4.2 Consensus size: 28
1686 TTTTTTTTAA
*
1696 TAATTACCAAAATATCACCCTTTTCGAAT
1 TAATT-CCAAAATAGCACCCTTTTCGAAT
* *
1725 TAATTCACATAATAGCACCAATTTT-GAAT
1 TAATTC-CAAAATAGCACC-CTTTTCGAAT
* * ** *
1754 TAATTCCCAAATATCACTTTTTTC-AAA
1 TAATTCCAAAATAGCACCCTTTTCGAAT
* *
1781 AAATTACCAAAATAGCA-CCTTTTCAAAT
1 TAATT-CCAAAATAGCACCCTTTTCGAAT
1809 TAATTCC
1 TAATTCC
1816 CCGAATAGTA
Statistics
Matches: 70, Mismatches: 16, Indels: 12
0.71 0.16 0.12
Matches are distributed among these distances:
27 17 0.24
28 24 0.34
29 25 0.36
30 4 0.06
ACGTcount: A:0.40, C:0.22, G:0.03, T:0.35
Consensus pattern (28 bp):
TAATTCCAAAATAGCACCCTTTTCGAAT
Found at i:1803 original size:28 final size:27
Alignment explanation
Indices: 1677--1815 Score: 91
Period size: 28 Copynumber: 5.0 Consensus size: 27
1667 CATTTTACAC
* **
1677 AAATAGCACTTTTTTTTAATAATTACCA
1 AAATAGCACCTTTTTCAAATAATT-CCA
* * *
1705 AAATATCACCCTTTTCGAATTAATTCACA
1 AAATAGCACCTTTTTC-AAATAATTC-CA
* * * * *
1734 TAATAGCACCAATTTTGAATTAATTCCC
1 AAATAGCACC-TTTTTCAAATAATTCCA
* * *
1762 AAATATCACTTTTTTCAAAAAATTACCA
1 AAATAGCACCTTTTTCAAATAATT-CCA
1790 AAATAGCACC-TTTTCAAATTAATTCC
1 AAATAGCACCTTTTTCAAA-TAATTCC
1816 CCGAATAGTA
Statistics
Matches: 84, Mismatches: 22, Indels: 11
0.72 0.19 0.09
Matches are distributed among these distances:
27 20 0.24
28 35 0.42
29 25 0.30
30 4 0.05
ACGTcount: A:0.40, C:0.20, G:0.04, T:0.37
Consensus pattern (27 bp):
AAATAGCACCTTTTTCAAATAATTCCA
Found at i:1880 original size:12 final size:13
Alignment explanation
Indices: 1855--1909 Score: 58
Period size: 17 Copynumber: 4.0 Consensus size: 13
1845 AAATAAAACC
1855 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1868 GGTCAACGGTCGGGTCG
1 GGTCAA----CGGGTCG
1885 GGTCAAC-GGTCG
1 GGTCAACGGGTCG
*
1897 GGTAAACGGGTCG
1 GGTCAACGGGTCG
1910 TGACTGGTCA
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
12 11 0.31
13 12 0.33
17 13 0.36
ACGTcount: A:0.16, C:0.22, G:0.45, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:1883 original size:17 final size:17
Alignment explanation
Indices: 1861--1899 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
1851 AACCGGTCAA
1861 CGGGTCGGGTCAACGGT
1 CGGGTCGGGTCAACGGT
1878 CGGGTCGGGTCAACGGT
1 CGGGTCGGGTCAACGGT
1895 CGGGT
1 CGGGT
1900 AAACGGGTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.10, C:0.23, G:0.49, T:0.18
Consensus pattern (17 bp):
CGGGTCGGGTCAACGGT
Found at i:1919 original size:30 final size:30
Alignment explanation
Indices: 1855--1920 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
1845 AAATAAAACC
* *
1855 GGTCAACGGGTCGGGTCAACGGTCGGGTCG
1 GGTCAACGGGTCGGGTAAACGGTCGGGACG
* *
1885 GGTCAAC-GGTCGGGTAAACGGGTCGTGACT
1 GGTCAACGGGTCGGGTAAAC-GGTCGGGACG
1915 GGTCAA
1 GGTCAA
1921 ACCGATCAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 11 0.35
30 20 0.65
ACGTcount: A:0.18, C:0.21, G:0.42, T:0.18
Consensus pattern (30 bp):
GGTCAACGGGTCGGGTAAACGGTCGGGACG
Found at i:1932 original size:10 final size:10
