Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008984.1 Hibiscus syriacus cultivar Beakdansim tig00112348_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: 146169
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.32
Found at i:1949 original size:29 final size:28
Alignment explanation
Indices: 1917--2007 Score: 83
Period size: 29 Copynumber: 3.1 Consensus size: 28
1907 TAAGTTATAG
1917 TTTAGGAATGAAATTAAAATGTTCAAAAT
1 TTTAGG-ATGAAATTAAAATGTTCAAAAT
* * * *
1946 TTTAAGGATTAATTTAAAATGAATCATAAT
1 TTT-AGGATGAAATTAAAATG-TTCAAAAT
* * * *
1976 TTGAGGATGAAATTAGAATATTCAAAAG
1 TTTAGGATGAAATTAAAATGTTCAAAAT
2004 TTTA
1 TTTA
2008 AGAACATTGT
Statistics
Matches: 47, Mismatches: 13, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
28 8 0.17
29 28 0.60
30 11 0.23
ACGTcount: A:0.46, C:0.03, G:0.14, T:0.36
Consensus pattern (28 bp):
TTTAGGATGAAATTAAAATGTTCAAAAT
Found at i:2000 original size:58 final size:59
Alignment explanation
Indices: 1856--2009 Score: 172
Period size: 58 Copynumber: 2.6 Consensus size: 59
1846 TATTTGGATA
* * *
1856 AATTTG-GGATGAAATTGGAATATTTCAAAAGTTTATGGACCAATTTAGAAATAAGTTAT
1 AATTTGAGGATGAAATTAGAATA-TTCAAAAGTTTAAGGACCAATTTAGAAATAAGTCAT
* * * * **
1915 AGTTT-AGGAATGAAATTAAAATGTTCAAAATTTTAAGGATTAATTTA-AAATGAA-TCAT
1 AATTTGAGG-ATGAAATTAGAATATTCAAAAGTTTAAGGACCAATTTAGAAAT-AAGTCAT
1973 AATTTGAGGATGAAATTAGAATATTCAAAAGTTTAAG
1 AATTTGAGGATGAAATTAGAATATTCAAAAGTTTAAG
2010 AACATTGTAA
Statistics
Matches: 78, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
58 36 0.46
59 31 0.40
60 11 0.14
ACGTcount: A:0.44, C:0.04, G:0.17, T:0.35
Consensus pattern (59 bp):
AATTTGAGGATGAAATTAGAATATTCAAAAGTTTAAGGACCAATTTAGAAATAAGTCAT
Found at i:2548 original size:20 final size:21
Alignment explanation
Indices: 2514--2554 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
2504 TAATTATATA
*
2514 ATTTTAATAAATTTAATAATT
1 ATTTTAATAAATTTAAAAATT
*
2535 ATTTT-ATAATTTTAAAAATT
1 ATTTTAATAAATTTAAAAATT
2555 TAATATCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTTTAATAAATTTAAAAATT
Found at i:3592 original size:150 final size:143
Alignment explanation
Indices: 3372--3647 Score: 372
Period size: 150 Copynumber: 1.9 Consensus size: 143
3362 ACATATATAA
* *
3372 ATATATATTAATCTATTTATCATTATTTTTTATAAAAATATTTTTATATTTTTTTTTAATATCAA
1 ATATATATCAATCTATTTATCATTATTTTTTAGAAAAATATTTTTATATTTTTTTTTAATATCAA
* * *
3437 AGAAAAGAGTTGTCTTAAAGCACCTAGAAGCCCTTTTATGATATTTCTAAATAAGTAAATAACTT
66 AGAAAAGAGCTGTCTTAAAGCACCTAGAAGCCATTTTATGATATTTCTAAATAAATAAATAACTT
3502 ACTTTTATAAATT
131 ACTTTTATAAATT
* * *
3515 ATATGTATCAATCTATTTATTATTATTATTTTTAGAAAAATGTTTTTATATTTATTCATTTTTCA
1 ATATATATCAATCTATTTATCATTA-T-TTTTTAGAAAAATATTTTTATA-TT-TT--TTTTT-A
* * * * *
3580 ATATCGAAGAAAAGAGCTGTCTTAAGGTACCTAGAAGTCATTTTCTGATATTTCTAAATAAATAA
59 ATATCAAAGAAAAGAGCTGTCTTAAAGCACCTAGAAGCCATTTTATGATATTTCTAAATAAATAA
3645 ATA
124 ATA
3648 TTTTATTTAT
Statistics
Matches: 113, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
143 22 0.19
144 1 0.01
145 20 0.18
146 2 0.02
147 2 0.02
149 5 0.04
150 61 0.54
ACGTcount: A:0.38, C:0.09, G:0.08, T:0.45
Consensus pattern (143 bp):
ATATATATCAATCTATTTATCATTATTTTTTAGAAAAATATTTTTATATTTTTTTTTAATATCAA
AGAAAAGAGCTGTCTTAAAGCACCTAGAAGCCATTTTATGATATTTCTAAATAAATAAATAACTT
ACTTTTATAAATT
Found at i:9054 original size:18 final size:17
Alignment explanation
Indices: 9029--9073 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
9019 TATTATACTT
*
9029 GAAAAAAAAACAACAAAAA
1 GAAAAAAAAA-AA-AAAAG
9048 GAAAAAAGAAAAAAAAAG
1 GAAAAAA-AAAAAAAAAG
9066 GAAAAAAA
1 GAAAAAAA
9074 TGGAGAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 1 0.04
18 11 0.46
19 9 0.38
20 3 0.12
ACGTcount: A:0.84, C:0.04, G:0.11, T:0.00
Consensus pattern (17 bp):
GAAAAAAAAAAAAAAAG
Found at i:11397 original size:114 final size:114
Alignment explanation
Indices: 11197--11419 Score: 365
Period size: 114 Copynumber: 2.0 Consensus size: 114
11187 TGCCATGTGA
* *
11197 TCATAGTAGAAATAAGAAGACTCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGA
1 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
* * **
11262 TTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTGC
66 TTCGGTAGGAACCCCAAAACCAATCATTGGAGATGAAAGATGAATTTGC
* *
11311 TCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
1 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
*
11376 TTCGGTAGGAACCCCAGAACCAATCATTGGAGATGAAAGATGAA
66 TTCGGTAGGAACCCCAAAACCAATCATTGGAGATGAAAGATGAA
11420 CTGCATGATC
Statistics
Matches: 100, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 100 1.00
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (114 bp):
TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
TTCGGTAGGAACCCCAAAACCAATCATTGGAGATGAAAGATGAATTTGC
