Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001061.1 Hibiscus syriacus cultivar Beakdansim tig00002098_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: 160210
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1825 original size:20 final size:20
Alignment explanation
Indices: 1784--1833 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
1774 AATAATAATT
*
1784 TTTTTAATAAATTTATGATA
1 TTTTTAATAAATTAATGATA
*
1804 TTTTTAA-AAATTAATTATTA
1 TTTTTAATAAATTAATGA-TA
1824 TTTTATAATA
1 TTTT-TAATA
1834 TTTAATAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 8 0.32
20 13 0.52
21 3 0.12
22 1 0.04
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
TTTTTAATAAATTAATGATA
Found at i:1869 original size:27 final size:26
Alignment explanation
Indices: 1822--1898 Score: 118
Period size: 27 Copynumber: 2.9 Consensus size: 26
1812 AATTAATTAT
1822 TATTTTATAATATTTAATAAATTTAA
1 TATTTTATAATATTTAATAAATTTAA
* *
1848 TATTTTGTAATTATTTGATAAATTTAA
1 TATTTTATAA-TATTTAATAAATTTAA
1875 TATTTTATAATATATTAATAAATT
1 TATTTTATAATAT-TTAATAAATT
1899 ATATAAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
26 12 0.27
27 33 0.73
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.55
Consensus pattern (26 bp):
TATTTTATAATATTTAATAAATTTAA
Found at i:1884 original size:16 final size:16
Alignment explanation
Indices: 1829--1894 Score: 52
Period size: 16 Copynumber: 4.3 Consensus size: 16
1819 TATTATTTTA
*
1829 TAATATTTAATAAATT
1 TAATATTTTATAAATT
*
1845 TAATATTTTGT-AA--
1 TAATATTTTATAAATT
*
1858 T--TATTTGATAAATT
1 TAATATTTTATAAATT
1872 TAATATTTTATAATATAT
1 TAATATTTTATAA-AT-T
1890 TAATA
1 TAATA
1895 AATTATATAA
Statistics
Matches: 38, Mismatches: 5, Indels: 12
0.69 0.09 0.22
Matches are distributed among these distances:
11 6 0.16
12 2 0.05
13 1 0.03
14 1 0.03
15 2 0.05
16 18 0.47
17 2 0.05
18 6 0.16
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TAATATTTTATAAATT
Found at i:1900 original size:18 final size:17
Alignment explanation
Indices: 1826--1901 Score: 57
Period size: 18 Copynumber: 4.3 Consensus size: 17
1816 AATTATTATT
1826 TTATAATATTTAATAAA
1 TTATAATATTTAATAAA
* *
1843 TT-TAATATTTTGTAATTAT
1 TTATAATA--TT-TAATAAA
**
1862 TTGATAA-ATTTAATATT
1 TT-ATAATATTTAATAAA
1879 TTATAATATATTAATAAA
1 TTATAATAT-TTAATAAA
1897 TTATA
1 TTATA
1902 TAAATATAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
16 9 0.20
17 11 0.24
18 15 0.33
19 7 0.15
20 1 0.02
21 3 0.07
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
TTATAATATTTAATAAA
Found at i:4089 original size:31 final size:31
Alignment explanation
Indices: 4051--4122 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
4041 CGGCGGTGAT
4051 CGATTTGTTATAAATAGATAACATTAGTAAC
1 CGATTTGTTATAAATAGATAACATTAGTAAC
* * * *
4082 CGATTTGTTATAGATCGATAACATTTGTGAC
1 CGATTTGTTATAAATAGATAACATTAGTAAC
*
4113 CAATTTGTTA
1 CGATTTGTTA
4123 CTTTTGAAAC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.39
Consensus pattern (31 bp):
CGATTTGTTATAAATAGATAACATTAGTAAC
Found at i:4353 original size:62 final size:61
Alignment explanation
Indices: 4256--4378 Score: 228
Period size: 62 Copynumber: 2.0 Consensus size: 61
4246 GGACATAAAG
*
4256 GTGACCTCAAGAAGATATCAACAATTTCAAAGTAAAAGCACAAAGCCCAGTGTCCAAAAACT
1 GTGACCTCAAGAAGATATCAACAATTTCAAAGTAAAAGCAC-AAGCCCAGGGTCCAAAAACT
4318 GTGACCTCAAGAAGATATCAACAATTTCAAAGTAAAAGCACAAGCCCAGGGTCCAAAAACT
1 GTGACCTCAAGAAGATATCAACAATTTCAAAGTAAAAGCACAAGCCCAGGGTCCAAAAACT
4379 ATGTCATGGT
Statistics
Matches: 60, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
61 19 0.32
62 41 0.68
ACGTcount: A:0.45, C:0.23, G:0.15, T:0.17
Consensus pattern (61 bp):
GTGACCTCAAGAAGATATCAACAATTTCAAAGTAAAAGCACAAGCCCAGGGTCCAAAAACT
Found at i:18542 original size:21 final size:21
Alignment explanation
Indices: 18518--18629 Score: 97
Period size: 21 Copynumber: 5.3 Consensus size: 21
18508 TTAAAGTTTG
18518 CGTTGCGATTTATTCCAAATT
1 CGTTGCGATTTATTCCAAATT