Alignment explanation
Indices: 1915--1964 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
1905 GGTCGTGACT
1915 GGTC-AAACC
1 GGTCAAAACC
*
1924 GATCAAAA-C
1 GGTCAAAACC
1933 GGTTCAAAACC
1 GG-TCAAAACC
**
1944 GGTTTAAACC
1 GGTCAAAACC
1954 GGTCAAAACC
1 GGTCAAAACC
1964 G
1 G
1965 TTTCCAGCGT
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
9 5 0.16
10 24 0.75
11 3 0.09
ACGTcount: A:0.38, C:0.26, G:0.20, T:0.16
Consensus pattern (10 bp):
GGTCAAAACC
Found at i:3767 original size:23 final size:23
Alignment explanation
Indices: 3724--3767 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
3714 TGTAGTTATG
*
3724 TTATATTTGTTTTCTTATCATAT
1 TTATATTTGTTTTATTATCATAT
*
3747 TTATATTT-TTGTTATTTTCAT
1 TTATATTTGTT-TTATTATCAT
3768 GTCAAGTACT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 16 0.89
ACGTcount: A:0.20, C:0.07, G:0.05, T:0.68
Consensus pattern (23 bp):
TTATATTTGTTTTATTATCATAT
Found at i:4732 original size:41 final size:41
Alignment explanation
Indices: 4687--4764 Score: 97
Period size: 41 Copynumber: 1.9 Consensus size: 41
4677 ATAAAGAAGT
*
4687 ATTG-TGAAAAAAATGTGATATCCT-AATTTAAAATGTTTGAC
1 ATTGTTGAAAAAAA-GT-ATATCCTAAAGTTAAAATGTTTGAC
* *
4728 ATTGTTGTAAAAAAGTATATTCTAAAGTTAAAATGTT
1 ATTGTTGAAAAAAAGTATATCCTAAAGTTAAAATGTT
4765 GATTTTAGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 6 0.19
41 18 0.56
42 8 0.25
ACGTcount: A:0.42, C:0.05, G:0.14, T:0.38
Consensus pattern (41 bp):
ATTGTTGAAAAAAAGTATATCCTAAAGTTAAAATGTTTGAC
Found at i:7093 original size:16 final size:17
Alignment explanation
Indices: 7072--7113 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
7062 ATGTAAAAAT
7072 AAATATTTAAATTTA-A
1 AAATATTTAAATTTATA
* *
7088 AAATA-TAAAATTTATT
1 AAATATTTAAATTTATA
7104 AAATATTTAA
1 AAATATTTAA
7114 TCAAGTAGGG
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
15 8 0.38
16 10 0.48
17 3 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AAATATTTAAATTTATA
Found at i:9244 original size:31 final size:31
Alignment explanation
Indices: 9209--9282 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 31
9199 CAACCATTCC
*** *
9209 CAACTTTTTCCAAAATTTTGAATTGGTCCCT
1 CAACTTTTTCCAAAATTACAAAATGGTCCCT
*
9240 CAAC-TTTTCAAAAATTACAAAATGGTCCCT
1 CAACTTTTTCCAAAATTACAAAATGGTCCCT
*
9270 -AAATTTTTCCAAA
1 CAACTTTTTCCAAA
9283 GCCTGTAAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
29 2 0.06
30 29 0.83
31 4 0.11
ACGTcount: A:0.35, C:0.22, G:0.07, T:0.36
Consensus pattern (31 bp):
CAACTTTTTCCAAAATTACAAAATGGTCCCT
Found at i:10266 original size:30 final size:30
Alignment explanation
Indices: 10230--10288 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
10220 TTTGGTCCCT
* *
10230 AAACTTT-TCAAATTTTATACTTCGGTCACC
1 AAACTTTACCAAA-TTTATAATTCGGTCACC
*
10260 AAACTTTACCAAATTTATAATTTGGTCAC
1 AAACTTTACCAAATTTATAATTCGGTCAC
10289 TAAATAAATC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.34, C:0.20, G:0.07, T:0.39
Consensus pattern (30 bp):