Found at i:14631 original size:164 final size:164
Alignment explanation
Indices: 14323--14644 Score: 549
Period size: 164 Copynumber: 2.0 Consensus size: 164
14313 AAGAATGAAA
14323 ATTATCTTGAGTTGGGGCATGTTACCCAATCAACATGTTATTTCAAAAAATAATGAGAAAACGAT
1 ATTATCTTGAGTTGGGGCATGTTACCCAATCAACATGTTATTTCAAAAAATAATGAGAAAACGAT
** *
14388 TTCCATAGTTTCTCATTTTATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTCCT
66 TTCCATAGTTTCTCATTCAATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTCCA
*
14453 TAGTTTTTTTACTTAGTAAACTATTTCCAACAGT
131 TAGTTTTATTACTTAGTAAACTATTTCCAACAGT
**
14487 ATTATCTTGAGATT-GGGCATGTTACCCAATCAACATGTTATTTTGAAAAATAATGAGAAAACGA
1 ATTATCTTGAG-TTGGGGCATGTTACCCAATCAACATGTTATTTCAAAAAATAATGAGAAAACGA
*
14551 TTTCCATAGTTTCTCATTCAATCTTTTCTGAAAATGAAATTGTTGAATAGTAAGAAAACGATTTC
65 TTTCCATAGTTTCTCATTCAATCTTTTCT-AAAATGAAATTGTTGAAAAGTAAGAAAACGATTTC
14616 CATAG-TTTATTACTTAGTAAACTATTTCC
129 CATAGTTTTATTACTTAGTAAACTATTTCC
14645 CACATCTGTA
Statistics
Matches: 149, Mismatches: 7, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
164 109 0.73
165 40 0.27
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (164 bp):
ATTATCTTGAGTTGGGGCATGTTACCCAATCAACATGTTATTTCAAAAAATAATGAGAAAACGAT
TTCCATAGTTTCTCATTCAATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTCCA
TAGTTTTATTACTTAGTAAACTATTTCCAACAGT
Found at i:14779 original size:76 final size:76
Alignment explanation
Indices: 14647--14832 Score: 320
Period size: 76 Copynumber: 2.4 Consensus size: 76
14637 CTATTTCCCA
* *
14647 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTATTGATGTTTTCAA
14712 AACCTCAGGGT
66 AACCTCAGGGT
14723 -AGTCTGTAAGTCCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTATTGATGTTTTCA
1 CA-TCTGTAAGTCCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTATTGATGTTTTCA
*
14787 AACCCTCAGGGT
65 AAACCTCAGGGT
*
14799 CATCTGTAAGACCTACAGTGCATGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTTCAA
14833 TATTTCCATT
Statistics
Matches: 104, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
75 1 0.01
76 102 0.98
77 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTATTGATGTTTTCAA
AACCTCAGGGT
Found at i:14975 original size:3 final size:3
Alignment explanation
Indices: 14961--15040 Score: 74
Period size: 3 Copynumber: 26.7 Consensus size: 3
14951 TCATTTCGTT
** *
14961 TTA TTA TT- TTA TTA TTA AAA TTA TTA TTA TTA TTA ATA TTA -TA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
* * *
15008 TTA TTA TTA ATA ATA TTA TTAA ATA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TT
15041 TAAATAAAAA
Statistics
Matches: 63, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
2 4 0.06
3 54 0.86
4 5 0.08
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:15596 original size:13 final size:13
Alignment explanation
Indices: 15574--15608 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
15564 AACAGAACGG
*
15574 GAGACAAGCAACA
1 GAGACGAGCAACA
15587 GAGACGAGCAACA
1 GAGACGAGCAACA
15600 GAGACGAGC
1 GAGACGAGC
15609 CACGAACCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.46, C:0.23, G:0.31, T:0.00
Consensus pattern (13 bp):
GAGACGAGCAACA
Found at i:16783 original size:146 final size:147
Alignment explanation
Indices: 16587--16884 Score: 424
Period size: 150 Copynumber: 2.0 Consensus size: 147
16577 TATTTATTTT
* *
16587 ATATCTTACATATATAAATTATATATTAATCTATTTATCATTATTATTTTTATAAAAATATTTTT
1 ATATCTTACATATATAAATTATATATCAATCTATTTATCATTATTATTTTTAGAAAAATATTTTT
*
16652 ATATTT-TT-TTTTT-AATATCAAAGAAAAGAGCTGTCTTTAA-GCACCTAGAAGTCCTTTTCTG
66 ATATTTATTATTTTTCAATATCAAAGAAAAGAGCTGTC-TTAAGGCACCTAGAAGTCATTTTCTG
*
16713 ATATTTCTAAATAAGTAA
130 ATATTTCTAAATAAATAA
* * * * *
16731 ATATCTTACTTTTATAAATTATATGTATCAATCTATTTTTTATTATTATTTTTAGAAAAATGTTT
1 ATATCTTACATATATAAATTATA--TATCAATCTATTTATCATTATTATTTTTAGAAAAATATTT
* * *
16796 TTATATTTATTCATTTTTCAATATCGAAGAAAAGAGTTGTCTTAAGGTACCTAGAAGTCATTTTC
64 TTATATTTATT-ATTTTTCAATATCAAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGTCATTTTC
16861 TGATATTTCTAAATAAATAA
128 TGATATTTCTAAATAAATAA
16881 ATAT
1 ATAT
16885 TTTATTTATA
Statistics
Matches: 135, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
144 21 0.16
146 43 0.32
147 2 0.01
149 9 0.07
150 60 0.44
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.47
Consensus pattern (147 bp):
ATATCTTACATATATAAATTATATATCAATCTATTTATCATTATTATTTTTAGAAAAATATTTTT
ATATTTATTATTTTTCAATATCAAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGTCATTTTCTGA
TATTTCTAAATAAATAA
Found at i:24018 original size:20 final size:20
Alignment explanation
Indices: 23993--24045 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
23983 TTTTCCTAAT
23993 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
