Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008406.1 Hibiscus syriacus cultivar Beakdansim tig00111175_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: 31884
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Found at i:2036 original size:183 final size:183
Alignment explanation
Indices: 1573--2239 Score: 1195
Period size: 181 Copynumber: 3.7 Consensus size: 183
1563 TTAAAATTAC
*
1573 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
* *
1638 ATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
* *
1703 ATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
*
1756 CG--ACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
1819 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
1884 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
*
1937 CGACACTTTTTAACAAT-GTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAA
1 CGACACTTTTTTA-AATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAA
*
2001 GATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGT
65 TATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGT
2066 TATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
130 TATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
2120 CGACAC-TTTTTAAAT-GTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACAC-A-
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
*
2181 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCAAAAAACCGGTATATTTATA
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATA
2240 ATATGTTGAA
Statistics
Matches: 470, Mismatches: 11, Indels: 10
0.96 0.02 0.02
Matches are distributed among these distances:
179 58 0.12
180 1 0.00
181 223 0.47
182 5 0.01
183 180 0.38
184 3 0.01
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (183 bp):
CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
Found at i:2135 original size:17 final size:19
Alignment explanation
Indices: 2113--2150 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2103 TTCCGATGTG
2113 TAAATG-TCGACAC-TTTT
1 TAAATGATCGACACATTTT
2130 TAAATGTATCGACACATTTT
1 TAAATG-ATCGACACATTTT
2150 T
1 T
2151 CTTCCAATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.33
19 7 0.39
20 5 0.28
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.42
Consensus pattern (19 bp):
TAAATGATCGACACATTTT
Found at i:3708 original size:3 final size:3
Alignment explanation
Indices: 3700--3780 Score: 72
Period size: 3 Copynumber: 27.0 Consensus size: 3
3690 ACTTGTTTGG
* * * **
3700 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * * * *
3748 AGC TTC ATC GTC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
3781 GTCAGCTTCA
Statistics
Matches: 59, Mismatches: 19, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.23, C:0.35, G:0.06, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:3717 original size:12 final size:12
Alignment explanation
Indices: 3704--3792 Score: 88
Period size: 12 Copynumber: 7.4 Consensus size: 12
3694 GTTTGGATCA
* *
3704 TCATCTTCATCA
1 TCATCGTCATCT
* *
3716 TCATCATCATCA
1 TCATCGTCATCT
* *
3728 TCGTCATCATCT
1 TCATCGTCATCT
* *
3740 TCATCGCCAGCT
1 TCATCGTCATCT
*
3752 TCATCGTCATCA
1 TCATCGTCATCT
3764 TCATCGTCATCT
1 TCATCGTCATCT
*
3776 TCATCGTCAGCT
1 TCATCGTCATCT
3788 TCATC
1 TCATC
3793 TTCTGCGACC
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 65 1.00
ACGTcount: A:0.21, C:0.35, G:0.08, T:0.36
Consensus pattern (12 bp):
TCATCGTCATCT
Found at i:3723 original size:18 final size:18
Alignment explanation
Indices: 3704--3795 Score: 76
Period size: 18 Copynumber: 5.1 Consensus size: 18
3694 GTTTGGATCA
* *
3704 TCATCTTCATCATCATCA
1 TCATCATCATCATCATCT
*
3722 TCATCATCGTCATCATCT
1 TCATCATCATCATCATCT
** * * *
3740 TCATCGCCAGCTTCATCG
1 TCATCATCATCATCATCT
*
3758 TCATCATCATCGTCATCT
1 TCATCATCATCATCATCT
* * *
3776 TCATCGTCAGCTTCATCT
1 TCATCATCATCATCATCT
3794 TC
1 TC
3796 TGCGACCGCT
Statistics
Matches: 57, Mismatches: 17, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 57 1.00
ACGTcount: A:0.21, C:0.35, G:0.08, T:0.37
Consensus pattern (18 bp):
TCATCATCATCATCATCT
Found at i:3756 original size:36 final size:36
Alignment explanation
Indices: 3716--3792 Score: 118
Period size: 36 Copynumber: 2.1 Consensus size: 36
3706 ATCTTCATCA
*
3716 TCATCATCATCATCGTCATCATCTTCATCGCCAGCT
1 TCATCATCATCATCATCATCATCTTCATCGCCAGCT
* * *
3752 TCATCGTCATCATCATCGTCATCTTCATCGTCAGCT
1 TCATCATCATCATCATCATCATCTTCATCGCCAGCT
3788 TCATC
1 TCATC
3793 TTCTGCGACC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.21, C:0.35, G:0.09, T:0.35
