Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005738.1 Hibiscus syriacus cultivar Beakdansim tig00013415_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: 62705
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:992 original size:125 final size:128
Alignment explanation
Indices: 801--1042 Score: 373
Period size: 125 Copynumber: 1.9 Consensus size: 128
791 AATTTTCTTC
* * *
801 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACACATCATGATCATGTGCTAACACATGTCAGAT
**
866 CCTGGTTAAATGATTAA-T-TT-ATTATATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTATTAATTATATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * *
926 TAATTAGGTGGTGACATGTGTCACCAATGACACGCGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACACATCATGATCATGTGCTAACACATGTCAGAT
*
991 CCTAATTAAATGATTAATTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTATT-AATTATATTTAATTTAGGACCAAATTGAT
1043 TATATAAATA
Statistics
Matches: 104, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
125 74 0.71
126 1 0.01
127 2 0.02
129 27 0.26
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.35
Consensus pattern (128 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACACATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTATTAATTATATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:1466 original size:35 final size:35
Alignment explanation
Indices: 1427--1502 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
1417 TAATTGAATT
* *
1427 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
*
1462 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
1497 AATTGA
1 AATTGA
1503 GGACTGTTTG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.36, C:0.01, G:0.24, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
Found at i:1801 original size:35 final size:36
Alignment explanation
Indices: 1724--1804 Score: 94
Period size: 35 Copynumber: 2.3 Consensus size: 36
1714 TTTACCCTTA
* **
1724 AATTAAAATATATAAATATTATATATATTTTTAATT
1 AATTTAAATATATAAATATTATATATATTAATAATT
*
1760 AATTTAAAT-TATTAATATTATATATA-TAATAATT
1 AATTTAAATATATAAATATTATATATATTAATAATT
* *
1794 ATTTTTAATAT
1 AATTTAAATAT
1805 TTATCGGGCC
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
34 13 0.34
35 17 0.45
36 8 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (36 bp):
AATTTAAATATATAAATATTATATATATTAATAATT
Found at i:1850 original size:106 final size:106
Alignment explanation
Indices: 1721--1915 Score: 324
Period size: 106 Copynumber: 1.8 Consensus size: 106
1711 TACTTTACCC
1721 TTAAATTAAAATATATAAATATTATATATATTTTTAA-TTAATTTAAA-TTATTAATATTATATA
1 TTAAATTAAAATATATAAATATTATATATATTTTTAATTTAATTTAAATTTATTAATA-T-TATA
*
1784 TATAATAATTATTTTTAATATTTATCGGGCCGGGTATATATATA
64 TAT-ATAATTAATTTTAATATTTATCGGGCCGGGTATATATATA
*
1828 TTAAATT-AAATATATAAATATTATATATTTTTTTAATTTAATTTAAATTTATTAATATTATATA