24013 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
24033 TCGCAAAGCGAAT
1 TCGCAATGCGAAT
24046 CTGACTATCG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:24055 original size:20 final size:20
Alignment explanation
Indices: 24045--24098 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
24035 GCAAAGCGAA
24045 TCTGACTATCGCAACGAGAT
1 TCTGACTATCGCAACGAGAT
24065 TCTGACTATCGCAACGAGAT
1 TCTGACTATCGCAACGAGAT
24085 TCTGACTATCGCAA
1 TCTGACTATCGCAA
24099 TACTGAATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.26
Consensus pattern (20 bp):
TCTGACTATCGCAACGAGAT
Found at i:24960 original size:24 final size:24
Alignment explanation
Indices: 24933--24986 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
24923 GTATTCAAAA
24933 TTTGATATTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* * *
24957 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
24981 TTTGAT
1 TTTGAT
24987 GATTTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:27431 original size:20 final size:20
Alignment explanation
Indices: 27406--27494 Score: 135
Period size: 20 Copynumber: 4.5 Consensus size: 20
27396 CAACACGGAA
27406 ATCGCAACGC-GAATATGACT
1 ATCGCAACGCGGAA-ATGACT
* *
27426 ATCGCAACACAGAAATGACT
1 ATCGCAACGCGGAAATGACT
*
27446 ATCGCAACGCGGAATTGACT
1 ATCGCAACGCGGAAATGACT
27466 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGGAAATGACT
27486 ATCGCAACG
1 ATCGCAACG
27495 AGAGAATCGT
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
20 60 0.95
21 3 0.05
ACGTcount: A:0.36, C:0.26, G:0.21, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:27573 original size:33 final size:34
Alignment explanation
Indices: 27516--27611 Score: 149
Period size: 33 Copynumber: 2.9 Consensus size: 34
27506 ATTAGTTTCG
27516 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
*
27550 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
** *
27583 CGTTGCGATAGTCATTTTCGCGTTGCGAT
1 CGTTGCGATTTTCATTTTCGCATTGCGAT
27612 AGTCTATTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
33 30 0.53
34 27 0.47
ACGTcount: A:0.14, C:0.23, G:0.21, T:0.43
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
Found at i:27608 original size:20 final size:21
Alignment explanation
Indices: 27583--27621 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
27573 GCGATTCTCT
27583 CGTTGCGATAGTC-ATTTTCG
1 CGTTGCGATAGTCTATTTTCG
27603 CGTTGCGATAGTCTATTTT
1 CGTTGCGATAGTCTATTTT
27622 GCATTCAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.15, C:0.18, G:0.23, T:0.44
Consensus pattern (21 bp):
CGTTGCGATAGTCTATTTTCG
Found at i:29188 original size:42 final size:42
Alignment explanation
Indices: 29081--29192 Score: 111
Period size: 42 Copynumber: 2.7 Consensus size: 42
29071 TCTAGAATGT
* * * *
29081 TGGGAG-GGACCTCTTCAACGATGACAGTGGCTTCTTGAACGG
1 TGGGAGAGG-CCTCTTGAACGATGACAGGGGCCTCTTGAACGA
* * ** *
29123 TGGGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGA
1 TGGGAGAGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGA
29165 TAGGG-GAGGCCTCTTGAACGATGACAGG
1 T-GGGAGAGGCCTCTTGAACGATGACAGG
29193 TGAGTCAGGC
Statistics
Matches: 55, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
42 50 0.91
43 5 0.09
ACGTcount: A:0.22, C:0.18, G:0.38, T:0.21
Consensus pattern (42 bp):
TGGGAGAGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGA
Found at i:29699 original size:20 final size:20
Alignment explanation
Indices: 29676--29740 Score: 94
Period size: 20 Copynumber: 3.2 Consensus size: 20
29666 CTTAAAATCA
*
29676 CAACGCGAAAATGACTATTG
1 CAACGCGAAAATGACTATCG
29696 CAACGCGAAAATGACTATCG
1 CAACGCGAAAATGACTATCG
* **
29716 CAATGCGAATTTGACTATCG
1 CAACGCGAAAATGACTATCG
29736 CAACG
1 CAACG
29741 AGAGAATCGC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (20 bp):
CAACGCGAAAATGACTATCG
Found at i:29837 original size:20 final size:20
Alignment explanation
Indices: 29789--29941 Score: 120
Period size: 20 Copynumber: 8.3 Consensus size: 20
29779 CTTTCGTTGT
*
29789 GATAGTCAAATTT-GCATTGC
1 GATAGTC-ATTTTCGCATTGC
29809 GATAGTCATTTTCGCATTGC
1 GATAGTCATTTTCGCATTGC
* *
29829 GATAGTCATTTTCACGTTGC
1 GATAGTCATTTTCGCATTGC
29849 GAT--T--TTGTT-G--TTGC
1 GATAGTCATT-TTCGCATTGC
**
29863 GATTTTCA-TTTCGCATTGC
1 GATAGTCATTTTCGCATTGC
*
29882 GAT--TC--TCTCG--TTGC
1 GATAGTCATTTTCGCATTGC
*
29896 GATAGTCATTTTCGCGTTGC
1 GATAGTCATTTTCGCATTGC
29916 GATAGTCATTTTCGCATTGC
1 GATAGTCATTTTCGCATTGC
29936 GATAGT
1 GATAGT
29942 AAACAATTCT
Statistics
Matches: 111, Mismatches: 7, Indels: 30
0.75 0.05 0.20
Matches are distributed among these distances:
14 14 0.13
16 11 0.10
17 6 0.05
18 5 0.05
19 11 0.10
20 64 0.58
ACGTcount: A:0.18, C:0.18, G:0.22, T:0.42
Consensus pattern (20 bp):
GATAGTCATTTTCGCATTGC