Consensus pattern (36 bp):
TCATCATCATCATCATCATCATCTTCATCGCCAGCT
Found at i:3795 original size:6 final size:6
Alignment explanation
Indices: 3704--3795 Score: 67
Period size: 6 Copynumber: 15.3 Consensus size: 6
3694 GTTTGGATCA
* * * * * * * *
3704 TCATCT TCATCA TCATCA TCATCA TCGTCA TCATCT TCATCG CCAGCT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
* * * * *
3752 TCATCG TCATCA TCATCG TCATCT TCATCG TCAGCT TCATCT TC
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TC
3796 TGCGACCGCT
Statistics
Matches: 68, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 68 1.00
ACGTcount: A:0.21, C:0.35, G:0.08, T:0.37
Consensus pattern (6 bp):
TCATCT
Found at i:5549 original size:177 final size:180
Alignment explanation
Indices: 5253--6380 Score: 1295
Period size: 197 Copynumber: 5.9 Consensus size: 180
5243 TTTAAATTAG
5253 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
5318 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* * *
5383 CGACAC-TT-TATGGGT-GCACCCTGTT-T-TCCATTCATTCTGGAAAAAAA
131 CGACACTTTATATGGATCG-ACACT-TTATGTCCATTCATTCTTGAAAAAAA
5430 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
5495 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
5560 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTATTTTCCATTCATTCTGGAAAA
131 CGACAC---TT-TATATGGATCGACACTTTAT--GT----CC-A--TT-CATTC--T-T-G-AAA
5625 AAAA
177 AAAA
*
5629 TATCGACACAAACTATATTAGTGTCGACACATTATTT--ACATATTATCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
5692 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
5757 CGACACTTTTTATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAA
131 CGACAC--TTTATATGGATCGACAC--T-T---T--A---TG---TCCATTCATTCTTG-AAAAA
5822 AA
179 AA
* * **
5824 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTATCTCATAAAATTGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
5889 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
5954 CGACACTTTTTATATATGGATCGACACTTTATGGGTTCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACAC---TT-TATATGGATCGACAC----T---TT-A---TG---TCCATTCATTCTTG-AAA
6019 AAAA
177 AAAA
*
6023 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
6088 ATTGTACCGGTTAGATTG-AAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTCGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
6152 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACAC---TT-TATATGGATCGACAC--T-T---T--A---TG---TCCATTCATTCTTGAAAA
6217 AAA
178 AAA
* *
6220 TATCGACACAAACTATATTAGTGTCGACGCATTATTTAGACATATTCTCTCAT-AAACCGGTAGA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
* * *
6284 CTTGTACCGGTTAGATTG-AAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGATTTTGGGA
*
6348 TTGACACTTTTATATATGGATCGACACTTTATG
130 TCGACAC--TT-TATATGGATCGACACTTTATG
6381 GTAAATTTGC
Statistics
Matches: 876, Mismatches: 24, Indels: 94
0.88 0.02 0.09
Matches are distributed among these distances:
177 135 0.15
181 1 0.00
182 3 0.00
183 11 0.01
184 1 0.00
185 2 0.00
186 1 0.00
188 1 0.00
190 3 0.00
191 1 0.00
193 3 0.00
194 7 0.01
195 61 0.07
196 82 0.09
197 272 0.31
198 102 0.12
199 176 0.20
200 3 0.00
201 3 0.00
202 1 0.00
203 4 0.00
204 1 0.00
206 1 0.00
207 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.37
Consensus pattern (180 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTATATGGATCGACACTTTATGTCCATTCATTCTTGAAAAAAA
Found at i:6072 original size:199 final size:199
Alignment explanation
Indices: 5379--6381 Score: 1801
Period size: 197 Copynumber: 5.1 Consensus size: 199
5369 GATGATTTTG
5379 GGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAAAAAATATCGACACAAAC
1 GGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAAC
*
5443 TATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTTA
66 TATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTATAATTGTACCGGTTA
5508 GATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTAT
131 GATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTAT
5573 ATAT
196 ATAT
*
5577 GGATCGACACTTTATGGGTGCACCCTATTTTCCATTCATTCTGGAAAAAAAATATCGACACAAAC
1 GGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAAC
5642 TATATTAGTGTCGACACATTATTT--ACATATTATCTCATAAAACCGGTATAATTGTACCGGTTA
66 TATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTATAATTGTACCGGTTA
5705 GATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACAC-TTTT-T
131 GATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTAT
5768 ATAT
196 ATAT