1 TTAAATTAAAATATATAAATATTATATATATTTTTAATTTAATTTAAATTTATTAATATTATATA
1892 TATAATTAATTTTAATATTTATCG
66 TATAATTAATTTTAATATTTATCG
1916 AGACGGATAT
Statistics
Matches: 84, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
105 22 0.26
106 35 0.42
107 18 0.21
108 9 0.11
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (106 bp):
TTAAATTAAAATATATAAATATTATATATATTTTTAATTTAATTTAAATTTATTAATATTATATA
TATAATTAATTTTAATATTTATCGGGCCGGGTATATATATA
Found at i:1901 original size:37 final size:37
Alignment explanation
Indices: 1828--1903 Score: 98
Period size: 37 Copynumber: 2.1 Consensus size: 37
1818 TATATATATA
* **
1828 TTAAATTAAATATATAAATATTATATATTTTTTTAAT
1 TTAAATTAAATATATAAATATTATATATATAATTAAT
* * *
1865 TTAATTTAAATTTATTAATATTATATATATAATTAAT
1 TTAAATTAAATATATAAATATTATATATATAATTAAT
1902 TT
1 TT
1904 TAATATTTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (37 bp):
TTAAATTAAATATATAAATATTATATATATAATTAAT
Found at i:3486 original size:22 final size:22
Alignment explanation
Indices: 3460--3501 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
3450 TTAATTTATA
3460 AAACGT-TAAAGTATAAAGTACT
1 AAACGTAT-AAGTATAAAGTACT
*
3482 AAACGTATAATTATAAAGTA
1 AAACGTATAAGTATAAAGTA
3502 GTTAAAAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.52, C:0.07, G:0.12, T:0.29
Consensus pattern (22 bp):
AAACGTATAAGTATAAAGTACT
Found at i:5082 original size:23 final size:23
Alignment explanation
Indices: 5032--5083 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
5022 TTTTATAAAT
*
5032 ATTATATTTTTAATTAAATTACA
1 ATTATATTTTTAACTAAATTACA
* * *
5055 TTTATATTTTTAACTAATTTATA
1 ATTATATTTTTAACTAAATTACA
5078 ATTATA
1 ATTATA
5084 CGTTTAATAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (23 bp):
ATTATATTTTTAACTAAATTACA
Found at i:5395 original size:28 final size:28
Alignment explanation
Indices: 5342--5395 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
5332 GATTAGACGT
* **
5342 AATTAAATTTTTAAATTGAATTAAATTG
1 AATTAAATTTTTAAAATGAAAAAAATTG
5370 AATT-AATTTTTAAAAATGAAAAAAAT
1 AATTAAATTTTT-AAAATGAAAAAAAT
5396 AAATTTTTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 7 0.32
28 15 0.68
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.41
Consensus pattern (28 bp):
AATTAAATTTTTAAAATGAAAAAAATTG
Found at i:6126 original size:4 final size:4
Alignment explanation
Indices: 6110--6162 Score: 52
Period size: 4 Copynumber: 13.2 Consensus size: 4
6100 ATACAGAAGG
* * * * *
6110 TATC TAAC TATC TATC TATC TATC CATC GATT TATC TATC AATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
*
6158 CATC T
1 TATC T
6163 TTTCATATAA
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.28, C:0.26, G:0.02, T:0.43
Consensus pattern (4 bp):
TATC
Found at i:8707 original size:31 final size:32
Alignment explanation
Indices: 8671--8786 Score: 89