Found at i:31849 original size:20 final size:20
Alignment explanation
Indices: 31826--31914 Score: 99
Period size: 20 Copynumber: 4.5 Consensus size: 20
31816 CTGAAACTTT
31826 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
31846 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
** * **
31866 TTATCGCAACGCGAATTTGA
1 AAATCGCAACACGAAAATGA
** *
31886 CTATCGCAACGCG-AAATGA
1 AAATCGCAACACGAAAATGA
31905 AAATCGCAAC
1 AAATCGCAAC
31915 GACAGAATCG
Statistics
Matches: 59, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
19 12 0.20
20 47 0.80
ACGTcount: A:0.45, C:0.22, G:0.17, T:0.16
Consensus pattern (20 bp):
AAATCGCAACACGAAAATGA
Found at i:32312 original size:22 final size:22
Alignment explanation
Indices: 32251--32316 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
32241 TGACCGTGAA
* ***
32251 TGATTTCGCCGGAGATGAATAC
1 TGATTTCGTCGGAGATGGGGAC
32273 TGATATT-GTCGGAGATGGGGAC
1 TGAT-TTCGTCGGAGATGGGGAC
32295 TGATTTCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
32317 GGATGTCGCC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
21 2 0.05
22 34 0.89
23 2 0.05
ACGTcount: A:0.23, C:0.14, G:0.36, T:0.27
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:32523 original size:20 final size:20
Alignment explanation
Indices: 32495--32585 Score: 78
Period size: 20 Copynumber: 4.5 Consensus size: 20
32485 GCTATGTAAA
*
32495 TCGCATTGCGATAGTAAG-AT
1 TCGCGTTGCGAT-GTAAGTAT
* *
32515 TCGCGTTGCGATTTACGTAT
1 TCGCGTTGCGATGTAAGTAT
* *
32535 TCGCGTTGCGATTTACGTAT
1 TCGCGTTGCGATGTAAGTAT
* *
32555 TCGCATTGCGATTTACA-TAT
1 TCGCGTTGCGATGTA-AGTAT
*
32575 TCGCATTGCGA
1 TCGCGTTGCGA
32586 ATTAGGAAAA
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
19 3 0.05
20 61 0.95
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (20 bp):
TCGCGTTGCGATGTAAGTAT
Found at i:32606 original size:21 final size:21
Alignment explanation
Indices: 32582--32627 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
32572 TATTCGCATT
*
32582 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAAGAAAATCGCAAC
*
32603 GCGAATTAAGAAAATCGCAAT
1 GCGAATTAAGAAAATCGCAAC
32624 GCGA
1 GCGA
32628 TAGTCAGAAT
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:0.43, C:0.17, G:0.24, T:0.15
Consensus pattern (21 bp):
GCGAATTAAGAAAATCGCAAC
Found at i:35685 original size:30 final size:30
Alignment explanation
Indices: 35649--35706 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
35639 TTCGGTTGAA
*
35649 CATAATTAAAAAAGGAAAGAAAA-AACAATT
1 CATAATTAAAAAAAGAAA-AAAACAACAATT
35679 CATAATTAAAAAAAGAAAAAAACAACAA
1 CATAATTAAAAAAAGAAAAAAACAACAA
35707 CAACAATTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 4 0.15
30 22 0.85
ACGTcount: A:0.71, C:0.09, G:0.07, T:0.14
Consensus pattern (30 bp):
CATAATTAAAAAAAGAAAAAAACAACAATT
Found at i:40552 original size:30 final size:30
Alignment explanation
Indices: 40518--40614 Score: 131
Period size: 30 Copynumber: 3.2 Consensus size: 30
40508 CCGAAGGACT
40518 TATCCAGAGGTCATAAAGATCCTCGGTAAC
1 TATCCAGAGGTCATAAAGATCCTCGGTAAC
40548 TATCCAGAGGTCATAAAGATCCTCGGTAAC
1 TATCCAGAGGTCATAAAGATCCTCGGTAAC
* * * * * *
40578 TGTCCATAGGTCCTGAAGAACCTAGGTAAAC
1 TATCCAGAGGTCATAAAGATCCTCGGT-AAC
40609 TATCCA
1 TATCCA
40615 TATATTCCTT
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
30 51 0.86
31 8 0.14
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.24
Consensus pattern (30 bp):
TATCCAGAGGTCATAAAGATCCTCGGTAAC
Found at i:41308 original size:24 final size:20
Alignment explanation
Indices: 41251--41308 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
41241 TTCCCCTTGA
41251 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATTCTAC
*
41271 AGTGTATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
41294 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
41309 CTACTCATGC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 16 0.50
22 1 0.03
23 3 0.09
24 12 0.38
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.33
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:41383 original size:64 final size:62
Alignment explanation
Indices: 41296--41436 Score: 158
Period size: 64 Copynumber: 2.2 Consensus size: 62
41286 TCTTTAACAT
* * *
41296 GTGCATCGATGCACTACTCATGCATCGATACATAAATTACCTTCGATGTTTTCATT-TTAAAGG
1 GTGCATCGATGCACTACTCATGCATCGATACACAAATTACATTCGATG-TTTC-TTATTAAAGA
* * * * * *
41359 GATGCATCGATGCATTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCTTCATTAAAGA
1 G-TGCATCGATGCACTACTCATGCATCGATACACAAATTACATTCGATGTTTCTT-ATTAAAGA
41423 GTGCATCGATGCAC
1 GTGCATCGATGCAC
41437 ATTTAATATG
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
62 2 0.03
63 17 0.26
64 46 0.71
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (62 bp):
