Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008651.1 Hibiscus syriacus cultivar Beakdansim tig00111641_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: 314694
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 2 of 2
Found at i:290089 original size:23 final size:23
Alignment explanation
Indices: 290063--290125 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
290053 ATATAACCAC
290063 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
290086 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
290109 TACCTATTACATCATAT
1 TACCTATTACATTATAT
290126 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:290528 original size:25 final size:25
Alignment explanation
Indices: 290471--290536 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
290461 CACTCAAAAG
*
290471 ATGTATATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
***
290496 ACAAACATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
*
290521 TTGTACATACCTAAAT
1 ATGTACATACCTAAAT
290537 TTAATGATAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (25 bp):
ATGTACATACCTAAATATGTAGTTA
Found at i:290568 original size:19 final size:19
Alignment explanation
Indices: 290513--290570 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 19
290503 TACCTAAATA
290513 TGTAGTTATTGTACATACC
1 TGTAGTTATTGTACATACC
** * * *
290532 TAAATTTAATGATA-ATACT
1 TGTAGTTATTG-TACATACC
290551 TGTAGTTATTGTACATACC
1 TGTAGTTATTGTACATACC
290570 T
1 T
290571 AAATATGTAC
Statistics
Matches: 27, Mismatches: 10, Indels: 4
0.66 0.24 0.10
Matches are distributed among these distances:
18 2 0.07
19 23 0.85
20 2 0.07
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (19 bp):
TGTAGTTATTGTACATACC
Found at i:293316 original size:183 final size:183
Alignment explanation
Indices: 293002--293710 Score: 1301
Period size: 183 Copynumber: 3.9 Consensus size: 183
292992 TTAAAATTAC
* *
293002 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
* *
293067 ATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATATCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
293132 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
293185 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
* *
293250 ATTAAAAAGTGTTGATATAGGTTGTAGACCTGTTCGCGCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
293315 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
293368 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
293433 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
*
293498 TTATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
293551 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
*
293616 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCACATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
* * * **
293681 ATATTGCAAATTTACCTATTTTATTATAAT
131 ATATTACAAAATTATCTATTACATTATAAT
293711 ATGTTGAAAG
Statistics
Matches: 510, Mismatches: 16, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
183 510 1.00
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (183 bp):
CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
Found at i:295138 original size:3 final size:3
Alignment explanation
Indices: 295130--295174 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
295120 ACTTGTTTGG
* * *
295130 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
295175 GCCAGCTTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.27, C:0.33, G:0.02, T:0.38
Consensus pattern (3 bp):
ATC
Found at i:295147 original size:12 final size:12
Alignment explanation
Indices: 295134--295222 Score: 79
Period size: 12 Copynumber: 7.4 Consensus size: 12
295124 GTTTGGATCA
* *
295134 TCATCTTCATCA
1 TCATCGTCATCT
* *
295146 TCATCATCATCA
1 TCATCGTCATCT
* *
295158 TCGTCATCATCT
1 TCATCGTCATCT
* *
295170 TCATCGCCAGCT
1 TCATCGTCATCT
* *
295182 TTATCGTCATCA
1 TCATCGTCATCT
295194 TCATCGTCATCT
1 TCATCGTCATCT
*
295206 TCATCGTCAGCT
1 TCATCGTCATCT
295218 TCATC
1 TCATC
295223 TTCTGCGACC
Statistics
Matches: 63, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 63 1.00
ACGTcount: A:0.21, C:0.34, G:0.08, T:0.37
Consensus pattern (12 bp):
TCATCGTCATCT
Found at i:295153 original size:18 final size:18
Alignment explanation
Indices: 295134--295225 Score: 67
Period size: 18 Copynumber: 5.1 Consensus size: 18
295124 GTTTGGATCA
* *
295134 TCATCTTCATCATCATCA
1 TCATCATCATCATCATCT
*
295152 TCATCATCGTCATCATCT
1 TCATCATCATCATCATCT