Period size: 31 Copynumber: 3.7 Consensus size: 32
8661 AGTTTGACAG
* *
8671 TGCTCAACTCG-TGTTCGTTAAAAAAATTTAT
1 TGCTCAACTCGATGCTCGTTAAAAAAATTTAC
* ** *
8702 TGCTCAACTCGACT-CGTTGTTCATCAAAA-TT-G
1 TGCTCAACTCGA-TGC-TCGTT-AAAAAAATTTAC
*
8734 TGCTCGACTCG-TGCTCGTTAAAAAAATTTAC
1 TGCTCAACTCGATGCTCGTTAAAAAAATTTAC
* *
8765 TGCTCGACTCGTTGCTCGTTAA
1 TGCTCAACTCGATGCTCGTTAA
8787 GCTCGACTTG
Statistics
Matches: 67, Mismatches: 10, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
29 5 0.07
30 7 0.10
31 23 0.34
32 20 0.30
33 7 0.10
34 5 0.07
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.35
Consensus pattern (32 bp):
TGCTCAACTCGATGCTCGTTAAAAAAATTTAC
Found at i:8792 original size:21 final size:21
Alignment explanation
Indices: 8766--8811 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
8756 AAAATTTACT
*
8766 GCTCGACTCGTTGCTCGTTAA
1 GCTCGACTCGTTACTCGTTAA
*
8787 GCTCGACTTGTTACTCGTTAA
1 GCTCGACTCGTTACTCGTTAA
8808 GCTC
1 GCTC
8812 ACTAAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.15, C:0.28, G:0.22, T:0.35
Consensus pattern (21 bp):
GCTCGACTCGTTACTCGTTAA
Found at i:8953 original size:41 final size:41
Alignment explanation
Indices: 8901--8980 Score: 101
Period size: 41 Copynumber: 2.0 Consensus size: 41
8891 TTTTTGTATT
* *
8901 AAAATACTATTA-TTAA-TTAATAATATTTTATTATTTATTAA
1 AAAATAATATTAGTTAACTT-ATAAT-TTTTATTACTTATTAA
*
8942 AAAATAATATTAGTTAACTTATTATTTTTATTACTTATT
1 AAAATAATATTAGTTAACTTATAATTTTTATTACTTATT
8981 CATATTAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
41 24 0.71
42 8 0.24
43 2 0.06
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.53
Consensus pattern (41 bp):
AAAATAATATTAGTTAACTTATAATTTTTATTACTTATTAA
Found at i:9224 original size:23 final size:23
Alignment explanation
Indices: 9190--9241 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
9180 TCAACTCGTT
*
9190 AAACACCTCTAATCCAT-GGTACA
1 AAACACCCCTAAT-CATGGGTACA
9213 AAACACCCCTAATCATGGGTACA
1 AAACACCCCTAATCATGGGTACA
9236 AAACAC
1 AAACAC
9242 ATGTTCAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 3 0.11
23 24 0.89
ACGTcount: A:0.42, C:0.31, G:0.10, T:0.17
Consensus pattern (23 bp):
AAACACCCCTAATCATGGGTACA
Found at i:12607 original size:17 final size:19
Alignment explanation
Indices: 12585--12620 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
12575 ATTATTATTT
12585 TTATTAATT-TTG-TATAA
1 TTATTAATTATTGATATAA
12602 TTATTAATTATTGATATAA
1 TTATTAATTATTGATATAA
12621 GTAAATGTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 3 0.18
19 5 0.29
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.56
Consensus pattern (19 bp):
TTATTAATTATTGATATAA
Found at i:14842 original size:21 final size:21
Alignment explanation
Indices: 14818--14864 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
14808 AATATGTAAA