* * * *
18539 CGTTGTGA--TAGTCGAAGTT
1 CGTTGCGATTTATTCCAAATT
18558 CGCGTTGCGATTTATTCCAAATT
1 --CGTTGCGATTTATTCCAAATT
* * *
18581 CGTTGCGA--TAGTCGAAGTT
1 CGTTGCGATTTATTCCAAATT
18600 CGCGTTGCGATTTATTCCAAATT
1 --CGTTGCGATTTATTCCAAATT
18623 CGTTGCG
1 CGTTGCG
18630 GTAGTTCAAA
Statistics
Matches: 69, Mismatches: 14, Indels: 16
0.70 0.14 0.16
Matches are distributed among these distances:
19 16 0.23
21 37 0.54
23 16 0.23
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.38
Consensus pattern (21 bp):
CGTTGCGATTTATTCCAAATT
Found at i:18557 original size:42 final size:42
Alignment explanation
Indices: 18499--18634 Score: 227
Period size: 42 Copynumber: 3.2 Consensus size: 42
18489 GGAAACTGAT
** *
18499 TTGCGATAGTTAAAGTTTGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
18541 TTGTGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
18583 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
18625 TTGCGGTAGT
1 TTGCGATAGT
18635 TCAAAATCGC
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 88 1.00
ACGTcount: A:0.21, C:0.16, G:0.24, T:0.38
Consensus pattern (42 bp):
TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:19441 original size:19 final size:19
Alignment explanation
Indices: 19417--19550 Score: 115
Period size: 19 Copynumber: 6.5 Consensus size: 19
19407 GTGATTTTCA
19417 ACTATCGCAACGAACTTGG
1 ACTATCGCAACGAACTTGG
*
19436 ACTATCGCAACGCGAATTTGG
1 ACTATCGCAA--CGAACTTGG
* *
19457 AATAAATCACAACGCAAACTTGG
1 ACT--ATCGCAACG--AACTTGG
* *
19480 ACTATCACAACGAATTTGG
1 ACTATCGCAACGAACTTGG
* *
19499 AATAAATCGCAAAACGAACTTCG
1 ACT--ATCGC--AACGAACTTGG
19522 ACTATCGCAACGAACTTGG
1 ACTATCGCAACGAACTTGG
19541 ACTATCGCAA
1 ACTATCGCAA
19551 TGTGAATTTG
Statistics
Matches: 93, Mismatches: 12, Indels: 20
0.74 0.10 0.16
Matches are distributed among these distances:
19 38 0.41
21 30 0.32
23 25 0.27
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (19 bp):
ACTATCGCAACGAACTTGG
Found at i:19479 original size:23 final size:22
Alignment explanation
Indices: 19443--19506 Score: 71
Period size: 23 Copynumber: 3.0 Consensus size: 22
19433 TGGACTATCG
19443 CAACGCGAATTTGGAATAAATCA
1 CAACGC-AATTTGGAATAAATCA
* *
19466 CAACGCAAACTTGGACT--ATCA
1 CAACGC-AATTTGGAATAAATCA
19487 CAACG-AATTTGGAATAAATC
1 CAACGCAATTTGGAATAAATC
19507 GCAAAACGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
19 8 0.24
21 12 0.35
23 14 0.41
ACGTcount: A:0.42, C:0.20, G:0.16, T:0.22
Consensus pattern (22 bp):
CAACGCAATTTGGAATAAATCA
Found at i:19495 original size:42 final size:42
Alignment explanation
Indices: 19429--19541 Score: 145
Period size: 42 Copynumber: 2.6 Consensus size: 42
19419 TATCGCAACG
**
19429 AACTTGGACTATCGCAACGCGAATTTGGAATAAATCACAACGCA
1 AACTTGGACTATCGCAA--CGAATTTGGAATAAATCACAAAACA
* * *
19473 AACTTGGACTATCACAACGAATTTGGAATAAATCGCAAAACG
1 AACTTGGACTATCGCAACGAATTTGGAATAAATCACAAAACA
* *
19515 AACTTCGACTATCGCAACGAACTTGGA
1 AACTTGGACTATCGCAACGAATTTGGA
19542 CTATCGCAAT
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
42 45 0.74
44 16 0.26
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (42 bp):
AACTTGGACTATCGCAACGAATTTGGAATAAATCACAAAACA
Found at i:19601 original size:21 final size:21
Alignment explanation
Indices: 19575--19618 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
19565 ATTGCATTGT
19575 GATAGTCGAAGCTCGCGTTGC
1 GATAGTCGAAGCTCGCGTTGC
* *
19596 GATAGTCGATGTTCGCGTTGC
1 GATAGTCGAAGCTCGCGTTGC
19617 GA
1 GA
19619 ATCTGGAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.20, G:0.34, T:0.27
Consensus pattern (21 bp):
GATAGTCGAAGCTCGCGTTGC
Found at i:24206 original size:30 final size:30
Alignment explanation
Indices: 24172--24238 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 30
24162 AAGGAACATA
24172 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
*
24202 TGGATAGTTACGGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
24232 TGGATAG
1 TGGATAG