AAACTTTACCAAATTTATAATTCGGTCACC
Found at i:11304 original size:9 final size:8
Alignment explanation
Indices: 11290--11349 Score: 57
Period size: 9 Copynumber: 6.9 Consensus size: 8
11280 TCTCTCATAT
11290 TTTTTTTC
1 TTTTTTTC
11298 ATTTTTTTC
1 -TTTTTTTC
*
11307 TGTTTTTC
1 TTTTTTTC
11315 TTTTTCTTC
1 TTTTT-TTC
*
11324 TTCTTCTTC
1 TT-TTTTTC
11333 TTTTTCTTC
1 TTTTT-TTC
11342 TTCTTTTT
1 TT-TTTTT
11350 AGTTTTTTAG
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
8 13 0.30
9 25 0.58
10 5 0.12
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.78
Consensus pattern (8 bp):
TTTTTTTC
Found at i:11318 original size:6 final size:6
Alignment explanation
Indices: 11309--11349 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
11299 TTTTTTTCTG
* * *
11309 TTTTTC TTTTTC TTCTTC TTCTTC TTTTTC TTCTTC TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
11350 AGTTTTTTAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTTTC
Found at i:11324 original size:3 final size:3
Alignment explanation
Indices: 11312--11346 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
11302 TTTTCTGTTT
* *
11312 TTC TTT TTC TTC TTC TTC TTC TTT TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
11347 TTTAGTTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (3 bp):
TTC
Found at i:11347 original size:12 final size:12
Alignment explanation
Indices: 11309--11349 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
11299 TTTTTTTCTG
*
11309 TTTTTCTTTTTC
1 TTTTTCTTCTTC
*
11321 TTCTTCTTCTTC
1 TTTTTCTTCTTC
11333 TTTTTCTTCTTC
1 TTTTTCTTCTTC
11345 TTTTT
1 TTTTT
11350 AGTTTTTTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTTCTTCTTC
Found at i:14135 original size:131 final size:131
Alignment explanation
Indices: 13901--14165 Score: 503
Period size: 131 Copynumber: 2.0 Consensus size: 131
13891 ACAAAGTTCT
*
13901 CCAACTTATAATTTGACCGAATTTTACATAATAATTTCTAGAAAGATCGAACATGTTTTAACCAT
1 CCAACTTATAATTTGACAGAATTTTACATAATAATTTCTAGAAAGATCGAACATGTTTTAACCAT
*
13966 AAATCATGCTTGGAAATGAATCTATAACCTTTGATTAATCAAGATTTATCATCAATTTCATGAAT
66 AAATCATGCTTGGAAATGAATCTATAACCTCTGATTAATCAAGATTTATCATCAATTTCATGAAT
14031 C
131 C
*
14032 CCAACTTATAATTTGACAGAATTTTACATAATAATTTCTAGAAAGATCGATCATGTTTTAACCAT
1 CCAACTTATAATTTGACAGAATTTTACATAATAATTTCTAGAAAGATCGAACATGTTTTAACCAT
14097 AAATCATGCTTGGAAATGAATCTATAACCTCTGATTAATCAAGATTTATCATCAATTTCATGAAT
66 AAATCATGCTTGGAAATGAATCTATAACCTCTGATTAATCAAGATTTATCATCAATTTCATGAAT
14162 C
131 C
14163 CCA
1 CCA
14166 TCATGAACAT
Statistics
Matches: 131, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
131 131 1.00
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (131 bp):
CCAACTTATAATTTGACAGAATTTTACATAATAATTTCTAGAAAGATCGAACATGTTTTAACCAT
AAATCATGCTTGGAAATGAATCTATAACCTCTGATTAATCAAGATTTATCATCAATTTCATGAAT
C
Found at i:20530 original size:23 final size:22
Alignment explanation
Indices: 20504--20576 Score: 69
Period size: 23 Copynumber: 3.3 Consensus size: 22
20494 GCATGTTATT