* *
14818 TCGCATTGCGATTTTTCAAAT
1 TCGCATTACGATTTTCCAAAT
*
14839 TCGCGTTACGATTTTCCAAAT
1 TCGCATTACGATTTTCCAAAT
14860 TCGCA
1 TCGCA
14865 ACTCGAAAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.38
Consensus pattern (21 bp):
TCGCATTACGATTTTCCAAAT
Found at i:14880 original size:20 final size:20
Alignment explanation
Indices: 14855--14950 Score: 115
Period size: 20 Copynumber: 4.8 Consensus size: 20
14845 TACGATTTTC
14855 CAAATTCGCAACTCGAAAGT
1 CAAATTCGCAACTCGAAAGT
* *
14875 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACTCGAAAGT
14895 CAAATTCGCAA-TGCGAAAGT
1 CAAATTCGCAACT-CGAAAGT
**
14915 CAAATTCGCAACT-GAATTT
1 CAAATTCGCAACTCGAAAGT
* *
14934 CATATTCGCAACGCGAA
1 CAAATTCGCAACTCGAA
14951 TTTAATTTCG
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
19 15 0.23
20 49 0.75
21 1 0.02
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.22
Consensus pattern (20 bp):
CAAATTCGCAACTCGAAAGT
Found at i:14953 original size:20 final size:20
Alignment explanation
Indices: 14855--14964 Score: 109
Period size: 20 Copynumber: 5.6 Consensus size: 20
14845 TACGATTTTC
* *
14855 CAAATTCGCAACTCGAAAGT
1 CAAATTCGCAACGCGAATGT
14875 CAAATTCGCAACGCG-ATAGT
1 CAAATTCGCAACGCGAAT-GT
* *
14895 CAAATTCGCAATGCGAAAGT
1 CAAATTCGCAACGCGAATGT
* *
14915 CAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACGCGAATGT
*
14934 CATATTCGCAACGCGAAT-T
1 CAAATTCGCAACGCGAATGT
* *
14953 TAATTTCGCAAC
1 CAAATTCGCAAC
14965 AGGTTTTAGT
Statistics
Matches: 74, Mismatches: 13, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
19 26 0.35
20 47 0.64
21 1 0.01
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.25
Consensus pattern (20 bp):
CAAATTCGCAACGCGAATGT
Found at i:15148 original size:16 final size:15
Alignment explanation
Indices: 15122--15158 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
15112 CCCCATCTCT
15122 ATTTTTTTTTACATA
1 ATTTTTTTTTACATA
*
15137 ATTTTATTTTTATATA
1 ATTTT-TTTTTACATA
15153 ATTTTT
1 ATTTTT
15159 CAATGATTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (15 bp):
ATTTTTTTTTACATA
Found at i:15910 original size:24 final size:24
Alignment explanation
Indices: 15852--15898 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
15842 AGTCAGTATT
*
15852 CGAAATTTGATCTTGGTCAATACC
1 CGAACTTTGATCTTGGTCAATACC
15876 CGAACTTTGATCTTGGTCAATAC
1 CGAACTTTGATCTTGGTCAATAC
15899 TCGGATTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (24 bp):
CGAACTTTGATCTTGGTCAATACC
Found at i:17048 original size:475 final size:474
Alignment explanation
Indices: 16159--17113 Score: 1865
Period size: 475 Copynumber: 2.0 Consensus size: 474
16149 ATAACTGGAA
16159 TATGCCATAATTACTTCAGATACCGGAAGAAAAATTGGTAAAGATATCAGTTGATTGTTACACAA
1 TATGCCATAATTACTTCAGATACCGGAAGAAAAATTGGTAAAGATATCAGTTGATTGTTACACAA