24239 GTCTTTCGGG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (30 bp):
TGGATAGTTACCGAGGATCTTTATGACCTC
Found at i:26791 original size:11 final size:11
Alignment explanation
Indices: 26775--26799 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
26765 ATTAAGTTAA
26775 TTAAATATTTT
1 TTAAATATTTT
26786 TTAAATATTTT
1 TTAAATATTTT
26797 TTA
1 TTA
26800 TTACATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TTAAATATTTT
Found at i:26842 original size:27 final size:28
Alignment explanation
Indices: 26780--26844 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 28
26770 GTTAATTAAA
*
26780 TATTTTTTAAATATTTTTTATTACATAT
1 TATTTTTTAAATATTTTTTATTACATAG
*
26808 TATATTTTAATATATTTTTTA-TACAT-G
1 TATTTTTTAA-ATATTTTTTATTACATAG
26835 TATTTTTTAA
1 TATTTTTTAA
26845 CTAGATATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 9 0.27
28 14 0.42
29 10 0.30
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (28 bp):
TATTTTTTAAATATTTTTTATTACATAG
Found at i:33071 original size:2 final size:2
Alignment explanation
Indices: 33064--33103 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
33054 AGAACCCTGC
* *
33064 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
33104 AACTGACTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:37864 original size:17 final size:18
Alignment explanation
Indices: 37839--37874 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
37829 AATATCTATC
*
37839 ATTTTTAAA-TTATCTAA
1 ATTTGTAAATTTATCTAA
37856 ATTTGTAAATTTATCTAA
1 ATTTGTAAATTTATCTAA
37874 A
1 A
37875 AATTAAATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.50
Consensus pattern (18 bp):
ATTTGTAAATTTATCTAA
Found at i:41294 original size:21 final size:21
Alignment explanation
Indices: 41270--41325 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
41260 TAGAAATATT
*
41270 TATTTTAGGTAGCGAAATTAA
1 TATTTTAGGTAGCGAAAATAA
* **
41291 TATTTTCA-ATAGAAAAAATAA
1 TATTTT-AGGTAGCGAAAATAA
41312 TATTTTAGGTAGCG
1 TATTTTAGGTAGCG
41326 TTCTACCAAA
Statistics
Matches: 26, Mismatches: 7, Indels: 4
0.70 0.19 0.11
Matches are distributed among these distances:
20 1 0.04
21 24 0.92
22 1 0.04
ACGTcount: A:0.41, C:0.05, G:0.16, T:0.38
Consensus pattern (21 bp):
TATTTTAGGTAGCGAAAATAA
Found at i:41471 original size:30 final size:29
Alignment explanation
Indices: 41439--41496 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
41429 GATTAATATT
41439 TTTTTTAATGT-TTTTTAAAAT-ATTTTTA
1 TTTTTTAAT-TATTTTTAAAATAATTTTTA
41467 TTTTTTAATTAATTTTTAAAATAATTTTTA
1 TTTTTTAATT-ATTTTTAAAATAATTTTTA
41497 ATATATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 1 0.04
28 9 0.33
29 10 0.37
30 7 0.26
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (29 bp):
TTTTTTAATTATTTTTAAAATAATTTTTA
Found at i:42068 original size:50 final size:51
Alignment explanation
Indices: 41955--42072 Score: 132
Period size: 50 Copynumber: 2.4 Consensus size: 51
41945 GATTTGGCGC
* * * * *
41955 CACGTGGGGTATAGCGCGCTCCCTGCACCGCGCTATACGCTAACTGGGTTA
1 CACGTGGGGTATAGCGCGCGCCCTGCACCGCACTATACGCTAACTAGCTGA
* * ** *
42006 CACGT-GGCTATAGCGCGCGCCCTGCTCCGCACTATAC-CTATTTATCTGA
1 CACGTGGGGTATAGCGCGCGCCCTGCACCGCACTATACGCTAACTAGCTGA
42055 CACGTGGGGTATAGCGCG
1 CACGTGGGGTATAGCGCG
42073 GTGCAGGGGG
Statistics
Matches: 55, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
49 11 0.20
50 39 0.71
51 5 0.09
ACGTcount: A:0.18, C:0.31, G:0.28, T:0.23
Consensus pattern (51 bp):
CACGTGGGGTATAGCGCGCGCCCTGCACCGCACTATACGCTAACTAGCTGA
Found at i:42274 original size:17 final size:18
Alignment explanation
Indices: 42237--42277 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
42227 ATATTCTGTA
*
42237 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
42255 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
42272 TTTACT
1 TTTACT
42278 AATATAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:44329 original size:23 final size:23
Alignment explanation
