Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002947.1 Hibiscus syriacus cultivar Beakdansim tig00006081_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: 56556
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.33
Found at i:13 original size:4 final size:4
Alignment explanation
Indices: 1--943 Score: 1326
Period size: 4 Copynumber: 240.8 Consensus size: 4
* * * *
1 TGTA -GTA TGTA TGTA TATT TGTA TATA TGTA TGTA TGTA TATA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
* *
48 TGTA TGTA TGTA TGTA TG-- TGTA TGTA TGTA TGTC TATA -GTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
* * * * * * *
93 TGTC TGTA TGTC TG-- TGTC TGTC TGT- TGTC TATA TGTC TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
138 TGTA TGTA TGTA TGTA TGTA TGTA TGTA -GTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
185 TGTA TGTA TGTA TGTA TGTA TGTA TGTA -GTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
232 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA -GTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
279 TGTA TGGTA TGTA TGTA TGTA TGTA TGTA TGTA TGATA GTGTA TGTA TGTA
1 TGTA T-GTA TGTA TGTA TGTA TGTA TGTA TGTA TG-TA -TGTA TGTA TGTA
*
330 TGTA TGGATA TGTA TGTA TGTA TGTA TGTA TGTA GGTA TG-A TGTA TGTA
1 TGTA T-G-TA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
379 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
427 TGTA -G-A TGTA TG-- TGTA TGTA TGTA TGTA TGTA TG-A TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
*
470 TGTA TGTA TG-A TGTA TGTA TGTG TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
*
517 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TATA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
* * * * *
565 TGTA TG-A TGTA TGTG TGTG TGT- GGTA TGTA TGTTG TGTG TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG-TA TGTA TGTA TGTA
*
612 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTG
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
* * *
660 TGTG TG-G TGTG TGT- TGTA -GTA TGTA -GTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
* * *
704 TGTA TGTA TGTG TGTA TGTT TGTA TGTA TGTA TGTA TGTC TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
* * * * *
752 TGTT TGTA TGTA TGTA TGTC TGTA TGTA TGTC TGTA TATA TGTA TGTC
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
* * *
800 TGTA TGTA TGTC TGTC TGTC TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
848 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA -GTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
895 TGTA TGTA TG-- TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
941 TGT
1 TGT
944 GTTGATGTAT
Statistics
Matches: 857, Mismatches: 50, Indels: 64
0.88 0.05 0.07
Matches are distributed among these distances:
2 9 0.01
3 48 0.06
4 782 0.91
5 13 0.02
6 5 0.01
ACGTcount: A:0.23, C:0.01, G:0.26, T:0.49
Consensus pattern (4 bp):
TGTA
Found at i:2146 original size:11 final size:11
Alignment explanation
Indices: 2132--2179 Score: 51
Period size: 11 Copynumber: 4.1 Consensus size: 11
2122 TGCTTTTGTC
2132 TTCTTTTTCTT
1 TTCTTTTTCTT
2143 TTCTTTTTCTT
1 TTCTTTTTCTT
2154 TTGCTAATTTTCTT
1 TT-CT--TTTTCTT
**
2168 TGATTTTTCTT
1 TTCTTTTTCTT
2179 T
1 T
2180 GTACTCTGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
11 21 0.66
12 2 0.06
13 1 0.03
14 8 0.25
ACGTcount: A:0.06, C:0.15, G:0.04, T:0.75
Consensus pattern (11 bp):
TTCTTTTTCTT
Found at i:2770 original size:20 final size:20
Alignment explanation
Indices: 2732--2770 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2722 GGATAAATGC
*
2732 AATGTTTCAATGTCACAAAG
1 AATGTTTCAAGGTCACAAAG
*
2752 AATGTTTCAAGGTCTCAAA