16224 AAGTTATTCGTATCAAGAAAGATGATTGTTTGATACAAAGGAAGACTTGAAGATAGCTTTGTATA
66 AAGTTATTCGTATCAAGAAAGATGATTGTTTGATACAAAGGAAGACTTGAAGATAGCTTTGTATA
16289 CGAAATGTGTGGAAGATGGCTATCAACTAAGAGTTAACAAATCAAGCAAAGATCGTTTCGAAACA
131 CGAAATGTGTGGAAGATGGCTATCAACTAAGAGTTAACAAATCAAGCAAAGATCGTTTCGAAACA
*
16354 AGGTGTATGATTGACAAAAACTGTATGTGGCGTATGATTGCAAAGAGGATAAAAGATTGCGAAAT
196 AGGTGTATGATTGACAAAAACTGTATGTGGCGTATGATTGCAAAGAGGATAAAAGATTACGAAAT
16419 GTTTCAAGTTAGGACTTTTATTGATAAACATACATGTTCAAGAACCCAAGTTTTTCCTCACCATA
261 GTTTCAAGTTAGGACTTTTATTGATAAACATACATGTTCAAGAACCCAAGTTTTTCCTCACCATA
16484 GACAGGCAAACAAAAAGGTGTTGGGTGATTTTCTGGCTAAGTTAATGTTTTTGAATAGAAGGGTA
326 GACAGGCAAACAAAAAGGTGTTGGGTGATTTTCTGGCTAAGTTAATGTTTTTGAATAGAAGGGTA
16549 TATCGGGGACATAAAATTATGACTGACATGAATGCTCGATTCATGATTAGTATCTCATATTCTCA
391 TATCGGGGACATAAAATTATGACTGACATGAATGCTCGATTCATGATTAGTATCTCATATTCTCA
16614 AGCTTGGAGAGCCAAATGT
456 AGCTTGGAGAGCCAAATGT
*
16633 TATGCCATAATTGCTTCAGATACCGGAAGAAAAATTGGTAAAGATATCAGTTGATTGTTACACAA
1 TATGCCATAATTACTTCAGATACCGGAAGAAAAATTGGTAAAGATATCAGTTGATTGTTACACAA
16698 AAGTTATTCGTATCAAGAAAGATGATTGTTTTGATACAAAGGAAGACTTGAAGATAGCTTTGTAT
66 AAGTTATTCGTATCAAGAAAGATGATTG-TTTGATACAAAGGAAGACTTGAAGATAGCTTTGTAT
16763 ACGAAATGTGTGGAAGATGGCTATCAACTAAGAGTTAACAAATCAAGCAAAGATCGTTTCGAAAC
130 ACGAAATGTGTGGAAGATGGCTATCAACTAAGAGTTAACAAATCAAGCAAAGATCGTTTCGAAAC
16828 AAGGTGTATGATTGACAAAAACTGTATGTGGCGTATGATTGCAAAGAGGATAAAAGATTACGAAA
195 AAGGTGTATGATTGACAAAAACTGTATGTGGCGTATGATTGCAAAGAGGATAAAAGATTACGAAA
*
16893 TGTTTCCAGTTAGGACTTTTATTGATAAACATACATGTTCAAGAACCCAAGTTTTTCCTCACCAT
260 TGTTTCAAGTTAGGACTTTTATTGATAAACATACATGTTCAAGAACCCAAGTTTTTCCTCACCAT
*
16958 AGACAGGCAAACAAAAAGGTGTTGGGTGATTTTCTGGCTAAGTTAATGTTTTTGAATGGAAGGGT
325 AGACAGGCAAACAAAAAGGTGTTGGGTGATTTTCTGGCTAAGTTAATGTTTTTGAATAGAAGGGT
17023 ATATCGGGGACATAAAATTATGACTGACATGAATGCTCGATTCATGATTAGTATCTCATATTCTC
390 ATATCGGGGACATAAAATTATGACTGACATGAATGCTCGATTCATGATTAGTATCTCATATTCTC
17088 AAGCTTGGAGAGCCAAATGT
455 AAGCTTGGAGAGCCAAATGT
17108 TATGCC
1 TATGCC
17114 TTGGAATTGT
Statistics
Matches: 476, Mismatches: 4, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
474 92 0.19
475 384 0.81
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (474 bp):
TATGCCATAATTACTTCAGATACCGGAAGAAAAATTGGTAAAGATATCAGTTGATTGTTACACAA
AAGTTATTCGTATCAAGAAAGATGATTGTTTGATACAAAGGAAGACTTGAAGATAGCTTTGTATA
CGAAATGTGTGGAAGATGGCTATCAACTAAGAGTTAACAAATCAAGCAAAGATCGTTTCGAAACA
AGGTGTATGATTGACAAAAACTGTATGTGGCGTATGATTGCAAAGAGGATAAAAGATTACGAAAT
GTTTCAAGTTAGGACTTTTATTGATAAACATACATGTTCAAGAACCCAAGTTTTTCCTCACCATA
GACAGGCAAACAAAAAGGTGTTGGGTGATTTTCTGGCTAAGTTAATGTTTTTGAATAGAAGGGTA
TATCGGGGACATAAAATTATGACTGACATGAATGCTCGATTCATGATTAGTATCTCATATTCTCA
AGCTTGGAGAGCCAAATGT
Found at i:19065 original size:25 final size:25
Alignment explanation
Indices: 19024--19073 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