Indices: 44303--44347 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
44293 CACCACAGCT
*
44303 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
44326 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
44348 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:44585 original size:149 final size:149
Alignment explanation
Indices: 44328--44629 Score: 559
Period size: 149 Copynumber: 2.0 Consensus size: 149
44318 AAGTGCCCCG
* *
44328 TAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACGTAGAATTCTTTAAGAATCA
1 TAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAATCA
44393 TATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATACA
66 TATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATACA
44458 TATGTCCCGAAGAACCGCA
131 TATGTCCCGAAGAACCGCA
44477 TAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAATCA
1 TAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAATCA
*
44542 TATACATATGCTAGGGATCAAGTATGTGTCTTTCTAGACTTCACACATGTTCCAAAGAATATACA
66 TATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATACA
* *
44607 TATGTCTCGAAGAACCGCG
131 TATGTCCCGAAGAACCGCA
44626 TAGA
1 TAGA
44630 CCCTCGACTC
Statistics
Matches: 148, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 148 1.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (149 bp):
TAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAATCA
TATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATACA
TATGTCCCGAAGAACCGCA
Found at i:45465 original size:18 final size:18
Alignment explanation
Indices: 45442--45476 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
45432 TCCCATCTAG
45442 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
45460 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
45477 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:46085 original size:21 final size:21
Alignment explanation
Indices: 46055--46099 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
46045 ATTCTGTCGT
* *
46055 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
46076 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
46097 TTG
1 TTG
46100 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:48383 original size:23 final size:23
Alignment explanation
Indices: 48357--48401 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
48347 CACCACAGCT
*
48357 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
48380 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
48402 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:48639 original size:149 final size:149
Alignment explanation
Indices: 48382--48683 Score: 550
Period size: 149 Copynumber: 2.0 Consensus size: 149
48372 AAGTGCCCCG
* *
48382 TAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACGTAGAATTCTTTAAGAATCA
1 TAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAATCA
*
48447 TATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCTAAAGAATATACA
66 TATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATACA
48512 TATGTCCCGAAGAACCGCA
131 TATGTCCCGAAGAACCGCA
48531 TAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAATCA
1 TAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAATCA
*
48596 TATACATATGCTAGGGATCAAGTATGTGTCTTTCTAGACTTCACACATGTTCCAAAGAATATACA
66 TATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATACA
* *
48661 TATGTCTCGAAGAACCGCG
131 TATGTCCCGAAGAACCGCA
48680 TAGA
1 TAGA
48684 CCCTCGACTC
Statistics
Matches: 147, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
149 147 1.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (149 bp):
TAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAATCA
TATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATACA
TATGTCCCGAAGAACCGCA
Found at i:49515 original size:18 final size:18
Alignment explanation
Indices: 49492--49526 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
49482 TCCCATCTAG
49492 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