5772 GGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAAC
1 GGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAAC
* **
5837 TATATTAGTGTCGACACATTATTTATACATATTATCTCATAAAATTGGTATAATTGTACCGGTTA
66 TATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTATAATTGTACCGGTTA
5902 GATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTAT
131 GATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTAT
5967 ATAT
196 ATAT
*
5971 GGATCGACACTTTATGGGTTCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAAC
1 GGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAAC
6036 TATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTATAATTGTACCGGTTA
66 TATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTATAATTGTACCGGTTA
*
6101 GATTG-AAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTCGGATCGACACTTTTTAT
131 GATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTAT
6165 ATAT
196 ATAT
6169 GGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAAAAAATATCGACACAAAC
1 GGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAAC
* * * *
6233 TATATTAGTGTCGACGCATTATTTAGACATATTCTCTCAT-AAACCGGTAGACTTGTACCGGTTA
66 TATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTATAATTGTACCGGTTA
* * *
6297 GATTG-AAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATTGACAC-TTTTA
131 GATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGATTTTGGGATCGACACTTTTTA
6360 TATAT
195 TATAT
6365 GGATCGACACTTTATGG
1 GGATCGACACTTTATGG
6382 TAAATTTGCC
Statistics
Matches: 780, Mismatches: 19, Indels: 14
0.96 0.02 0.02
Matches are distributed among these distances:
195 93 0.12
196 86 0.11
197 269 0.34
198 152 0.19
199 180 0.23
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (199 bp):
GGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAAC
TATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTATAATTGTACCGGTTA
GATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTAT
ATAT
Found at i:6536 original size:19 final size:18
Alignment explanation
Indices: 6490--6536 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
6480 TTATATTCAC
*
6490 ATACAAAAATATAATCGT
1 ATACAAAATTATAATCGT
*
6508 ATAC-AAATTATAAATCTT
1 ATACAAAATTAT-AATCGT
6526 ATACAAAATTA
1 ATACAAAATTA
6537 ACCCTACATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 6 0.24
18 13 0.52
19 6 0.24
ACGTcount: A:0.55, C:0.11, G:0.02, T:0.32
Consensus pattern (18 bp):
ATACAAAATTATAATCGT
Found at i:8365 original size:33 final size:33
Alignment explanation
Indices: 8319--8384 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
8309 CCATCTTATA
*
8319 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
8352 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
8385 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:8443 original size:21 final size:21
Alignment explanation
Indices: 8418--8482 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
8408 CCCCTTATGC
* *
8418 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
* *
8439 CTCTCGAGTTTCTCTACGACT
1 CTCTCAAGTTTCTCTTCGACT
**
8460 CGATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
8481 CT
1 CT
8483 TGATTGTCTT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.17, C:0.31, G:0.14, T:0.38
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:10730 original size:17 final size:18
Alignment explanation
Indices: 10708--10750 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
10698 ATATATCCGG
10708 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
10725 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
10745 TATCAT
1 TATCAT
10751 ATTTTTACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:10921 original size:20 final size:20
Alignment explanation
Indices: 10894--10940 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
10884 TCCGGTAACG
10894 TTTTACCGGTTTTATCAT-T
1 TTTTACCGGTTTTATCATAT
10913 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCATAT
10934 TTTTACC
1 TTTTACC
10941 TGGTATATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:10993 original size:181 final size:181
Alignment explanation
Indices: 10680--11151 Score: 687
Period size: 181 Copynumber: 2.6 Consensus size: 181
10670 CGTACTTACG
* * *
10680 AAAGTATCGACACTTTCAATATATCCGGTATCATTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * * * *
10745 TATCATATTTTTACATGTTATATCGTTGTGGATCGATATATTTTTTTAAAGTATTGACACATTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
*
10810 AGGCGCTATAACTGCTTCTCTTTTAAATTCACAAAATGTCGATCCTTATA-T