19014 AAATCAATTA
* *
19024 AACATTGTTGTGTGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
19049 AACATTGTTATGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
19074 GAAAAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.26, C:0.08, G:0.20, T:0.46
Consensus pattern (25 bp):
AACATTGTTATGGGTACATTATTTG
Found at i:19492 original size:39 final size:39
Alignment explanation
Indices: 19449--19535 Score: 138
Period size: 39 Copynumber: 2.2 Consensus size: 39
19439 TCCAATGCTC
*
19449 ATCAAAATCCAAAGCTCACATGGTGCCAAACAAAAGGAA
1 ATCAAAATCCAAAGATCACATGGTGCCAAACAAAAGGAA
* * *
19488 ATCAAAATCCAAATATCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGATCACATGGTGCCAAACAAAAGGAA
19527 ATCAAAATC
1 ATCAAAATC
19536 TACAACTTGA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.49, C:0.21, G:0.14, T:0.16
Consensus pattern (39 bp):
ATCAAAATCCAAAGATCACATGGTGCCAAACAAAAGGAA
Found at i:19798 original size:20 final size:20
Alignment explanation
Indices: 19773--19810 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
19763 GCAACGCTTA
19773 TTTCGCATTGCGAATTTGAC
1 TTTCGCATTGCGAATTTGAC
*
19793 TTTCGCGTTGCGAATTTG
1 TTTCGCATTGCGAATTTG
19811 TACCTTCAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.42
Consensus pattern (20 bp):
TTTCGCATTGCGAATTTGAC
Found at i:20641 original size:21 final size:20
Alignment explanation
Indices: 20601--20672 Score: 63
Period size: 21 Copynumber: 3.5 Consensus size: 20
20591 GCGGGCGGGA
* *
20601 CCTCTTAAACGATGACAGGGG
1 CCTCTTGAAC-ATGAGAGGGG
*
20622 CCTCTTGAACAGTGGGAGGGG
1 CCTCTTGAACA-TGAGAGGGG
* **
20643 CTTCTTCGATGATGAGAGGGG
1 CCTCTT-GAACATGAGAGGGG
20664 CCTCTTGAA
1 CCTCTTGAA
20673 TAATAGGAGT
Statistics
Matches: 40, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
20 3 0.08
21 34 0.85
22 3 0.08
ACGTcount: A:0.22, C:0.21, G:0.33, T:0.24
Consensus pattern (20 bp):
CCTCTTGAACATGAGAGGGG
Found at i:23153 original size:22 final size:22
Alignment explanation
Indices: 23125--23175 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
23115 GATGGAGATA
23125 GACGGATTTCGTCGGAAATGGG
1 GACGGATTTCGTCGGAAATGGG
* *
23147 GACGGATTTCGTCTGAGATGGG
1 GACGGATTTCGTCGGAAATGGG
23169 GACGGAT
1 GACGGAT
23176 GTCGCCGTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.22, C:0.14, G:0.41, T:0.24
Consensus pattern (22 bp):
GACGGATTTCGTCGGAAATGGG
Found at i:24424 original size:80 final size:80
Alignment explanation
Indices: 24264--24425 Score: 245
Period size: 80 Copynumber: 2.0 Consensus size: 80
24254 ATTAATATTT
*
24264 TTTAACATTTCCGGTAAAGCGCTACATAAAACATTATTTTTTTTTACCGAAAATGTTAATATTGG
1 TTTAACATTTCCGGTAAAGCGCTACATAAAACATTATTTTTTTCTACCGAAAATGTTAATATTGG
*
24329 ACGCTACCTAAAATG
66 ACGCTACCGAAAATG
* *
24344 TTTAACATTTTCGGTAAAGCGCTACATAAAATATTATTTTTTTCTACC-AGAAATGTTAATATTG