49510 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
49527 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:50128 original size:21 final size:21
Alignment explanation
Indices: 50098--50142 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
50088 ATTCTGTCGT
*
50098 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTATCGATTCCCC
*
50119 TTGAATGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
50140 TTG
1 TTG
50143 CCCAGAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.16, C:0.22, G:0.29, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTATCGATTCCCC
Found at i:55254 original size:50 final size:51
Alignment explanation
Indices: 55144--55268 Score: 139
Period size: 50 Copynumber: 2.5 Consensus size: 51
55134 TCTACACAGA
* * * * *
55144 TATAGCGCGGTTCAGGGTGAGCGCTATACCCCACGTGTAACCTAGTTAGCAG
1 TATAGCGCGGTGCAGGG-GAGCGCTATACCCCACGTGGAACCAAATCAGCAG
* *
55196 -ATAGCGCGGTGCAGGGGCGCGCTATACCCCACGTGGAGCCAAATCAGC-G
1 TATAGCGCGGTGCAGGGGAGCGCTATACCCCACGTGGAACCAAATCAGCAG
*
55245 TATAACGCGG-GTCAGGGGAGCGCT
1 TATAGCGCGGTG-CAGGGGAGCGCT
55269 TTACTACTAT
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
49 2 0.03
50 45 0.73
51 15 0.24
ACGTcount: A:0.22, C:0.26, G:0.34, T:0.18
Consensus pattern (51 bp):
TATAGCGCGGTGCAGGGGAGCGCTATACCCCACGTGGAACCAAATCAGCAG
Found at i:69364 original size:32 final size:32
Alignment explanation
Indices: 69314--69396 Score: 98
Period size: 32 Copynumber: 2.6 Consensus size: 32
69304 TCGGATCGGG
* * *
69314 TATCGGGTCGGTTG-TTTTCAGTTC-GGATCAA
1 TATCGGATCGGTTGATTTTCAGGTCAGG-GCAA
* *
69345 TATCGGATTGGTTGATTTTCGGGTCAGGGCAA
1 TATCGGATCGGTTGATTTTCAGGTCAGGGCAA
69377 TATCGGATCGGTTGATTTTC
1 TATCGGATCGGTTGATTTTC
69397 TGTTTAGGTC
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
31 12 0.27
32 30 0.68
33 2 0.05
ACGTcount: A:0.17, C:0.14, G:0.30, T:0.39
Consensus pattern (32 bp):
TATCGGATCGGTTGATTTTCAGGTCAGGGCAA
Found at i:70739 original size:32 final size:33
Alignment explanation
Indices: 70703--70766 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 33
70693 CAATATGTTT
*
70703 GGGTTGCTTTTTGG-TCGGGTT-AAATTCGGTTC
1 GGGTTGC-TTTCGGATCGGGTTAAAATTCGGTTC
*
70735 GGGTTGCTTTCGGATTGGGTTAAAATTCGGTT
1 GGGTTGCTTTCGGATCGGGTTAAAATTCGGTT
70767 TGGATCAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 5 0.18
32 13 0.46
33 10 0.36
ACGTcount: A:0.12, C:0.11, G:0.34, T:0.42
Consensus pattern (33 bp):
GGGTTGCTTTCGGATCGGGTTAAAATTCGGTTC
Found at i:81097 original size:6 final size:6
Alignment explanation
Indices: 81086--81112 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
81076 AAACACTTCT
81086 CCATTC CCATTC CCATTC CCATTC CCA
1 CCATTC CCATTC CCATTC CCATTC CCA
81113 ACTCCAAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.52, G:0.00, T:0.30
Consensus pattern (6 bp):
CCATTC
Found at i:85577 original size:15 final size:15
Alignment explanation
Indices: 85557--85585 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
85547 GAATAACAGA
85557 AAAACTATTATATAG
1 AAAACTATTATATAG
85572 AAAACTATTATATA
1 AAAACTATTATATA
85586 AGGAATCCAC
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:0.55, C:0.07, G:0.03, T:0.34
Consensus pattern (15 bp):
AAAACTATTATATAG
Found at i:91550 original size:31 final size:31
Alignment explanation
Indices: 91505--91587 Score: 91
Period size: 31 Copynumber: 2.7 Consensus size: 31
91495 GTCACTTAAC
91505 TTTT-AAAAATTATAAAATGAT-CATTAAAT
1 TTTTCAAAAATTATAAAATGATACATTAAAT
* *
91534 TTTTCAAACAATTATAAAA-CATACATTAAGT
1 TTTTCAAA-AATTATAAAATGATACATTAAAT
*
91565 TTTATCAAAATATTACAAAATGA
1 TTT-TCAAAA-ATTATAAAATGA
91588 CAACGAAATT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
29 4 0.09
30 5 0.11
31 21 0.48
32 13 0.30
33 1 0.02
ACGTcount: A:0.51, C:0.08, G:0.04, T:0.37
Consensus pattern (31 bp):
TTTTCAAAAATTATAAAATGATACATTAAAT
Found at i:93551 original size:2 final size:2
Alignment explanation