** * * * *
295170 TCATCGCCAGCTTTATCG
1 TCATCATCATCATCATCT
*
295188 TCATCATCATCGTCATCT
1 TCATCATCATCATCATCT
* * *
295206 TCATCGTCAGCTTCATCT
1 TCATCATCATCATCATCT
295224 TC
1 TC
295226 TGCGACCGCT
Statistics
Matches: 55, Mismatches: 19, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
18 55 1.00
ACGTcount: A:0.21, C:0.34, G:0.08, T:0.38
Consensus pattern (18 bp):
TCATCATCATCATCATCT
Found at i:295225 original size:6 final size:6
Alignment explanation
Indices: 295134--295225 Score: 58
Period size: 6 Copynumber: 15.3 Consensus size: 6
295124 GTTTGGATCA
* * * * * * * *
295134 TCATCT TCATCA TCATCA TCATCA TCGTCA TCATCT TCATCG CCAGCT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
* * * * * *
295182 TTATCG TCATCA TCATCG TCATCT TCATCG TCAGCT TCATCT TC
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TC
295226 TGCGACCGCT
Statistics
Matches: 66, Mismatches: 20, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
6 66 1.00
ACGTcount: A:0.21, C:0.34, G:0.08, T:0.38
Consensus pattern (6 bp):
TCATCT
Found at i:297021 original size:198 final size:198
Alignment explanation
Indices: 296683--297851 Score: 2275
Period size: 198 Copynumber: 5.9 Consensus size: 198
296673 TTTAAATTAG
296683 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
296748 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
296813 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
296878 AAA
196 AAA
296881 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
296946 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
297011 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
297076 AAA
196 AAA
297079 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
297144 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
297209 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
297274 AAA
196 AAA
297277 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
297342 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
297407 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
297472 AAA
196 AAA
*
297475 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
297540 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
297605 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAA
297670 AAAA
195 AAAA
297674 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
* *
297739 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGATTTTGGGA
*
297804 TTGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
130 TCGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
297852 GGCCATATTG
Statistics
Matches: 963, Mismatches: 5, Indels: 3
0.99 0.01 0.00
Matches are distributed among these distances:
198 784 0.81
199 118 0.12
200 21 0.02
201 40 0.04
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.37
Consensus pattern (198 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
AAA
Found at i:298016 original size:19 final size:19
Alignment explanation
Indices: 297970--298018 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
297960 TTATATTCAC
* *
297970 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATAGT
*
297989 ATACAAAATTATAAATATT
1 ATACAAAATTATAAATAGT
298008 ATACAAAATTA
1 ATACAAAATTA
298019 ACCCTACATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.59, C:0.08, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATAGT
Found at i:299848 original size:33 final size:33
Alignment explanation
Indices: 299811--299876 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
299801 CATCTTAATA
*
299811 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
*
299844 TCACCCCTCAACACCCCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
299877 CCATCTATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.23, C:0.50, G:0.00, T:0.27
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:299950 original size:21 final size:21
Alignment explanation
Indices: 299910--299974 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
299900 CCCCTTATGC
* *
299910 CTCTCGAGTGTATCTTCGACT
1 CTCTCGAGTTTCTCTTCGACT
*
299931 CTCTCGAGTTTCTCTACGACT
1 CTCTCGAGTTTCTCTTCGACT
* *
299952 -TGATCAAGTTTCTCTTCGACT
1 CT-CTCGAGTTTCTCTTCGACT
299973 CT
1 CT
299975 TGATTGTCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.15, C:0.29, G:0.15, T:0.40
Consensus pattern (21 bp):
CTCTCGAGTTTCTCTTCGACT
Found at i:302246 original size:20 final size:20
Alignment explanation