1 AATGTTTCAAGGTCACAAA
2771 AGGAGGGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (20 bp):
AATGTTTCAAGGTCACAAAG
Found at i:3983 original size:30 final size:30
Alignment explanation
Indices: 3949--4006 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
3939 GAAAAATGAC
*
3949 ACAAACAAAAGAGAAAAACGAGTTAGTAAA
1 ACAAACAAAACAGAAAAACGAGTTAGTAAA
3979 ACAAACAAAACAGAAAAACGAGTTAGTA
1 ACAAACAAAACAGAAAAACGAGTTAGTA
4007 CAAGCAAGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.62, C:0.12, G:0.16, T:0.10
Consensus pattern (30 bp):
ACAAACAAAACAGAAAAACGAGTTAGTAAA
Found at i:6006 original size:24 final size:24
Alignment explanation
Indices: 5959--6007 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
5949 ATGTAATCTA
5959 ATATAATATACACTTACATAAAAAT
1 ATATAATATACAC-TACATAAAAAT
5984 ATATGAATATACA-TACATGAAAAA
1 ATAT-AATATACACTACAT-AAAAA
6008 ATAAGAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 5 0.23
25 9 0.41
26 8 0.36
ACGTcount: A:0.57, C:0.10, G:0.04, T:0.29
Consensus pattern (24 bp):
ATATAATATACACTACATAAAAAT
Found at i:6338 original size:27 final size:27
Alignment explanation
Indices: 6256--6344 Score: 88
Period size: 30 Copynumber: 3.1 Consensus size: 27
6246 TGACATAGCT
**
6256 AAAATAGAAGTTTAAAGGACTAAAATGACA
1 AAAATAGAAAATTAAAGG-CTAAAAT-A-A
* *
6286 AAAATAGAAAATTAAAGGATGTAAATAA
1 AAAATAGAAAATTAAAGGCT-AAAATAA
* *
6314 AAAATAGAAAATTTAGGGCTAAAATAA
1 AAAATAGAAAATTAAAGGCTAAAATAA
6341 AAAA
1 AAAA
6345 CTGAAACATC
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
27 10 0.20
28 18 0.36
29 2 0.04
30 20 0.40
ACGTcount: A:0.62, C:0.03, G:0.15, T:0.20
Consensus pattern (27 bp):
AAAATAGAAAATTAAAGGCTAAAATAA
Found at i:6343 original size:28 final size:28
Alignment explanation
Indices: 6256--6344 Score: 81
Period size: 28 Copynumber: 3.1 Consensus size: 28
6246 TGACATAGCT
** *
6256 AAAATAGAAGTTTAAAGGACTAAAATGACA
1 AAAATAGAAAATTAAAGG-CTAAAAT-AAA
* *
6286 AAAATAGAAAATTAAAGGATGTAAAT-AA
1 AAAATAGAAAATTAAAGGCT-AAAATAAA
* *
6314 AAAATAGAAAATTTAGGGCTAAAATAAA
1 AAAATAGAAAATTAAAGGCTAAAATAAA
6342 AAA
1 AAA
6345 CTGAAACATC
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
27 4 0.08
28 23 0.48
29 1 0.02
30 20 0.42
ACGTcount: A:0.62, C:0.03, G:0.15, T:0.20
Consensus pattern (28 bp):
AAAATAGAAAATTAAAGGCTAAAATAAA
Found at i:7678 original size:3 final size:3
Alignment explanation
Indices: 7670--7711 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
7660 TAATTACTAT
7670 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
7712 ATAAAAAAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:10188 original size:14 final size:13
Alignment explanation
Indices: 10169--10217 Score: 71
Period size: 14 Copynumber: 3.6 Consensus size: 13
10159 TTTGGGCTTG
10169 TAATAATTATTTAA
1 TAATAA-TATTTAA
*
10183 TAATAATATACTAA
1 TAATAATAT-TTAA
10197 TAATAATATTTAA
1 TAATAATATTTAA
10210 TAATAATA
1 TAATAATA
10218 ATAAATTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
13 14 0.44
14 18 0.56
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (13 bp):
TAATAATATTTAA
Found at i:10227 original size:18 final size:19
Alignment explanation
Indices: 10194--10233 Score: 73
Period size: 18 Copynumber: 2.2 Consensus size: 19
10184 AATAATATAC
10194 TAATAATAATATTTAATAA
1 TAATAATAATATTTAATAA
10213 TAATAATAA-ATTTAATAA
1 TAATAATAATATTTAATAA
10231 TAA
1 TAA
10234 AAACAATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TAATAATAATATTTAATAA
Found at i:10233 original size:3 final size:3
Alignment explanation
Indices: 10180--10221 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
10170 AATAATTATT
* *