Indices: 93544--93581 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
93534 ATAAATTTAT
*
93544 TA TA TA TA TA TA TT 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 TA TA TA TA TA TA
93582 ATTGATATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:101332 original size:23 final size:23
Alignment explanation
Indices: 101306--101351 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
101296 CACCACAGCT
*
101306 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
*
101329 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
101352 TATAATAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:101568 original size:149 final size:151
Alignment explanation
Indices: 101329--101634 Score: 589
Period size: 149 Copynumber: 2.0 Consensus size: 151
101319 CGAAGTGCCA
101329 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
101394 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAG-A-ATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
101457 TATATATATCCCGAAGGACCG
131 TATATATATCCCGAAGGACCG
*
101478 TGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
101543 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
101608 TATATATATCCCGAAGGACCG
131 TATATATATCCCGAAGGACCG
101629 CGTAGA
1 CGTAGA
101635 CCCTCTACCA
Statistics
Matches: 153, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
149 123 0.80
150 1 0.01
151 29 0.19
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (151 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
TATATATATCCCGAAGGACCG
Found at i:102196 original size:63 final size:63
Alignment explanation
Indices: 102090--102248 Score: 203
Period size: 63 Copynumber: 2.5 Consensus size: 63
102080 TAATGGAGAC
* * *
102090 ATGCATCGATGCACTCCTGATGCATCGATGCACTGAAGGCATTCGATGTTCAT-TTTATTAGAA
1 ATGCATCGATGCACTCCTTATGCATCGATGCACTGAAGACATTCGATGTTCATATTTA-AAGAA
* ** **
102153 ATGCATCGATGCACTCCTTATGCATCGATGCACTGACGACATTCGATGTTTGTATTTAAATTA
1 ATGCATCGATGCACTCCTTATGCATCGATGCACTGAAGACATTCGATGTTCATATTTAAAGAA
***
102216 ATGCATCGATGCACTTAATATGCATCGATGCAC
1 ATGCATCGATGCACTCCTTATGCATCGATGCAC
102249 CTTCAACAAA
Statistics
Matches: 84, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
63 80 0.95
64 4 0.05
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTTATGCATCGATGCACTGAAGACATTCGATGTTCATATTTAAAGAA
Found at i:108348 original size:23 final size:23
Alignment explanation
Indices: 108322--108367 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
108312 CACCACAGCT
*
108322 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
*
108345 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
108368 TATAATAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:108611 original size:146 final size:149
Alignment explanation
Indices: 108345--108645 Score: 563
Period size: 146 Copynumber: 2.0 Consensus size: 149
108335 CGAAGTGCCA
108345 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
*
108410 CATATACATATACCAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACA-GA-ATA
66 CATATACATATACCAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACATAATATA
108473 TATATATCCCGAAGGACCG
131 TATATATCCCGAAGGACCG
108492 C-TAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
*
108556 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACATAATATA
66 CATATACATATACCAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACATAATATA
108621 TATATATCCCGAAGGACCG
131 TATATATCCCGAAGGACCG
108640 CGTAGA
1 CGTAGA
108646 CCCTCTACCC
Statistics
Matches: 149, Mismatches: 2, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
146 120 0.81
147 2 0.01
148 23 0.15
149 4 0.03
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
CATATACATATACCAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACATAATATA
TATATATCCCGAAGGACCG
Found at i:109229 original size:63 final size:63
Alignment explanation
Indices: 109100--109258 Score: 185
Period size: 63 Copynumber: 2.5 Consensus size: 63
109090 TAATGGAGAC