Indices: 302199--302246 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
302189 TCCGGTATCA
302199 TTTTACCGGTTTTTATCATT
1 TTTTACCGGTTTTTATCATT
*
302219 TTGATACCGG-TTTTATCATAT
1 TT-TTACCGGTTTTTATCAT-T
302240 TTTTACC
1 TTTTACC
302247 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 15 0.62
21 9 0.38
ACGTcount: A:0.19, C:0.17, G:0.10, T:0.54
Consensus pattern (20 bp):
TTTTACCGGTTTTTATCATT
Found at i:302394 original size:20 final size:20
Alignment explanation
Indices: 302368--302413 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
302358 CACTTTTAAA
302368 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
302387 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
302408 TTTACC
1 TTTACC
302414 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:303440 original size:15 final size:15
Alignment explanation
Indices: 303418--303459 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
303408 AATTATTTTA
303418 TATATATATATAATAT
1 TATATATATATAAT-T
*
303434 T-TATATATTTAATT
1 TATATATATATAATT
*
303448 TAAATATATATA
1 TATATATATATA
303460 CTCGACCCGA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
14 2 0.09
15 19 0.86
16 1 0.05
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATATATATATAATT
Found at i:305201 original size:41 final size:41
Alignment explanation
Indices: 305156--305311 Score: 165
Period size: 41 Copynumber: 3.8 Consensus size: 41
305146 GAATAAGTAA
** *
305156 ATCGCAACGCGA-AATGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGATAAT-ACAAAATCGCAACGCGATACTGACT
305197 ATCGCAACGCGATAATACAAAATCGCAACGCGATACTGACT
1 ATCGCAACGCGATAATACAAAATCGCAACGCGATACTGACT
* * ** *
305238 TTCGCAACGCGATACTGAC--TTTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATAAT-ACAAAATCGCAACGCGATACTGACT
* * * *
305278 TTCGCAACGAGATAATACAGAATCGCAATGCGAT
1 ATCGCAACGCGATAATACAAAATCGCAACGCGAT
305312 TTTCAAAGTT
Statistics
Matches: 98, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
39 2 0.02
40 32 0.33
41 59 0.60
42 5 0.05
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.21
Consensus pattern (41 bp):
ATCGCAACGCGATAATACAAAATCGCAACGCGATACTGACT
Found at i:305202 original size:20 final size:20
Alignment explanation
Indices: 305177--305291 Score: 133
Period size: 20 Copynumber: 5.7 Consensus size: 20
305167 AAATGGGAAA
*
305177 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
305197 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
305218 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
305238 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
305258 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
* *
305278 TTCGCAACGAGATA
1 ATCGCAACGCGATA
305292 ATACAGAATC
Statistics
Matches: 83, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
19 2 0.02
20 64 0.77
21 15 0.18
22 2 0.02
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:305223 original size:21 final size:22
Alignment explanation
Indices: 305154--305236 Score: 84
Period size: 21 Copynumber: 4.0 Consensus size: 22
305144 GCGAATAAGT
**
305154 AAATCGCAACGCGA-AATGGGA
1 AAATCGCAACGCGATAATGACA
* *
305175 AAATCGCAATGCGATACTGAC-
1 AAATCGCAACGCGATAATGACA
*
305196 -TATCGCAACGCGATAAT-ACA
1 AAATCGCAACGCGATAATGACA
*
305216 AAATCGCAACGCGATACTGAC
1 AAATCGCAACGCGATAATGAC
305237 TTTCGCAACG
Statistics
Matches: 49, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
19 2 0.04
20 14 0.29
21 28 0.57
22 5 0.10
ACGTcount: A:0.40, C:0.24, G:0.20, T:0.16
Consensus pattern (22 bp):
AAATCGCAACGCGATAATGACA
Found at i:307302 original size:20 final size:20
Alignment explanation
Indices: 307267--307304 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
307257 ATTCATTTGA
* *
307267 CTATCGCAATGCGAAAATGG
1 CTATCGCAACGAGAAAATGG
307287 CTATCGCAACGAGAAAAT
1 CTATCGCAACGAGAAAAT
307305 CGCAATGCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.18
Consensus pattern (20 bp):
CTATCGCAACGAGAAAATGG
Found at i:307364 original size:19 final size:19
Alignment explanation
Indices: 307323--307406 Score: 124
Period size: 19 Copynumber: 4.7 Consensus size: 19
307313 GAAATGAAAA
307323 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
307339 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
307356 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
307375 TCGCATTACGATTTTCATT
1 TCGCATTGCGATTTTCATT
307394 TCGCATTGCGATT
1 TCGCATTGCGATT
307407 CTCTCGTTAC
Statistics
Matches: 61, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