GTGCATCGATGCACTACTCATGCATCGATACACAAATTACATTCGATGTTTCTTATTAAAGA
Found at i:41924 original size:3 final size:3
Alignment explanation
Indices: 41916--41958 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
41906 GCTTACAGGG
*
41916 AGA AGA AGA AGA AGA AGA AGA AGA AGA AAA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
41959 AATAAGCTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:44835 original size:30 final size:30
Alignment explanation
Indices: 44801--44928 Score: 184
Period size: 30 Copynumber: 4.2 Consensus size: 30
44791 CCCGAAGGAC
44801 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
44831 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
44861 CTATCCAGAGGTCATAAAGATCCTCGATAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* * * * * *
44891 CTGTCCATAGGTCCTGAAGAACCTAGGTTAA
1 CTATCCAGAGGTCATAAAGATCCTCGG-TAA
44922 CTATCCA
1 CTATCCA
44929 TATGTTCCTT
Statistics
Matches: 88, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
30 79 0.90
31 9 0.10
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:44964 original size:31 final size:32
Alignment explanation
Indices: 44888--44964 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 32
44878 AGATCCTCGA
* *
44888 TAACTGTCCATA-GGTCCTGAAGAACCTAGGT
1 TAACTGTCCATATGTTCCTGAAGAACATAGGT
* *
44919 TAACTATCCATATGTTCCT-TAGAACATAGG-
1 TAACTGTCCATATGTTCCTGAAGAACATAGGT
44949 TATACTGTCCATATGT
1 TA-ACTGTCCATATGT
44965 CTCGAAAGAC
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
30 2 0.05
31 32 0.82
32 5 0.13
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (32 bp):
TAACTGTCCATATGTTCCTGAAGAACATAGGT
Found at i:45622 original size:24 final size:20
Alignment explanation
Indices: 45565--45622 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
45555 TTCCCCTTGA
45565 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATTCTAC
*
45585 AGTGTATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
45608 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
45623 CTACTCATGC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 16 0.50
22 1 0.03
23 3 0.09
24 12 0.38
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.33
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:45697 original size:64 final size:62
Alignment explanation
Indices: 45610--45750 Score: 158
Period size: 64 Copynumber: 2.2 Consensus size: 62
45600 TCTTTAACAT
* * *
45610 GTGCATCGATGCACTACTCATGCATCGATACATAAATTACCTTCGATGTTTTCATT-TTAAAGG
1 GTGCATCGATGCACTACTCATGCATCGATACACAAATTACATTCGATG-TTTC-TTATTAAAGA
* * * * * *
45673 GATGCATCGATGCATTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCTTCATTAAAGA
1 G-TGCATCGATGCACTACTCATGCATCGATACACAAATTACATTCGATGTTTCTT-ATTAAAGA
45737 GTGCATCGATGCAC
1 GTGCATCGATGCAC
45751 ATTTAATATG
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
62 2 0.03
63 17 0.26
64 46 0.71
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (62 bp):
GTGCATCGATGCACTACTCATGCATCGATACACAAATTACATTCGATGTTTCTTATTAAAGA
Found at i:49584 original size:27 final size:27
Alignment explanation
Indices: 49548--49608 Score: 122
Period size: 27 Copynumber: 2.3 Consensus size: 27
49538 ATTATATGAA
49548 ACACTCAGGTGCATACTCGTATCTGAC
1 ACACTCAGGTGCATACTCGTATCTGAC
49575 ACACTCAGGTGCATACTCGTATCTGAC
1 ACACTCAGGTGCATACTCGTATCTGAC
49602 ACACTCA
1 ACACTCA
49609 AATCCGATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.28, C:0.31, G:0.16, T:0.25
Consensus pattern (27 bp):
ACACTCAGGTGCATACTCGTATCTGAC
Found at i:57352 original size:31 final size:31
Alignment explanation
Indices: 57314--57378 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
57304 AACGACCGGT
*
57314 GACCATATTGCAAACAGACTAAATGTTGGGG
1 GACCATATTGCAAACAGACTAAATGTTAGGG
*
57345 GACCATATTGCAAACGGACTAAATGTTAGGG
1 GACCATATTGCAAACAGACTAAATGTTAGGG
57376 GAC
1 GAC
57379 TGTATAGCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.35, C:0.17, G:0.26, T:0.22
Consensus pattern (31 bp):
GACCATATTGCAAACAGACTAAATGTTAGGG
Found at i:57825 original size:31 final size:33
Alignment explanation
Indices: 57787--57854 Score: 95
Period size: 31 Copynumber: 2.1 Consensus size: 33
57777 TTGTTCATTT
*
57787 TTTTTATAAATACATG-AATTTTATATA-AATA
1 TTTTTATAAAGACATGCAATTTTATATATAATA
* *
57818 TTTTTATACAGACATGCATTTTTATATATAATA
1 TTTTTATAAAGACATGCAATTTTATATATAATA
57851 TTTT
1 TTTT
57855 ATTTTATCTG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
31 14 0.44
32 10 0.31
33 8 0.25
ACGTcount: A:0.38, C:0.06, G:0.04, T:0.51
Consensus pattern (33 bp):
TTTTTATAAAGACATGCAATTTTATATATAATA
Found at i:58499 original size:30 final size:30
Alignment explanation
Indices: 58418--58500 Score: 139
Period size: 30 Copynumber: 2.8 Consensus size: 30
58408 GGCCTATCTA
* *