* * * *
109100 ATGCATCGATGCTCTCCTGATGCATCGATGCACTGAAGGCATTCGATGTTCATTTTATTAGAA
1 ATGCATCGATGCACTCCTTATGCATCGATGCACTGAAGACATTCGATGTTCATTTTATAAGAA
* * ** **
109163 ATGCATCGATGAACTCCTTATGCATCGATGCACTGACGACATTCGATGTTTGTATTTA-AATTA
1 ATGCATCGATGCACTCCTTATGCATCGATGCACTGAAGACATTCGATGTTCAT-TTTATAAGAA
***
109226 ATGCATCGATGCACTTAATATGCATCGATGCAC
1 ATGCATCGATGCACTCCTTATGCATCGATGCAC
109259 CTTCAACAAA
Statistics
Matches: 81, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
63 77 0.95
64 4 0.05
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTTATGCATCGATGCACTGAAGACATTCGATGTTCATTTTATAAGAA
Found at i:111334 original size:30 final size:30
Alignment explanation
Indices: 111299--111371 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
111289 CCCGAAGGAC
* *
111299 CTATCCAGAGGTTATAAAGATCCTCGGTAA
1 CTATCCATAGGTCATAAAGATCCTCGGTAA
111329 CTATCCATAGGTCATAAAGATCCTCGGTAA
1 CTATCCATAGGTCATAAAGATCCTCGGTAA
*
111359 CTGTCCATAGGTC
1 CTATCCATAGGTC
111372 CCGAAGAACC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.27
Consensus pattern (30 bp):
CTATCCATAGGTCATAAAGATCCTCGGTAA
Found at i:111388 original size:30 final size:30
Alignment explanation
Indices: 111314--111398 Score: 107
Period size: 30 Copynumber: 2.8 Consensus size: 30
111304 CAGAGGTTAT
* *
111314 AAAGATCCTCGGTAACTATCCATAGGTCAT
1 AAAGATCCTCGGTAACTGTCCATAGGTCAC
*
111344 AAAGATCCTCGGTAACTGTCCATAGGTCCC
1 AAAGATCCTCGGTAACTGTCCATAGGTCAC
* * *
111374 GAAGAACCTAGGTAAACTGTCCATA
1 AAAGATCCTCGGT-AACTGTCCATA
111399 TGTTCCTTAG
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 37 0.77
31 11 0.23
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.24
Consensus pattern (30 bp):
AAAGATCCTCGGTAACTGTCCATAGGTCAC
Found at i:111411 original size:31 final size:30
Alignment explanation
Indices: 111376--111483 Score: 105
Period size: 33 Copynumber: 3.5 Consensus size: 30
111366 TAGGTCCCGA
*
111376 AGAACCTAGGTAAACTGTCCATATGTTCCTT
1 AGAACATAGGTAAACTGTCCATATGTT-CTT
*
111407 AGAAC--AGGTATACTGTCCATATG-TCTT
1 AGAACATAGGTAAACTGTCCATATGTTCTT
*
111434 GAAAGACATAGGTAAAAACTGTCCATATGTTCTGT
1 -AGA-ACATAGGT--AAACTGTCCATATGTTCT-T
*
111469 AGAGCATAGGTAAAC
1 AGAACATAGGTAAAC
111484 CCTCGACTCT
Statistics
Matches: 64, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
27 3 0.05
28 3 0.05
29 19 0.30
31 13 0.20
33 20 0.31
34 5 0.08
35 1 0.02
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (30 bp):
AGAACATAGGTAAACTGTCCATATGTTCTT
Found at i:111574 original size:17 final size:17
Alignment explanation
Indices: 111552--111587 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
111542 TTTCTTTTAT
111552 ACTTATCATTTCACATA
1 ACTTATCATTTCACATA
111569 ACTTATCATTTCACATA
1 ACTTATCATTTCACATA
111586 AC
1 AC
111588 ACATAGTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (17 bp):
ACTTATCATTTCACATA
Found at i:112850 original size:21 final size:20
Alignment explanation
Indices: 112820--112863 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
112810 TTTTGTTCGT
* *
112820 TTGAAGGGTATCGGTTCCCC
1 TTGAAGGGTACCGATTCCCC
112840 TTGAATGGGTACCGATTCCCC
1 TTGAA-GGGTACCGATTCCCC
112861 TTG
1 TTG
112864 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.16, C:0.25, G:0.27, T:0.32
Consensus pattern (20 bp):
TTGAAGGGTACCGATTCCCC
Found at i:116181 original size:30 final size:30
Alignment explanation
Indices: 116146--116218 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
116136 CCCGAAGGAC
*
116146 CTATCCAGAGGTTATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
116176 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
116206 CTGTCCATAGGTC
1 CTATCCAGAGGTC
116219 CCGAAGAACC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:116242 original size:31 final size:31
Alignment explanation
Indices: 116204--116331 Score: 116
Period size: 31 Copynumber: 4.1 Consensus size: 31
116194 GATCCTCGGT
* *
116204 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
* * **