131 AGGAGCTA-AACTGCTTCTCTTTTAAATTCACAAAATGTCGATCCTTATATT
* *
10861 AAAGTATCGACACTTTTAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGTTACCGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
10926 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
** * *
10991 AGGATTTAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
131 AGGAGCTAAACTGCTTCTCTTTTAAATTCACAAAATGTCGATCCTTATATT
* * * * *
11042 AAAGTACCGACACTTTAAATGTATCCGGTAGCGCTTGACCGGTTTTATCATTTCT-ATACCGGTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTT-TGATACCGGTT
* * *
11106 TTGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTT
65 TTATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
11152 AATTTGGATC
Statistics
Matches: 262, Mismatches: 27, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
180 39 0.15
181 222 0.85
182 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (181 bp):
AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
AGGAGCTAAACTGCTTCTCTTTTAAATTCACAAAATGTCGATCCTTATATT
Found at i:11617 original size:229 final size:228
Alignment explanation
Indices: 11218--11702 Score: 850
Period size: 229 Copynumber: 2.1 Consensus size: 228
11208 ACCTACTTTT
11218 ATAAGTATGGACACTTTTATAAAAATG--ATATACTTCTTTGAAAGTTATGTAATTTATGTTTCA
1 ATAAGTATGGACACTTTTATAAAAATGATATATACTTCTTTGAAAGTTATGTAATTTATGTTTCA
11281 ATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTAATTTACACAAA
66 ATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTAATTTACACAAA
*
11346 ATATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATA-TAAC
131 AAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAAC
* *
11410 CAAATATAATAATAAATATGTTTTTCAACAGTGAA
196 CAAAGATAATAATAAATAT-ATTTTC-ACAGTGAA
*
11445 ATAAGTATGGACACTTTTATAAAAATGATATATACTTTTTTGAAAGTTATGTAATTTATGTTTCA
1 ATAAGTATGGACACTTTTATAAAAATGATATATACTTCTTTGAAAGTTATGTAATTTATGTTTCA
* *
11510 ATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAA
66 ATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTAATTTACACAAA
*
11575 AAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGATTTTAAATTTAACAATATTAAC
131 AAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAAC
*
11640 TAAAGATAATAATAAATATATTTTCACAGTGAA
196 CAAAGATAATAATAAATATATTTTCACAGTGAA
*
11673 ATAAGTATGGACACTTTTATAAAAAGGATA
1 ATAAGTATGGACACTTTTATAAAAATGATA
11703 GATAATTTAC
Statistics
Matches: 246, Mismatches: 9, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
227 27 0.11
228 37 0.15
229 161 0.65
230 21 0.09
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (228 bp):
ATAAGTATGGACACTTTTATAAAAATGATATATACTTCTTTGAAAGTTATGTAATTTATGTTTCA
ATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTAATTTACACAAA
AAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAAC
CAAAGATAATAATAAATATATTTTCACAGTGAA
Found at i:15573 original size:30 final size:31
Alignment explanation
Indices: 15537--15602 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
15527 TAATATTTGA
15537 TCACTTTC-GTTTTATTTAATTAAAATGTGG
1 TCACTTTCAGTTTTATTTAATTAAAATGTGG
* *
15567 TCACTTTCATTTTTATTTAATTAAGATGTGG
1 TCACTTTCAGTTTTATTTAATTAAAATGTGG
15598 TCACT
1 TCACT
15603 GAGGGTTAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
30 8 0.24
31 25 0.76
ACGTcount: A:0.26, C:0.12, G:0.12, T:0.50
Consensus pattern (31 bp):
TCACTTTCAGTTTTATTTAATTAAAATGTGG
Found at i:17147 original size:21 final size:21
Alignment explanation
Indices: 17101--17147 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
17091 TAATGATAAT
*
17101 GTGACGATCTACGATAATTAC
1 GTGACGATCTACGATAATGAC
*
17122 ATGACGATCTACGATAATGAC
1 GTGACGATCTACGATAATGAC
17143 GTGAC
1 GTGAC
17148 AATTCATGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (21 bp):
GTGACGATCTACGATAATGAC
Found at i:17769 original size:21 final size:23
Alignment explanation
Indices: 17743--17790 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
17733 GTCCCCTCAA
* *
17743 AATTAT-ATTAAATTT-TAAGTT
1 AATTATCATAAAATTTATAACTT
17764 AATTATCATAAAATTTATAACTT
1 AATTATCATAAAATTTATAACTT
17787 AATT
1 AATT
17791 TCGACTCTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 6 0.26
22 8 0.35
23 9 0.39
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (23 bp):
AATTATCATAAAATTTATAACTT
Found at i:19336 original size:5 final size:5
Alignment explanation
Indices: 19321--19372 Score: 79
Period size: 5 Copynumber: 10.6 Consensus size: 5
19311 GTATCATGTT
* *
19321 TATAA -ATAA TATAA TATAA TATAA TGTAA TGTAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
19370 TAT
1 TAT