58418 TGCTTTTCCTTGGCTTGTCCCGGGTATCAG
1 TGCTTTTCCTTGGTTTGTCCCTGGTATCAG
*
58448 TGCTTTTCCTAGGTTTGTCCCTGGTATCAG
1 TGCTTTTCCTTGGTTTGTCCCTGGTATCAG
58478 TGCTTTTCCTTGGTTTGTCCCTG
1 TGCTTTTCCTTGGTTTGTCCCTG
58501 CGGTCGATGC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.06, C:0.25, G:0.24, T:0.45
Consensus pattern (30 bp):
TGCTTTTCCTTGGTTTGTCCCTGGTATCAG
Found at i:66019 original size:28 final size:28
Alignment explanation
Indices: 65987--66080 Score: 82
Period size: 28 Copynumber: 3.2 Consensus size: 28
65977 GGACATAATG
65987 AATAGTCGGGTGACAATTTATAACTTTT
1 AATAGTCGGGTGACAATTTATAACTTTT
***
66015 AATAGTCGGG-GACTAAAAAAATAACTTTCT
1 AATAGTCGGGTGAC--AATTTATAACTTT-T
* * * *
66045 ATATAGTCAGATGACTATTTGTAACTTTT
1 A-ATAGTCGGGTGACAATTTATAACTTTT
66074 AATAGTC
1 AATAGTC
66081 TAGGCGCTTA
Statistics
Matches: 51, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
27 3 0.06
28 16 0.31
29 12 0.24
30 10 0.20
31 7 0.14
32 3 0.06
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (28 bp):
AATAGTCGGGTGACAATTTATAACTTTT
Found at i:66733 original size:31 final size:31
Alignment explanation
Indices: 66674--66735 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
66664 TAACATTTTT
**
66674 AGGGTTAATATGATATTTTACCTGAAGTTTA
1 AGGGTTAATATGATATTTTACCAAAAGTTTA
*
66705 AGGGTTAA-ATTGATATTTTATCAAAAGTTTA
1 AGGGTTAATA-TGATATTTTACCAAAAGTTTA
66736 GAGATCAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 1 0.04
31 26 0.96
ACGTcount: A:0.35, C:0.05, G:0.18, T:0.42
Consensus pattern (31 bp):
AGGGTTAATATGATATTTTACCAAAAGTTTA
Found at i:69315 original size:60 final size:60
Alignment explanation
Indices: 69230--69387 Score: 176
Period size: 60 Copynumber: 2.6 Consensus size: 60
69220 GAATTTAGGG
* * * * *
69230 ATGAAATTGGAAGA-TCTAAAAGTTTAGGGACTGATTTAGAATGAGATTCATAATTTGTGG
1 ATGAAATTGGAATATTC-AAAAGTTTAAGGACTGATTTAGAATGAGAGTCATAATTTGAGC
* * ** *
69290 AT-AAGATTGGGATGTTCAAAAGTTTAAGGACTGATACAGAATGAGAGTCATAGTTTGAGC
1 ATGAA-ATTGGAATATTCAAAAGTTTAAGGACTGATTTAGAATGAGAGTCATAATTTGAGC
* *
69350 ATGAAATTGGAATATTTAAAAGTTTAAGGACTAATTTA
1 ATGAAATTGGAATATTCAAAAGTTTAAGGACTGATTTA
69388 AAAGAAGGGA
Statistics
Matches: 79, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
59 2 0.03
60 73 0.92
61 4 0.05
ACGTcount: A:0.39, C:0.06, G:0.23, T:0.32
Consensus pattern (60 bp):
ATGAAATTGGAATATTCAAAAGTTTAAGGACTGATTTAGAATGAGAGTCATAATTTGAGC
Found at i:70544 original size:14 final size:14
Alignment explanation
Indices: 70525--70558 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
70515 AAGAACAAAG
70525 GAAGATGGAAAA-TA
1 GAAGAT-GAAAAGTA
70539 GAAGATGAAAAGTA
1 GAAGATGAAAAGTA
70553 GAAGAT
1 GAAGAT
70559 TAAATCAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.56, C:0.00, G:0.29, T:0.15
Consensus pattern (14 bp):
GAAGATGAAAAGTA
Found at i:79588 original size:19 final size:19
Alignment explanation
Indices: 79572--79613 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
79562 GTCGGGTCGG
*
79572 ACCGGTTCAGACCGGTCAA
1 ACCGATTCAGACCGGTCAA
*
79591 ACCGATTCAGATCGGTCAA
1 ACCGATTCAGACCGGTCAA
79610 ACCG
1 ACCG
79614 GTTTTCCAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.29, C:0.31, G:0.24, T:0.17
Consensus pattern (19 bp):
ACCGATTCAGACCGGTCAA
Found at i:82575 original size:65 final size:65
Alignment explanation
Indices: 82442--82601 Score: 209
Period size: 65 Copynumber: 2.5 Consensus size: 65
82432 TGCACTAAGA
* * *
82442 GTGCACCGATGCATCAAGTGCATTCGATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCTG
* * *
82506 GTGCATCGATACATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGATGCATGG-T
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAGCCACAGTGCATCGATGCATGGCT
*
82569 AT
65 -G
*
82571 GTGCATCGATGCATGAAATGCATTCGATGTT
1 GTGCATCGATGCATCAAATGCATTCGATGTT
82602 CAATTTAATT
Statistics
Matches: 84, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
64 27 0.32
65 54 0.64
66 3 0.04
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCTG
Found at i:83726 original size:21 final size:21
Alignment explanation
Indices: 83692--83756 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
83682 CCGGAGGAGG
* *
83692 AGGAGGAGCACGAGAAGAGCT
1 AGGAGCAGCTCGAGAAGAGCT
*
83713 AGGAGCTGCTCGAGAAGAGCT
1 AGGAGCAGCTCGAGAAGAGCT
*
83734 AGGAGCAGCTCGTGAAGAGCT
1 AGGAGCAGCTCGAGAAGAGCT
83755 AG
1 AG
83757 CTCCCGGGGT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.32, C:0.17, G:0.40, T:0.11
Consensus pattern (21 bp):
AGGAGCAGCTCGAGAAGAGCT
Found at i:85363 original size:22 final size:22
Alignment explanation
Indices: 85310--85366 Score: 80
Period size: 21 Copynumber: 2.6 Consensus size: 22
85300 GCATGGCCCT
* *
85310 ATGCATCGATGTACATTCATGG
1 ATGCATCGATGCACATTCAAGG
*
85332 -TGTATCGATGCACATTCAAGG