1 TTTAACATTTCCGGTAAAGCGCTACATAAAACATTATTTTTTTCTACCGA-AAATGTTAATATTG
* * *
24408 GGCGTTACCGATAATG
65 GACGCTACCGAAAATG
24424 TT
1 TT
24426 ATTTTTTCTA
Statistics
Matches: 74, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
79 1 0.01
80 73 0.99
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (80 bp):
TTTAACATTTCCGGTAAAGCGCTACATAAAACATTATTTTTTTCTACCGAAAATGTTAATATTGG
ACGCTACCGAAAATG
Found at i:32763 original size:175 final size:174
Alignment explanation
Indices: 32459--32818 Score: 560
Period size: 175 Copynumber: 2.1 Consensus size: 174
32449 TTTTGAGTTG
* * *
32459 TCAATATAGTTGTAGAACTTTATTAGACTTGTACGAGTAAGACAATTGTTGCCCTCACAAATTGA
1 TCAATA-AATTGTAGAACTTGATTAGACTTGTAAGAGTAAGACAATTGTTGCCCTCACAAATTGA
*
32524 CTTTTAATCTTTATACTTTTGAACCCATAAGTGATATCGGTGGTAAAAAGAACTATTACTCTTTA
65 CTTTTAATCCTTATACTTTTGAACCCATAAGTGATATCGGTGGTAAAAAGAACTATTACTCTTTA
*
32589 AAGATCTTAGATTCGAGCAATTACGTCCGTAAAATATATGAATTA
130 AAGATCTTAGATTCGAGCAATTACGTCCATAAAATATATGAATTA
*
32634 TCAATACAATTGTAGAACTTGATTAGAGTTGTAAGAGTAAGACAATTGTTGCCCTCACAAATTGA
1 TCAATA-AATTGTAGAACTTGATTAGACTTGTAAGAGTAAGACAATTGTTGCCCTCACAAATTGA
* *
32699 CTTTTAATCCTTATACTTTTGAACCCATAAGTGATCTCGGTGGT-AAAAGAAACTATTGCTCTTT
65 CTTTTAATCCTTATACTTTTGAACCCATAAGTGATATCGGTGGTAAAAAG-AACTATTACTCTTT
* * * * * *
32763 AAAGATTTTAGGTTCGAGCAATTACGTCTATAAAATGTATGTATTG
129 AAAGATCTTAGATTCGAGCAATTACGTCCATAAAATATATGAATTA
32809 TCAATAAATT
1 TCAATAAATT
32819 AATAAAATTA
Statistics
Matches: 169, Mismatches: 15, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
174 9 0.05
175 160 0.95
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (174 bp):
TCAATAAATTGTAGAACTTGATTAGACTTGTAAGAGTAAGACAATTGTTGCCCTCACAAATTGAC
TTTTAATCCTTATACTTTTGAACCCATAAGTGATATCGGTGGTAAAAAGAACTATTACTCTTTAA
AGATCTTAGATTCGAGCAATTACGTCCATAAAATATATGAATTA
Found at i:36156 original size:39 final size:39
Alignment explanation
Indices: 36112--36190 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
36102 CACTCTTATA
36112 AATATTTTTAGATCTATCACTGCTAAGTGTTAATCGGCC
1 AATATTTTTAGATCTATCACTGCTAAGTGTTAATCGGCC
* *
36151 AATATTTTTAGATCTATTATTGCTAAGTGTTAATCGGCC
1 AATATTTTTAGATCTATCACTGCTAAGTGTTAATCGGCC
36190 A
1 A
36191 TTAAATGTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (39 bp):
AATATTTTTAGATCTATCACTGCTAAGTGTTAATCGGCC
Found at i:52603 original size:17 final size:17
Alignment explanation
Indices: 52581--52615 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
52571 AGTCACCATC
*
52581 GACATTTGTGTTAGGTA
1 GACATTTGGGTTAGGTA
52598 GACATTTGGGTTAGGTA
1 GACATTTGGGTTAGGTA
52615 G
1 G
52616 GTAGAACACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.23, C:0.06, G:0.34, T:0.37
Consensus pattern (17 bp):
GACATTTGGGTTAGGTA
Found at i:53079 original size:223 final size:222
Alignment explanation
Indices: 52692--53338 Score: 1001