10180 TAA TAA TAA T-A TAC TAA TAA TAA TATT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA
10222 ATTTAATAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
2 2 0.06
3 29 0.88
4 2 0.06
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:10630 original size:76 final size:76
Alignment explanation
Indices: 10494--11020 Score: 957
Period size: 76 Copynumber: 6.9 Consensus size: 76
10484 TTTTTTTTTT
* *
10494 TTTGGAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGAT
10559 GACCCGAAGGC
66 GACCCGAAGGC
10570 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGAT
10635 GACCCGAAGGC
66 GACCCGAAGGC
10646 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG-AACATCATGCACTGAAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGAT
10710 GACCCGAAGGC
66 GACCCGAAGGC
10721 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGAT
10786 GACCCGAAGGC
66 GACCCGAAGGC
10797 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGAT
10862 GACCCGAAGGC
66 GACCCGAAGGC
10873 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGAT
*
10938 GACCCGAAGGTTTTTTT
66 GACCCGAAGG------C
*
10955 TTTGGAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGAT
11020 G
66 G
11021 TGGGAAATAG
Statistics
Matches: 440, Mismatches: 4, Indels: 8
0.97 0.01 0.02
Matches are distributed among these distances:
75 75 0.17
76 300 0.68
82 65 0.15
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.23
Consensus pattern (76 bp):
TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGAT
GACCCGAAGGC
Found at i:10774 original size:151 final size:152
Alignment explanation
Indices: 10494--11020 Score: 957
Period size: 151 Copynumber: 3.4 Consensus size: 152
10484 TTTTTTTTTT
* *
10494 TTTGGAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGAT
10559 GACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAG
66 GACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAG
10624 GACTTACAGATGACCCGAAGGC
131 GACTTACAGATGACCCGAAGGC
10646 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG-AACATCATGCACTGAAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGAT
10710 GACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAG
66 GACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAG
10775 GACTTACAGATGACCCGAAGGC
131 GACTTACAGATGACCCGAAGGC
10797 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGAT
10862 GACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAG
66 GACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAG
*
10927 GACTTACAGATGACCCGAAGGTTTTTTT
131 GACTTACAGATGACCCGAAGG------C
*
10955 TTTGGAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGAT
11020 G
66 G
11021 TGGGAAATAG
Statistics
Matches: 364, Mismatches: 4, Indels: 8
0.97 0.01 0.02
Matches are distributed among these distances:
151 150 0.41
152 149 0.41
158 65 0.18
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.23
Consensus pattern (152 bp):
TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGAT
GACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAG
GACTTACAGATGACCCGAAGGC
Found at i:10850 original size:227 final size:229
Alignment explanation
Indices: 10363--11020 Score: 1113
Period size: 227 Copynumber: 2.8 Consensus size: 229
10353 GATGGAAATG
* * *
10363 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATTAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
*
10428 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTTTTTT
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG---------T
*
10493 TTTTGGAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGA
122 TTTTGGAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGA
10558 TGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