14 11 0.18
16 3 0.05
17 3 0.05
19 44 0.72
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:307396 original size:38 final size:33
Alignment explanation
Indices: 307323--307419 Score: 131
Period size: 38 Copynumber: 2.8 Consensus size: 33
307313 GAAATGAAAA
*
307323 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTACGATTTTCATT
307356 TCGCATTGCGATTTTCATTTCGCATTACGATTTTCATT
1 TCGCATTGCGATTTTC---TCG--TTACGATTTTCATT
*
307394 TCGCATTGCGATTCTCTCGTTACGAT
1 TCGCATTGCGATTTTCTCGTTACGAT
307420 AGTCAGTTTC
Statistics
Matches: 57, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
33 23 0.40
35 3 0.05
36 3 0.05
38 28 0.49
ACGTcount: A:0.15, C:0.23, G:0.16, T:0.45
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCGTTACGATTTTCATT
Found at i:307565 original size:14 final size:14
Alignment explanation
Indices: 307546--307582 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
307536 CATCAATTAA
307546 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
307560 ACAAATCATCTTTT
1 ACAAATCAACATTT
307574 ACAAATCAA
1 ACAAATCAA
307583 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:309464 original size:20 final size:20
Alignment explanation
Indices: 309441--309494 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
309431 GAAACTTAAA
*
309441 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACG
* *
309461 ATCGCAACGCGGAAATGGCG
1 ATCGCAACGCGAAAATGACG
*
309481 ATCGCAATGCGAAA
1 ATCGCAACGCGAAA
309495 TGAAAATCTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.37, C:0.24, G:0.26, T:0.13
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACG
Found at i:309523 original size:33 final size:32
Alignment explanation
Indices: 309481--309591 Score: 122
Period size: 33 Copynumber: 3.4 Consensus size: 32
309471 GGAAATGGCG
*
309481 ATCGCAATGCGAAATGAAAATCTTAACGACAAA
1 ATCGCAACGCGAAATGAAAATC-TAACGACAAA
* *
309514 ATCGCAATGCGAAATGAAAATC--GCGACAAA
1 ATCGCAACGCGAAATGAAAATCTAACGACAAA
309544 ATCGCAACGCGAAA-G-AAATCGCAATAACGACAAA
1 ATCGCAACGCGAAATGAAAAT--C--TAACGACAAA
309578 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
309592 CAAAAATCAC
Statistics
Matches: 69, Mismatches: 3, Indels: 11
0.83 0.04 0.13
Matches are distributed among these distances:
28 4 0.06
29 1 0.01
30 21 0.30
33 22 0.32
34 21 0.30
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.13
Consensus pattern (32 bp):
ATCGCAACGCGAAATGAAAATCTAACGACAAA
Found at i:309562 original size:17 final size:16
Alignment explanation
Indices: 309535--309591 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 16
309525 AAATGAAAAT
*
309535 CGCGACAAAATCGCAA
1 CGCGAAAAAATCGCAA
309551 CGCGAAAGAAATCGCAA
1 CGCGAAA-AAATCGCAA
** *
309568 TAACGACAAAATCGCAA
1 -CGCGAAAAAATCGCAA
309585 CGCGAAA
1 CGCGAAA
309592 CAAAAATCAC
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
16 10 0.31
17 18 0.56
18 4 0.12
ACGTcount: A:0.47, C:0.26, G:0.19, T:0.07
Consensus pattern (16 bp):
CGCGAAAAAATCGCAA
Found at i:309625 original size:19 final size:19
Alignment explanation
Indices: 309603--309733 Score: 84
Period size: 19 Copynumber: 7.3 Consensus size: 19
309593 AAAAATCACA
309603 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
309622 TTGCGA-TTT--TGT--CG
1 TTGCGATTTTCATTTCGCG
*
309636 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCG
*
309655 TTGCGA-TTT--TGT--CG
1 TTGCGATTTTCATTTCGCG
*
309669 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCG
***
309688 TTGCGATAGCCATTTCCGCG
1 TTGCGATTTTCATTT-CGCG
** *
309708 TTGCGATAGTCATTTTCGTG
1 TTGCGATTTTCA-TTTCGCG
309728 TTGCGA
1 TTGCGA
309734 AAGTAAACTA
Statistics
Matches: 87, Mismatches: 13, Indels: 23
0.71 0.11 0.19
Matches are distributed among these distances:
14 15 0.17
15 6 0.07
16 4 0.05
17 4 0.05
18 6 0.07
19 26 0.30
20 23 0.26
21 3 0.03
ACGTcount: A:0.13, C:0.20, G:0.23, T:0.44
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:309639 original size:14 final size:14
Alignment explanation
Indices: 309620--309678 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
309610 TTTCATTTCG
309620 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
309634 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
309651 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
309667 CGTTGCGATTTT
1 CGTTGCGATTTT
309679 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 18 0.47
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 6 0.16