Period size: 223 Copynumber: 2.9 Consensus size: 222
52682 GTATGCGCTT
* * * *
52692 TTCAAATATTCATTTTAGGTTCGGGCGTTGATTACGCATGGGGAAGAGTTAGCTCCCCACAACGT
1 TTCAAATATTCATTTTAGGTTCGGGAGTCGATTACGCATGGGGAAGAGTTAGCACCCCACAACGC
* * *
52757 CCAAAGATTAGTACCTAATCGCTTGTATGTTGTCGTGGTGGTGGAAATTATAATTTCGAATAGAA
66 CCAAAAATTGGTACCTAATCGCTTGTATGTTGTCGTGGTGGTGGAAATTATAAATTCGAATAGAA
52822 AATTAAATTATGATCCATTTATTGAACATTGATTAATTTGTTTCGAATTATTTAATAAAGAACAT
131 AATTAAATTATGATCCATTTATTGAACATTGATTAATTTGTTTCGAATTATTTAATAAAGAACAT
* *
52887 TCCATATTCCGAGAAGAGACCACGAGA
196 TCCATATTACGAGAAAAGACCACGAGA
*
52914 TTCAAATATTCATTTTAGGTTCGGGAGTCGATTACGCATGGGGAAGAGTTAGCACCCCCACAATG
1 TTCAAATATTCATTTTAGGTTCGGGAGTCGATTACGCATGGGGAAGAGTTAGCA-CCCCACAACG
* * * * *
52979 CCCAAAAATTGGTACCTAATCGCTTGTATGTTGTTGTAGTGGTGGAAATTATAAACTCGGATAAA
65 CCCAAAAATTGGTACCTAATCGCTTGTATGTTGTCGTGGTGGTGGAAATTATAAATTCGAATAGA
*** *
53044 AAATTAAATTCCAATCCATTTATTGAACGTTGATTAATTTGTTTCGAATTATTTAATAAAGAACA
130 AAATTAAATTATGATCCATTTATTGAACATTGATTAATTTGTTTCGAATTATTTAATAAAGAACA
* *
53109 TTCCATATTATGAGAAAAGACCACGGGA
195 TTCCATATTACGAGAAAAGACCACGAGA
* * *
53137 TTCAAAGATTTA-TTTAGGATT-GGGAGTCCATTACGCATGGGGAAGAGTTAGCACCCCACAACG
1 TTCAAATATTCATTTTAGG-TTCGGGAGTCGATTACGCATGGGGAAGAGTTAGCACCCCACAACG
*
53200 CCCAAAAATTGGTACCTAATCGCTTGTTTGTTGTCGTGGTGGTGGAAATTATAAATTCGAATAGA
65 CCCAAAAATTGGTACCTAATCGCTTGTATGTTGTCGTGGTGGTGGAAATTATAAATTCGAATAGA
* * * *
53265 AAATTAAATTTTGATTCATTTATTGAACATTGATTAATTTATTTCGAATTATTTAATAAAGAACG
130 AAATTAAATTATGATCCATTTATTGAACATTGATTAATTTGTTTCGAATTATTTAATAAAGAACA
53330 TTCCATATT
195 TTCCATATT
53339 TAAGACCAAG
Statistics
Matches: 385, Mismatches: 38, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
221 135 0.35
222 88 0.23
223 162 0.42
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.34
Consensus pattern (222 bp):
TTCAAATATTCATTTTAGGTTCGGGAGTCGATTACGCATGGGGAAGAGTTAGCACCCCACAACGC
CCAAAAATTGGTACCTAATCGCTTGTATGTTGTCGTGGTGGTGGAAATTATAAATTCGAATAGAA
AATTAAATTATGATCCATTTATTGAACATTGATTAATTTGTTTCGAATTATTTAATAAAGAACAT
TCCATATTACGAGAAAAGACCACGAGA
Found at i:57408 original size:39 final size:39
Alignment explanation
Indices: 57365--57501 Score: 186
Period size: 39 Copynumber: 3.5 Consensus size: 39
57355 ACATGATGGA
* *
57365 GCATCGAGAGCTGCAAGCCCGGGTGATGAGCATCCTGCT
1 GCATCGAGAGCTGCAAGTCCGGATGATGAGCATCCTGCT
*
57404 GCATCGAGAGCTGCAAGTCCGGATGATGAGCATCCTGTT
1 GCATCGAGAGCTGCAAGTCCGGATGATGAGCATCCTGCT
* * *
57443 ACATCGAGAGTTGCAAGTCCGGATGATGAGCATTCTGCT
1 GCATCGAGAGCTGCAAGTCCGGATGATGAGCATCCTGCT
* *
57482 GCGTCAAGAG-TGGCAAGTCC
1 GCATCGAGAGCT-GCAAGTCC
57502 TGTTTGGTTA
Statistics
Matches: 87, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
38 1 0.01
39 86 0.99
ACGTcount: A:0.23, C:0.24, G:0.31, T:0.21
Consensus pattern (39 bp):
GCATCGAGAGCTGCAAGTCCGGATGATGAGCATCCTGCT
Done.