116235 AACTGTCCATATATTCCTTAGAACATAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
* * *
116266 TACTGTCCATATGTCTCGAA-AGGCATAGGTAA
1 AACTGTCCATATGTCCCGAAGA-ACATAGGT-A
* *
116298 AACTGTCCATATGTTCTGTAA-AACATAGGTA
1 AACTGTCCATATGTCCCG-AAGAACATAGGTA
116329 AAC
1 AAC
116332 CCTCGACTCT
Statistics
Matches: 76, Mismatches: 18, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
30 1 0.01
31 50 0.66
32 22 0.29
33 3 0.04
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.27
Consensus pattern (31 bp):
AACTGTCCATATGTCCCGAAGAACATAGGTA
Found at i:117703 original size:21 final size:21
Alignment explanation
Indices: 117664--117703 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
117654 TTTTGTTCGT
* *
117664 TTGAAGGGGTATCGGTTCCAC
1 TTGAAGGGGTACCGATTCCAC
*
117685 TTGAATGGGTACCGATTCC
1 TTGAAGGGGTACCGATTCC
117704 CGTTGCCCAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCAC
Found at i:135590 original size:3 final size:3
Alignment explanation
Indices: 135584--135666 Score: 55
Period size: 3 Copynumber: 27.7 Consensus size: 3
135574 TTCATTTGAA
* * * * * * *
135584 TAT TAT T-T ATAT TAT TAT TAT TAT TAA AAT AAT AAT AAT AAT AAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
135629 TAT TAT TAT TA- TAT ATAT TA- TAT ATAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT -TAT TAT TAT -TAT TAT TAT TAT TA
135667 AAAAATAATT
Statistics
Matches: 70, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
2 5 0.07
3 58 0.83
4 7 0.10
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (3 bp):
TAT
Found at i:137063 original size:18 final size:18
Alignment explanation
Indices: 137040--137082 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
137030 CTGTTTTATG
137040 ATATTTTTAAATAAATAA
1 ATATTTTTAAATAAATAA
137058 ATATTTTTAAATAAATAA
1 ATATTTTTAAATAAATAA
137076 ATATTTT
1 ATATTTT
137083 ACTTTTATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATATTTTTAAATAAATAA
Found at i:137236 original size:29 final size:29
Alignment explanation
Indices: 137194--137253 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
137184 ATATTTCTGA
137194 ATAAATAAATATTTAATTT-ATAAATATAT
1 ATAAATAAATATTT-ATTTCATAAATATAT
* * *
137223 ATAAATTAATATTTTTTTCATAATTATAT
1 ATAAATAAATATTTATTTCATAAATATAT
137252 AT
1 AT
137254 TTGAAATGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 3 0.11
29 24 0.89
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (29 bp):
ATAAATAAATATTTATTTCATAAATATAT
Found at i:141488 original size:12 final size:12
Alignment explanation
Indices: 141469--141500 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
141459 TTGTGATGGG
141469 AAAGTAAAGTAA
1 AAAGTAAAGTAA
*
141481 ATAGTAAAGTAA
1 AAAGTAAAGTAA
141493 AAAGTAAA
1 AAAGTAAA
141501 TTTTAAGAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.16, T:0.19
Consensus pattern (12 bp):
AAAGTAAAGTAA
Found at i:155016 original size:33 final size:35
Alignment explanation
Indices: 154949--155019 Score: 119
Period size: 35 Copynumber: 2.1 Consensus size: 35
154939 ATTTTCGGGA
*
154949 TTTGCTATTTTTGGCAAAATTCGAATAAATACGAT
1 TTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
154984 TTTGCTATTTTTGGC-AAATTCG-ATAAAGACGAT
1 TTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
155017 TTT
1 TTT
155020 TTTAGCTATA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
33 13 0.37
34 7 0.20
35 15 0.43
ACGTcount: A:0.31, C:0.11, G:0.15, T:0.42
Consensus pattern (35 bp):
TTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:158837 original size:30 final size:30
Alignment explanation
Indices: 158797--158868 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
158787 CCTGAAGGAC
* *
158797 CTATCTAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGAAA
158827 CTATCCAGAGGTCATAAAGATCCTCGGAAA
1 CTATCCAGAGGTCATAAAGATCCTCGGAAA
* *
158857 CTGTCCATAGGT
1 CTATCCAGAGGT
158869 TCCGAAGAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGAAA
Done.