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:309645 original size:33 final size:33
Alignment explanation
Indices: 309603--309694 Score: 175
Period size: 33 Copynumber: 2.8 Consensus size: 33
309593 AAAAATCACA
*
309603 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
309636 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
309669 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
309695 AGCCATTTCC
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:309713 original size:20 final size:19
Alignment explanation
Indices: 309679--309733 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
309669 TTGCGATTTT
*
309679 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
309698 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
309718 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
309734 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:310236 original size:18 final size:18
Alignment explanation
Indices: 310210--310254 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
310200 GGTCGATCAA
*
310210 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
310228 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
310246 TGATGGCTC
1 TGATGGCTC
310255 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:311619 original size:20 final size:20
Alignment explanation
Indices: 311571--311629 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
311561 AATAGTTTCT
** *
311571 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
311591 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
311611 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
311630 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:311919 original size:22 final size:22
Alignment explanation
Indices: 311892--311935 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
311882 GATGGAGATA
311892 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
311914 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
311936 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:312154 original size:20 final size:20
Alignment explanation
Indices: 312124--312237 Score: 140
Period size: 20 Copynumber: 5.7 Consensus size: 20
312114 GATTATGTAT
*
312124 TATCGCATTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
312144 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
312164 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
** *
312184 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
*
312205 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
312225 TATCGCATTGCGA
1 TATCGCGTTGCGA
312238 TTTTCCCAAT
Statistics
Matches: 82, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
19 3 0.04
20 63 0.77
21 14 0.17
22 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:312241 original size:41 final size:41
Alignment explanation
Indices: 312104--312239 Score: 177
Period size: 41 Copynumber: 3.3 Consensus size: 41
312094 CGCTTTGAAA
* *
312104 ATCGCATTGCGATTATGTATTATCGCATTGCGAAAGTCAGA
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
* * *
312145 ATCGCGTTGCGA--AAGTCAGTATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTATGT-ATTATCGCGTTGCGAAAGTCAGT
* * *
312185 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
312226 ATCGCATTGCGATT
1 ATCGCATTGCGATT
312240 TTCCCAATTC
Statistics
Matches: 82, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
39 3 0.04
40 32 0.39
41 45 0.55
42 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (41 bp):
ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
Found at i:312252 original size:41 final size:41
Alignment explanation
Indices: 312104--312259 Score: 136
Period size: 41 Copynumber: 3.8 Consensus size: 41
312094 CGCTTTGAAA
* ** * * * *
312104 ATCGCATTGCGATTATGTATTATCGCATTGCGAAAGTCAGA
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTCAGT
* *** * *
312145 ATCGCGTTGCGAAAGT-CAGTATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTCAGT
* ** *
312185 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTCAGT
312226 ATCGCATTGCGATTTTCCCAAT-TCGCGTTGCGAT
1 ATCGCATTGCGATTTT-CCAATATCGCGTTGCGAT
312260 TTACTTATTC
Statistics
Matches: 95, Mismatches: 18, Indels: 4
0.81 0.15 0.03
Matches are distributed among these distances:
40 33 0.35
41 60 0.63
42 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (41 bp):
ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTCAGT
Done.