19373 GAAAAATAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
4 4 0.09
5 40 0.91
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (5 bp):
TATAA
Found at i:21602 original size:13 final size:14
Alignment explanation
Indices: 21584--21612 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
21574 AGGCGACAAT
21584 GGAGC-AACGTTTA
1 GGAGCAAACGTTTA
21597 GGAGCAAACGTTTA
1 GGAGCAAACGTTTA
21611 GG
1 GG
21613 TAAACCCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.31, C:0.14, G:0.34, T:0.21
Consensus pattern (14 bp):
GGAGCAAACGTTTA
Found at i:21797 original size:3 final size:3
Alignment explanation
Indices: 21791--21823 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
21781 TATTATTTAT
21791 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
21824 TAAATATTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:23060 original size:2 final size:2
Alignment explanation
Indices: 23042--23087 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
23032 TTGATATTTC
23042 AT AT -T AT AT A- AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23081 AT AT AT A
1 AT AT AT A
23088 GGGATGATGA
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
1 3 0.07
2 38 0.93
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:23181 original size:3 final size:3
Alignment explanation
Indices: 23173--23203 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
23163 TACACTTATT
*
23173 TAA TAA TAA TAA TAA TAA TAA TCA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
23204 TAAAATAGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:23346 original size:16 final size:16
Alignment explanation
Indices: 23325--23355 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
23315 AATACGAATT
*
23325 ATGAATATAATAATAA
1 ATGAATATAAAAATAA
23341 ATGAATATAAAAATA
1 ATGAATATAAAAATA
23356 TAAAACCGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (16 bp):
ATGAATATAAAAATAA
Found at i:24749 original size:2 final size:2
Alignment explanation
Indices: 24742--24792 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
24732 CATTAAACCC
24742 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
24784 TA TA TA TA T
1 TA TA TA TA T
24793 CCAGGGCCGC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:25118 original size:2 final size:2
Alignment explanation
Indices: 25111--25135 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
25101 TAGTTATACA
25111 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
25136 ATTCATAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:26052 original size:32 final size:32
Alignment explanation
Indices: 26015--26075 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
26005 TAGATTACTT
26015 AAAAATTATCTTACGTAAAATGAATTATATGA
1 AAAAATTATCTTACGTAAAATGAATTATATGA
* * * *
26047 AAAAATTGTTTTACTTAAAATTAATTATA
1 AAAAATTATCTTACGTAAAATGAATTATA
26076 ATTTTAGAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.39
Consensus pattern (32 bp):
AAAAATTATCTTACGTAAAATGAATTATATGA
Found at i:27414 original size:2 final size:2
Alignment explanation
Indices: 27407--27438 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
27397 ATTTTGTTAC
27407 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
27439 GAGGTCCCGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:27725 original size:19 final size:19
Alignment explanation
Indices: 27701--27745 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
27691 AAAAGTAATC
27701 AATATCACAGTTTACTATA
1 AATATCACAGTTTACTATA
27720 AATATCACAGTTTACTATA
1 AATATCACAGTTTACTATA
*
27739 AAAATCA
1 AATATCA
27746 AGGACATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.47, C:0.16, G:0.04, T:0.33
Consensus pattern (19 bp):
AATATCACAGTTTACTATA
Found at i:30024 original size:68 final size:69
Alignment explanation
Indices: 29897--30025 Score: 158
Period size: 68 Copynumber: 1.9 Consensus size: 69
29887 ATTAGGTCAT
* * * *
29897 AATTTCAATTTAATTTAATAATTTATTTCTCCAATCAAAGTGTGACACATTTTATCTTTTGTACA
1 AATTTCAATTTAATTTAATAATATATTTCTCCAATCAAAGTGTGACACATGTCACCTTTTGTACA
29962 ATGA
66 ATGA
*
29966 AATTT-AATTTAATTTAATAA-AT-TTTCAATCCGATCAAAAG-GTGACACATGTCACCTTTTG
1 AATTTCAATTTAATTTAATAATATATTTC--TCCAATC-AAAGTGTGACACATGTCACCTTTTG
30026 AATTGAAGTG
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
66 4 0.08
67 1 0.02
68 38 0.73
69 9 0.17
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.42
Consensus pattern (69 bp):
AATTTCAATTTAATTTAATAATATATTTCTCCAATCAAAGTGTGACACATGTCACCTTTTGTACA
ATGA
Done.