1 ATGCATCGATGCACATTCAAGG
85353 ATGCATCGATGCAC
1 ATGCATCGATGCAC
85367 TGTTAGGTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 18 0.60
22 12 0.40
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (22 bp):
ATGCATCGATGCACATTCAAGG
Found at i:85382 original size:20 final size:21
Alignment explanation
Indices: 85314--85385 Score: 76
Period size: 21 Copynumber: 3.4 Consensus size: 21
85304 GGCCCTATGC
* *
85314 ATCGATGTACATTCATGGTGT
1 ATCGATGCACATTCAAGGTGT
*
85335 ATCGATGCACATTCAAGGATGC
1 ATCGATGCACATTCAAGG-TGT
*
85357 ATCGATGCAC-TGT-TAGGTGT
1 ATCGATGCACAT-TCAAGGTGT
85377 ATCGATGCA
1 ATCGATGCA
85386 TAAAGCACAA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
20 11 0.25
21 20 0.45
22 13 0.30
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (21 bp):
ATCGATGCACATTCAAGGTGT
Found at i:87893 original size:33 final size:34
Alignment explanation
Indices: 87856--87919 Score: 87
Period size: 35 Copynumber: 1.9 Consensus size: 34
87846 AAATGAAAAT
*
87856 GGATTTTGAA-AATC-AAAATGAAATCTTGAAGAA
1 GGATTTAGAACAATCAAAAATGAAAT-TTGAAGAA
*
87889 GGATTTAGAACTATCAAAAATGAAATTTGAA
1 GGATTTAGAACAATCAAAAATGAAATTTGAA
87920 AGTATTGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
33 9 0.33
34 8 0.30
35 10 0.37
ACGTcount: A:0.48, C:0.06, G:0.17, T:0.28
Consensus pattern (34 bp):
GGATTTAGAACAATCAAAAATGAAATTTGAAGAA
Found at i:91875 original size:21 final size:21
Alignment explanation
Indices: 91849--91888 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
91839 CCCCCTTTGA
*
91849 AGGGGAACTGATTCCCCCCAC
1 AGGGGAACTGATACCCCCCAC
*
91870 AGGGGAATTGATACCCCCC
1 AGGGGAACTGATACCCCCC
91889 CTGGGGTTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.35, G:0.25, T:0.15
Consensus pattern (21 bp):
AGGGGAACTGATACCCCCCAC
Found at i:94929 original size:154 final size:154
Alignment explanation
Indices: 94683--94989 Score: 571
Period size: 154 Copynumber: 2.0 Consensus size: 154
94673 CTCCAAGTTG
94683 TTTTATTAATTGTTTTCACACTAAAACGGCTATATGATCTTCACTAATCATCCAAAACGTTCAGA
1 TTTTATTAATTGTTTTCACACTAAAACGGCTATATGATCTTCACTAATCATCCAAAACGTTCAGA
94748 AGTGATTCAAGGTGTATTTAAACAAGTTCTGAAGCCTTTGAAAGATAAGAAATCATAGAGAAACA
66 AGTGATTCAAGGTGTATTTAAACAAGTTCTGAAGCCTTTGAAAGATAAGAAATCATAGAGAAACA
94813 AGA-AAGAAAGCATCAAACACCAAT
131 AGAGAA-AAAGCATCAAACACCAAT
**
94837 TTTTATTAATTGTTTTCACACTAAAACGGCTATATGATCTTCACTAATCATCCCCAACGTTCAGA
1 TTTTATTAATTGTTTTCACACTAAAACGGCTATATGATCTTCACTAATCATCCAAAACGTTCAGA
*
94902 AGTGATTCAAGGTGTATTTAAATAAGTTCTGAAGCCTTTGAAAGATAAGAAATCATAGAGAAACA
66 AGTGATTCAAGGTGTATTTAAACAAGTTCTGAAGCCTTTGAAAGATAAGAAATCATAGAGAAACA
94967 AGAGAAAAAGCATCAAACACCAA
131 AGAGAAAAAGCATCAAACACCAA
94990 CTTTGTGCAA
Statistics
Matches: 149, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
154 147 0.99
155 2 0.01
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (154 bp):
TTTTATTAATTGTTTTCACACTAAAACGGCTATATGATCTTCACTAATCATCCAAAACGTTCAGA
AGTGATTCAAGGTGTATTTAAACAAGTTCTGAAGCCTTTGAAAGATAAGAAATCATAGAGAAACA
AGAGAAAAAGCATCAAACACCAAT
Found at i:98486 original size:22 final size:21
Alignment explanation
Indices: 98444--98483 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
98434 GAGTTTATTT
*
98444 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
98465 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
98484 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:100460 original size:64 final size:66
Alignment explanation
Indices: 100386--100531 Score: 190
Period size: 64 Copynumber: 2.2 Consensus size: 66
100376 TGGACCCTTA
* * *
100386 GTGCACCGATGCATCAAGTGCATTCGATGTTTT-A-AAATAGCCAGAGTGCATCGATGCATGG-C
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-AGCCACAGTGCATCGATGCATGGAC
100448 TG
65 TG
* * *
100450 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGATGCATGGATT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAAGCCACAGTGCATCGATGCATGGACT
100515 G
66 G
* *
100516 GTACATCGGTGCATCA
1 GTGCATCGATGCATCA
100532 CTCTGAAAAA
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
64 31 0.44
65 21 0.30
66 19 0.27
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.29
Consensus pattern (66 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAAGCCACAGTGCATCGATGCATGGACT
G
Found at i:100854 original size:30 final size:30
Alignment explanation
Indices: 100779--100855 Score: 100
Period size: 30 Copynumber: 2.6 Consensus size: 30
100769 TGTTTTCAAC
* * *
100779 AGTGTCCTTACACACCACAATGCTACACTG
1 AGTGTCCTTACACACTACAATGATACACTA
** *
100809 AGCATCCTTACACACTACAATGATATACTA
1 AGTGTCCTTACACACTACAATGATACACTA
100839 AGTGTCCTTACACACTA
1 AGTGTCCTTACACACTA
100856 TAGTACTGTA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.34, C:0.30, G:0.10, T:0.26
Consensus pattern (30 bp):