187 TGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
10601 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
* *
10666 CCCGAAGGCTTTTTGG-AACATCATGCACTGAAGGACTTACAGATGACCCGAAGG-CTTTGAAAA
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGGAAA
10729 CATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAA
131 CATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAA
10794 GGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
196 GGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
10828 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
10893 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTTTTTT
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG-----TTTTT
10958 GGAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
126 GGAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
11021 TGGGAAATAG
Statistics
Matches: 404, Mismatches: 9, Indels: 18
0.94 0.02 0.04
Matches are distributed among these distances:
227 186 0.46
228 38 0.09
234 65 0.16
237 37 0.09
238 78 0.19
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (229 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGGAAA
CATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAA
GGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
Found at i:11725 original size:22 final size:22
Alignment explanation
Indices: 11700--11779 Score: 79
Period size: 22 Copynumber: 3.6 Consensus size: 22
11690 CATAAAGCTT
*
11700 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTAAAAAGAGAATCTA
* * *
11722 TCATCTTTAAAAAGAAAATTTG
1 TCATCTTTAAAAAGAGAATCTA
* * **
11744 TCATCTCTGAAGTGAGAATCTA
1 TCATCTTTAAAAAGAGAATCTA
*
11766 TTATCTTTAAAAAG
1 TCATCTTTAAAAAG
11780 TGTAGATGTA
Statistics
Matches: 42, Mismatches: 16, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (22 bp):
TCATCTTTAAAAAGAGAATCTA
Found at i:14720 original size:93 final size:89
Alignment explanation
Indices: 14543--14908 Score: 451
Period size: 93 Copynumber: 4.2 Consensus size: 89
14533 TATTTCTACC
* * ** * * * *
14543 ATGAGCAAATTCATCTTTCAAATCCAATGATTGATT-TTGG--AGTTCATACCAAATCAGATAAT
1 ATGAGCATATTCATCTTCCAAATTTAATGATTGATTCTTGGTTA-TCCAAACCAGATCAGATAAC
14605 TCAAAGAACACTTCCAGAAGATGCT
65 TCAAAGAACACTTCCAGAAGATGCT
*
14630 ATGAGCACATTCATCTTCCAAATTTAATGATTGATTCTGTGGTTTTATACCAAACCAGATCAGAT
1 ATGAGCATATTCATCTTCCAAATTTAATGATTGATTCT-TGG--TTAT-CCAAACCAGATCAGAT
14695 AACTCAAAGAACACTTCCAGAAGATGCT
62 AACTCAAAGAACACTTCCAGAAGATGCT
* *
14723 ATGAGCATATTCATCTTCCAAATTCAATGATTGGTTC-T-G----CCAAACCAGATCAGATAACT
1 ATGAGCATATTCATCTTCCAAATTTAATGATTGATTCTTGGTTATCCAAACCAGATCAGATAACT
14782 CAAAGAACACTTCCAGAAGATGCT
66 CAAAGAACACTTCCAGAAGATGCT
*
14806 ATGAGCATATTCATCTTCC-AA-TTCA--A-TGA---TTGGTTATGCCAAACCAGATCAGATAAC
1 ATGAGCATATTCATCTTCCAAATTTAATGATTGATTCTTGGTTAT-CCAAACCAGATCAGATAAC
14863 TCAAAGAACACTTCCAGAAGATGCT
65 TCAAAGAACACTTCCAGAAGATGCT
14888 ATGAGCATATTCATCTTCCAA
1 ATGAGCATATTCATCTTCCAA
14909 TTTCTACTAT
Statistics
Matches: 250, Mismatches: 14, Indels: 34
0.84 0.05 0.11
Matches are distributed among these distances:
76 1 0.00
77 1 0.00
78 2 0.01
79 1 0.00
81 2 0.01
82 65 0.26
83 64 0.26
87 32 0.13
88 1 0.00
89 3 0.01
90 1 0.00
91 1 0.00
92 1 0.00
93 75 0.30
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (89 bp):
ATGAGCATATTCATCTTCCAAATTTAATGATTGATTCTTGGTTATCCAAACCAGATCAGATAACT
CAAAGAACACTTCCAGAAGATGCT
Found at i:14880 original size:82 final size:82
Alignment explanation
Indices: 14674--14910 Score: 447
Period size: 82 Copynumber: 2.9 Consensus size: 82
14664 TTCTGTGGTT
*
14674 TTATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCT
1 TTATGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCT
14739 TCCAAATTCAATGATTGG
66 TCC-AATTCAATGATTGG
*
14757 TTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCT
1 TTATGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCT
14822 TCCAATTCAATGATTGG
66 TCCAATTCAATGATTGG
14839 TTATGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCT
1 TTATGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCT
14904 TCCAATT
66 TCCAATT
14911 TCTACTATGA
Statistics
Matches: 151, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
82 85 0.56
83 66 0.44
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.27
Consensus pattern (82 bp):
TTATGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCT
TCCAATTCAATGATTGG
Found at i:23205 original size:3 final size:3
Alignment explanation
Indices: 23199--23246 Score: 62
Period size: 3 Copynumber: 16.0 Consensus size: 3
23189 AATAATTATT
* *
23199 TAA TAA TAA T-A TAC TAA TAA TAA TATT TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA
23244 TAA
1 TAA
23247 ATTTAATAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 35 0.90
4 2 0.05
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:23266 original size:16 final size:18
Alignment explanation
Indices: 23245--23278 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
23235 TAATAATAAT
23245 AAATTT-AAT-AAAAAAA
1 AAATTTAAATGAAAAAAA
23261 AAATTTAAATGAAAAAAA
1 AAATTTAAATGAAAAAAA
23279 TGATGTCTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 3 0.19
18 7 0.44
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (18 bp):
AAATTTAAATGAAAAAAA
Found at i:23277 original size:17 final size:16
Alignment explanation
Indices: 23245--23278 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
23235 TAATAATAAT
23245 AAATTTAATAAAAAAA
1 AAATTTAATAAAAAAA
*
23261 AAATTTAAATGAAAAAA
1 AAATTT-AATAAAAAAA
23278 A
1 A
23279 TGATGTCTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (16 bp):
AAATTTAATAAAAAAA
Found at i:27779 original size:64 final size:64
Alignment explanation
Indices: 27699--27849 Score: 180
Period size: 64 Copynumber: 2.3 Consensus size: 64
27689 ATGCACATTC
* * * * *
27699 ATAAGTGCATCGATGCATTTC-TTTAAAAGAAGAACATCGAATGCCTTTGATGCATCGATGCATA
1 ATAA-TGCATCGATGCATTCCTTTTAAAAGAAAAACATCGAATGCATTTGATGCACCGATGCACA
* *
27763 GATAATGCATCGATGCA-TCCTTTTAAAATAAAAACATCGAATGCATTTTATGCACCGATGCACA
1 -ATAATGCATCGATGCATTCCTTTTAAAAGAAAAACATCGAATGCATTTGATGCACCGATGCACA
* *
27827 AGTAGTGCATCGATGCATACCTT
1 A-TAATGCATCGATGCATTCCTT
27850 CATTGAAAGA
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
63 3 0.04
64 63 0.85
65 8 0.11
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.29
Consensus pattern (64 bp):
ATAATGCATCGATGCATTCCTTTTAAAAGAAAAACATCGAATGCATTTGATGCACCGATGCACA
Found at i:28541 original size:31 final size:31
Alignment explanation
Indices: 28503--28567 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
28493 AGAGTCGAGG
*
28503 GTTTACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTAGGTTCTAAGGAACATATGGACA
** * *
28534 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTAGGTTCTAAGGAACATATGGACA
28565 GTT
1 GTT
28568 ACCGAGGATC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (31 bp):
GTTTACCTAGGTTCTAAGGAACATATGGACA
Found at i:28587 original size:30 final size:30
Alignment explanation
Indices: 28526--28617 Score: 112
Period size: 30 Copynumber: 3.0 Consensus size: 30
28516 CTAAGGAACA
* * **
28526 TATGGACAGTTTACCTAGGTTCTTCGGGACC
1 TATGGACAG-TTACCGAGGATCTTTAGGACC
*
28557 TATGGACAGTTACCGAGGATCTTTATGACC
1 TATGGACAGTTACCGAGGATCTTTAGGACC
* *
28587 TCTGGATAGTTACCGAGGATCTTTAGGACC
1 TATGGACAGTTACCGAGGATCTTTAGGACC