20504 TACCTTTATGACAAGTTTATCTA
1 TACCTTTATGACAA-TTTATCTA
* * * *
20527 TACCTTTGTGGC-ATGT-TCTC
1 TACCTTTATGACAATTTATCTA
*
20547 TGCCTTTATGACACATTTATCTA
1 TACCTTTATGACA-ATTTATCTA
20570 TACCTTT
1 TACCTTT
20577 GTGGCACGTT
Statistics
Matches: 37, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
20 12 0.32
21 2 0.05
22 4 0.11
23 19 0.51
ACGTcount: A:0.22, C:0.22, G:0.11, T:0.45
Consensus pattern (22 bp):
TACCTTTATGACAATTTATCTA
Found at i:20553 original size:43 final size:43
Alignment explanation
Indices: 20487--20582 Score: 140
Period size: 43 Copynumber: 2.2 Consensus size: 43
20477 ATAATTATGT
* *
20487 CTTTGTAGCATGTTATTTACCTTTATGACA-AGTTTATCTATAC
1 CTTTGTGGCATGTTATCTACCTTTATGACACA-TTTATCTATAC
* *
20530 CTTTGTGGCATGTTCTCTGCCTTTATGACACATTTATCTATAC
1 CTTTGTGGCATGTTATCTACCTTTATGACACATTTATCTATAC
20573 CTTTGTGGCA
1 CTTTGTGGCA
20583 CGTTTTTCTC
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
43 47 0.98
44 1 0.02
ACGTcount: A:0.21, C:0.20, G:0.15, T:0.45
Consensus pattern (43 bp):
CTTTGTGGCATGTTATCTACCTTTATGACACATTTATCTATAC
Found at i:20598 original size:23 final size:23
Alignment explanation
Indices: 20542--20599 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
20532 TTGTGGCATG
20542 TTCTCTGCCTTTATGACACATTT
1 TTCTCTGCCTTTATGACACATTT
* * * * * *
20565 ATCTATACCTTTGTGGCACGTTT
1 TTCTCTGCCTTTATGACACATTT
20588 TTCTCTGCCTTT
1 TTCTCTGCCTTT
20600 TGGTAGTTTA
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.14, C:0.26, G:0.12, T:0.48
Consensus pattern (23 bp):
TTCTCTGCCTTTATGACACATTT
Found at i:21549 original size:19 final size:19
Alignment explanation
Indices: 21511--21549 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
21501 TGACCAGAAG
21511 TTTCGAAACTTCTACAAGAT
1 TTTCGAAACTTC-ACAAGAT
21531 TTTCGAAACATTC-CAAGAT
1 TTTCGAAAC-TTCACAAGAT
21550 AGTTTCCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 9 0.50
21 3 0.17
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.33
Consensus pattern (19 bp):
TTTCGAAACTTCACAAGAT
Found at i:24218 original size:19 final size:20
Alignment explanation
Indices: 24194--24245 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
24184 TTCCCAAAAT
24194 GTTTCGATACTTTA-C-AAGA
1 GTTTCGATACTTTACCTAA-A
*
24213 GTTTCGAAACTTTACCTAAA
1 GTTTCGATACTTTACCTAAA
24233 GTTTCGATACTTT
1 GTTTCGATACTTT
24246 GTGTCCAACG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 13 0.45
20 14 0.48
21 2 0.07
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.40
Consensus pattern (20 bp):
GTTTCGATACTTTACCTAAA
Found at i:28017 original size:18 final size:18
Alignment explanation
Indices: 27990--28024 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
27980 ACAGAGAAGT
* *
27990 AAATACTGAAATTTAAAA
1 AAATAATGAAATATAAAA
28008 AAATAATGAAATATAAA
1 AAATAATGAAATATAAA
28025 TATTGGAAAT
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:0.66, C:0.03, G:0.06, T:0.26
Consensus pattern (18 bp):
AAATAATGAAATATAAAA