AGTGTCCTTACACACTACAATGATACACTA
Found at i:107251 original size:30 final size:30
Alignment explanation
Indices: 107216--107284 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
107206 ACTGAGCATC
107216 CTTACACACTACAGTGCTGTACTAAGTG-T
1 CTTACACACTACAGTGCTGTACTAAGTGTT
**
107245 CTTTACACACTATGGTGCTGTACTAAGTGTT
1 C-TTACACACTACAGTGCTGTACTAAGTGTT
107276 CTTACACAC
1 CTTACACAC
107285 CATAGTACTA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
29 1 0.03
30 33 0.92
31 2 0.06
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.33
Consensus pattern (30 bp):
CTTACACACTACAGTGCTGTACTAAGTGTT
Found at i:107979 original size:63 final size:62
Alignment explanation
Indices: 107890--108047 Score: 176
Period size: 63 Copynumber: 2.5 Consensus size: 62
107880 ATGTACAGTT
* * * *
107890 CCACGGAAGAACAAAGTGGTGACTGTTTTTTGACAACA-ATGTCTCTTATGCCAAGTTATAGTC
1 CCACGGGAGAACAAAGTGGTGACTGTTTTTTGACAACACAGGTC-C-GATGCCAACTTATAGTC
* * *
107953 CCATGGGAGAACACAA-TGGTGGCTGTTTTTTTACAACACTAGGTCCGATGCCAACTTATAGTC
1 CCACGGGAGAACA-AAGTGGTGACTGTTTTTTGACAACAC-AGGTCCGATGCCAACTTATAGTC
* *
108016 CCACGGGAGAACATAGTTGTGACTGTTATTTT
1 CCACGGGAGAACAAAGTGGTGACTGTT-TTTT
108048 AGAACATCAG
Statistics
Matches: 79, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
62 1 0.01
63 67 0.85
64 7 0.09
65 4 0.05
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (62 bp):
CCACGGGAGAACAAAGTGGTGACTGTTTTTTGACAACACAGGTCCGATGCCAACTTATAGTC
Found at i:112355 original size:12 final size:12
Alignment explanation
Indices: 112335--112373 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
112325 CATAAGTCAC
*
112335 CTTATTTTTTTT
1 CTTAATTTTTTT
112347 CTTAATTTTTTTT
1 CTTAA-TTTTTTT
*
112360 CTTCATTTTTTT
1 CTTAATTTTTTT
112372 CT
1 CT
112374 CCATTTCATC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 13 0.54
13 11 0.46
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (12 bp):
CTTAATTTTTTT
Found at i:112356 original size:13 final size:13
Alignment explanation
Indices: 112338--112371 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
112328 AAGTCACCTT
112338 ATTTTTTTTCTTA
1 ATTTTTTTTCTTA
*
112351 ATTTTTTTTCTTC
1 ATTTTTTTTCTTA
112364 ATTTTTTT
1 ATTTTTTT
112372 CTCCATTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.79
Consensus pattern (13 bp):
ATTTTTTTTCTTA
Found at i:114427 original size:6 final size:6
Alignment explanation
Indices: 114408--114621 Score: 414
Period size: 6 Copynumber: 36.0 Consensus size: 6
114398 GGGAATCTAG
114408 ATATAC ATAT-- ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
114454 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
114502 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
114550 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
114598 ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC
114622 CAAAATTACC
Statistics
Matches: 206, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
4 4 0.02
6 202 0.98
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34
Consensus pattern (6 bp):
ATATAC
Found at i:121284 original size:15 final size:15
Alignment explanation
Indices: 121247--121286 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
121237 GAAAATTATA
121247 TTTTAATTTTATGTT
1 TTTTAATTTTATGTT
121262 TTTATAATTTTAAT-TT
1 TTT-TAATTTT-ATGTT
121278 TTTTAATTT
1 TTTTAATTT
121287 AATAATGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 9 0.39
16 12 0.52
17 2 0.09
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (15 bp):
TTTTAATTTTATGTT
Found at i:131045 original size:17 final size:18
Alignment explanation
Indices: 131023--131057 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
131013 TTTACCCTAT
131023 AAAAAATTAAATA-GAAA
1 AAAAAATTAAATATGAAA
131040 AAAAAATTAAATATGAAA
1 AAAAAATTAAATATGAAA
131058 GATTAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.20
Consensus pattern (18 bp):
AAAAAATTAAATATGAAA
Found at i:136146 original size:30 final size:29
Alignment explanation
Indices: 136110--136167 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
136100 TTTTATAAAT
136110 ATTTTTGAATATGTC-TTTTCTTTTCTTTTG
1 ATTTTTGAATA-GTCGTTTT-TTTTCTTTTG
**
136140 ATTTTTGTTTAGTCGTTTTTTTTCTTTT
1 ATTTTTGAATAGTCGTTTTTTTTCTTTT
136168 TTTCGTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 12 0.48
30 13 0.52
ACGTcount: A:0.10, C:0.09, G:0.10, T:0.71
Consensus pattern (29 bp):
ATTTTTGAATAGTCGTTTTTTTTCTTTTG
Found at i:144719 original size:11 final size:13
Alignment explanation
Indices: 144687--144716 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
144677 TGGCCAAAGA
144687 TGAAAAGGTATGT
1 TGAAAAGGTATGT
144700 TGAAAAGGTATG-
1 TGAAAAGGTATGT
144712 TGAAA
1 TGAAA
144717 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Done.