28617 T
1 T
28618 CTAGATAGGT
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
30 44 0.83
31 9 0.17
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.32
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGATCTTTAGGACC
Found at i:28618 original size:30 final size:30
Alignment explanation
Indices: 28552--28625 Score: 112
Period size: 30 Copynumber: 2.5 Consensus size: 30
28542 AGGTTCTTCG
* *
28552 GGACCTATGGACAGTTACCGAGGATCTTTA
1 GGACCTCTGGATAGTTACCGAGGATCTTTA
*
28582 TGACCTCTGGATAGTTACCGAGGATCTTTA
1 GGACCTCTGGATAGTTACCGAGGATCTTTA
*
28612 GGACCTCTAGATAG
1 GGACCTCTGGATAG
28626 GTCCTTCGGG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (30 bp):
GGACCTCTGGATAGTTACCGAGGATCTTTA
Found at i:30777 original size:19 final size:19
Alignment explanation
Indices: 30726--30783 Score: 54
Period size: 17 Copynumber: 3.3 Consensus size: 19
30716 TCAATAATAA
30726 ATTA-ATTTA-AATAAAAT
1 ATTAGATTTATAATAAAAT
* *
30743 -TGATATTTAT--TAAAAT
1 ATTAGATTTATAATAAAAT
30759 ATTAGATTTATAATAAAAT
1 ATTAGATTTATAATAAAAT
*
30778 AATAGA
1 ATTAGA
30784 AAGTTTAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
16 8 0.25
17 13 0.41
19 11 0.34
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.41
Consensus pattern (19 bp):
ATTAGATTTATAATAAAAT
Found at i:31632 original size:15 final size:15
Alignment explanation
Indices: 31612--31645 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
31602 AATTTAGACT
* *
31612 CAAAATTACTCAACC
1 CAAAATGACCCAACC
31627 CAAAATGACCCAACC
1 CAAAATGACCCAACC
31642 CAAA
1 CAAA
31646 CCCGATCCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.35, G:0.03, T:0.12
Consensus pattern (15 bp):
CAAAATGACCCAACC
Found at i:35889 original size:13 final size:13
Alignment explanation
Indices: 35841--35888 Score: 78
Period size: 13 Copynumber: 3.7 Consensus size: 13
35831 TGTGTCATAA
35841 ATTTATGACACGC
1 ATTTATGACACGC
*
35854 ATTTATGACACAC
1 ATTTATGACACGC
*
35867 ATTTATGACGCGC
1 ATTTATGACACGC
35880 ATTTATGAC
1 ATTTATGAC
35889 GTTCATTAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (13 bp):
ATTTATGACACGC
Found at i:35966 original size:85 final size:85
Alignment explanation
Indices: 35867--36032 Score: 210
Period size: 85 Copynumber: 2.0 Consensus size: 85
35857 TATGACACAC
* * * * * *
35867 ATTTATGACGCGCATTTATGACGTT-CATTAAGCGTCATTGAAGCCCCCGTCA-TAAATTAAGAT
1 ATTTATGACACGCATGTATGAC-TTACATTAAGCGTCATTGAAGCACACGCCATTAAA-AAAGAT
*
35930 GACACACATTTGTGTGTCATAA
64 GACACACATTCGTGTGTCATAA
** *
35952 ATTTATGACACGCATGTATGACTTACATTGCGTGTCATTGAAGCACACGCCATTAAAAAAGATGA
1 ATTTATGACACGCATGTATGACTTACATTAAGCGTCATTGAAGCACACGCCATTAAAAAAGATGA
36017 CACACATTCGTGTGTC
66 CACACATTCGTGTGTC
36033 GTGATTGCAT
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
84 2 0.03
85 63 0.91
86 4 0.06
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.30
Consensus pattern (85 bp):
ATTTATGACACGCATGTATGACTTACATTAAGCGTCATTGAAGCACACGCCATTAAAAAAGATGA
CACACATTCGTGTGTCATAA
Found at i:41490 original size:31 final size:31
Alignment explanation
Indices: 41452--41513 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
41442 ATAAACACTT
41452 GCAAAAACATACTCATGTTGTATTATTATTC
1 GCAAAAACATACTCATGTTGTATTATTATTC
41483 GCAAAAACATACTCATGTTGTATTATTATTC
1 GCAAAAACATACTCATGTTGTATTATTATTC
41514 AAGAAGAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (31 bp):
GCAAAAACATACTCATGTTGTATTATTATTC
Found at i:44333 original size:21 final size:21
Alignment explanation
Indices: 44302--44403 Score: 141
Period size: 21 Copynumber: 4.9 Consensus size: 21
44292 AAAGGAATTC
* * *
44302 GATGAATTACCTTGGTAAGTT
1 GATGAAGTACCTTGGTAAATA
*
44323 GAAGAAGTACCTTGGTAAATA