Found at i:28079 original size:30 final size:31
Alignment explanation
Indices: 28045--28168 Score: 86
Period size: 30 Copynumber: 4.2 Consensus size: 31
28035 TTAAAGGACA
28045 TAAAT-ATAAATAAATAAAAGTGCATAAATG
1 TAAATAATAAATAAATAAAAGTGCATAAATG
* * * * *
28075 TAAATGA-CAATAATTAAAGAATG--GAAA--
1 TAAATAATAAATAAATAAA-AGTGCATAAATG
28102 TAAATAAATAAATAAATCAAAAG-GCATAAATG
1 TAAAT-AATAAATAAAT-AAAAGTGCATAAATG
* *
28134 TAAATAATGAAA-AGAT-AAAGAGCATAAATG
1 TAAATAAT-AAATAAATAAAAGTGCATAAATG
28164 TAAAT
1 TAAAT
28169 GGTAGAAATG
Statistics
Matches: 73, Mismatches: 10, Indels: 22
0.70 0.10 0.21
Matches are distributed among these distances:
27 5 0.07
28 2 0.03
29 14 0.19
30 34 0.47
31 10 0.14
32 8 0.11
ACGTcount: A:0.60, C:0.04, G:0.12, T:0.23
Consensus pattern (31 bp):
TAAATAATAAATAAATAAAAGTGCATAAATG
Found at i:28857 original size:56 final size:57
Alignment explanation
Indices: 28656--28897 Score: 330
Period size: 57 Copynumber: 4.3 Consensus size: 57
28646 TGGCTTCCTA
* * * *
28656 AAAAATTCACTTAAAGTAATCATCAATAAA-CTCCTGAAAATCAGGA-TTAGCTTCTTT
1 AAAAATTCATTTGAAGTAATCATCAAGAAACCT-CTAAAAATCA-GACTTAGCTTCTTT
* * * *
28713 AAAAATTCACTTGAAGTACTCATAAAAAAACCTCTAAAAATCAGACTTAGCTTCTTT
1 AAAAATTCATTTGAAGTAATCATCAAGAAACCTCTAAAAATCAGACTTAGCTTCTTT
*
28770 AAAAATTCATTTGAAGTAATCATCAAGAAACCTCTAAAAATCATACTTAGCTTCTTT
1 AAAAATTCATTTGAAGTAATCATCAAGAAACCTCTAAAAATCAGACTTAGCTTCTTT
*
28827 -AAAATTCATTTGAAGTAATCATCAAGAAACC-CTTGAAAATCAGACTTAGCTTCTTT
1 AAAAATTCATTTGAAGTAATCATCAAGAAACCTC-TAAAAATCAGACTTAGCTTCTTT
*
28883 AAAAATTCTTTTGAA
1 AAAAATTCATTTGAA
28898 AACATCATAT
Statistics
Matches: 168, Mismatches: 13, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
55 1 0.01
56 54 0.32
57 111 0.66
58 2 0.01
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.32
Consensus pattern (57 bp):
AAAAATTCATTTGAAGTAATCATCAAGAAACCTCTAAAAATCAGACTTAGCTTCTTT
Found at i:30275 original size:28 final size:28
Alignment explanation
Indices: 30244--30309 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
30234 ATGTGGACTA
* *
30244 TTTCAGGTTGATTTGGGGAGGTAGA-GTG
1 TTTCAGGTTGATTCGAGGAGGTA-ATGTG
*
30272 TTTCGGGTTGATTCGAGGAGGTAATGTG
1 TTTCAGGTTGATTCGAGGAGGTAATGTG
*
30300 TTTCAAGTTG
1 TTTCAGGTTG
30310 GCTTCTATAG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 1 0.03
28 31 0.97
ACGTcount: A:0.18, C:0.06, G:0.38, T:0.38
Consensus pattern (28 bp):
TTTCAGGTTGATTCGAGGAGGTAATGTG
Found at i:41629 original size:20 final size:18
Alignment explanation
Indices: 41566--41634 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 18
41556 TCAATTTGAC
*
41566 ATCGATACTTAATCAAGT
1 ATCGATACTCAATCAAGT
41584 ATCGATACCTCAATACCAAAGT
1 ATCGATA-CTCAAT--C-AAGT
41606 ATCGATACTCAATCTAATGT
1 ATCGATACTCAATC-AA-GT
41626 ATCGATACT
1 ATCGATACT
41635 GCCTTATCCC
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
18 7 0.16
19 8 0.18
20 11 0.25
21 7 0.16
22 11 0.25
ACGTcount: A:0.38, C:0.22, G:0.10, T:0.30
Consensus pattern (18 bp):
ATCGATACTCAATCAAGT
Done.