1 GATGAAGTACCTTGGTAAATA
*
44344 GATGAAGTACCTTAGTAAATA
1 GATGAAGTACCTTGGTAAATA
*
44365 GATGAAGTACCTTAGTAAATA
1 GATGAAGTACCTTGGTAAATA
*
44386 GATGAAGTACCATGGTAA
1 GATGAAGTACCTTGGTAA
44404 GTGTCTCTGA
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 73 1.00
ACGTcount: A:0.39, C:0.10, G:0.23, T:0.28
Consensus pattern (21 bp):
GATGAAGTACCTTGGTAAATA
Found at i:45850 original size:19 final size:20
Alignment explanation
Indices: 45807--45855 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
45797 ATTTTGATTT
45807 AAAAATA-AAACTAACAATA
1 AAAAATAGAAACTAACAATA
* * *
45826 AGAAATTGAAACTAA-ACTA
1 AAAAATAGAAACTAACAATA
45845 AAAAATAGAAA
1 AAAAATAGAAA
45856 AAAATTTGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.69, C:0.08, G:0.06, T:0.16
Consensus pattern (20 bp):
AAAAATAGAAACTAACAATA
Found at i:46189 original size:15 final size:16
Alignment explanation
Indices: 46129--46189 Score: 51
Period size: 15 Copynumber: 4.1 Consensus size: 16
46119 AAAATAAAAA
*
46129 ATAAGGATAATAATA-
1 ATAAAGATAATAATAG
*
46144 AT-AAGATGGATAA-AG
1 ATAAAGAT-AATAATAG
*
46159 -TAAATATAATAATAG
1 ATAAAGATAATAATAG
46174 ATAAAGATAA-AATAG
1 ATAAAGATAATAATAG
46189 A
1 A
46190 GATATATAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
14 10 0.28
15 18 0.50
16 8 0.22
ACGTcount: A:0.61, C:0.00, G:0.15, T:0.25
Consensus pattern (16 bp):
ATAAAGATAATAATAG
Found at i:49550 original size:154 final size:152
Alignment explanation
Indices: 49256--49558 Score: 371
Period size: 154 Copynumber: 2.0 Consensus size: 152
49246 CAATGACCAT
* * * * * *
49256 CCAATCACTTGATTTCATAAACTTTTGATTGATATATCATTTCAATTCAGTGATATATTAGACAT
1 CCAATCACTTCATTTCAGAAACTTTTCAGTGATACATCATTTCAATTCAGTGATATATCAGACAT
* * * *
49321 TGAATGTTGTTTTTGACTTGTTTCCCTTTAATGAAAAAATGTCATTTTCTTATATCATTTAAAAC
66 TGAATGATGCTTTTGACTTGTTTCCCTTTAATGAAAAAA-GTCATTTTCTCATACCATTTAAAAC
49386 ACAATGAAAAAAACTTTTCAGTGG
130 ACAATG-AAAAAACTTTTCAGTGG
*
49410 CCAATCACTTCATTTCAGAAACTTTTCAGTGATACATCACTTT-AATTTAGTGATATATCAGACC
1 CCAATCACTTCATTTCAGAAACTTTTCAGTGATACATCA-TTTCAATTCAGTGATATATCAGA-C
* * * *
49474 ATTGAATGATGCTTTTGA-TTTTTTTCCTTTAATGAAAAACA-TCCTTTTCTCATACCA-TTAAT
64 ATTGAATGATGCTTTTGACTTGTTTCCCTTTAATGAAAAA-AGTCATTTTCTCATACCATTTAAA
*
49536 ACATAATGACAAAAATCTTTTCA
128 ACACAATGA-AAAAA-CTTTTCA
49559 ATGAAATATC
Statistics
Matches: 128, Mismatches: 16, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
151 1 0.01
152 16 0.12
153 20 0.16
154 70 0.55
155 21 0.16
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.41
Consensus pattern (152 bp):
CCAATCACTTCATTTCAGAAACTTTTCAGTGATACATCATTTCAATTCAGTGATATATCAGACAT
TGAATGATGCTTTTGACTTGTTTCCCTTTAATGAAAAAAGTCATTTTCTCATACCATTTAAAACA
CAATGAAAAAACTTTTCAGTGG
Found at i:50543 original size:24 final size:24
Alignment explanation
Indices: 50494--50543 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
50484 AAAAACTAGG
* *
50494 TTAGTGACTAAATTGTAAGATTTT
1 TTAGAGACTAAATTGTAAAATTTT
*
50518 TTAGAGACTTAATTG-AAAATTCTT
1 TTAGAGACTAAATTGTAAAATT-TT
50542 TT
1 TT
50544 TGTAGGAGTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.34, C:0.06, G:0.14, T:0.46
Consensus pattern (24 bp):
TTAGAGACTAAATTGTAAAATTTT
Found at i:51992 original size:23 final size:23
Alignment explanation
Indices: 51934--51985 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
51924 AAATCACTGG
51934 GTTAACTCGTTGACATTGATCGA
1 GTTAACTCGTTGACATTGATCGA
* * *
51957 ATCAACTCGTTGACATTGCTCGA
1 GTTAACTCGTTGACATTGATCGA
51980 GTTAAC
1 GTTAAC
51986 CCATTGAACG
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:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (23 bp):
GTTAACTCGTTGACATTGATCGA
Done.