Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007860.1 Hibiscus syriacus cultivar Beakdansim tig00110223_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: 2941097
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 16
Found at i:2876626 original size:199 final size:199
Alignment explanation
Indices: 2876285--2878252 Score: 3733
Period size: 199 Copynumber: 9.9 Consensus size: 199
2876275 TTTAAATTAG
2876285 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
2876350 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
**
2876415 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGAAAA
2876480 AAAA
196 AAAA
*
2876484 AATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
2876549 ATTGTACAGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
2876614 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGAAAA
2876679 AAAA
196 AAAA
2876683 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
2876748 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
2876813 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGAAAA
2876878 AAAA
196 AAAA
2876882 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
2876947 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
**
2877012 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGAAAA
2877077 AAAA
196 AAAA
2877081 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
2877146 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
2877211 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGAAAA
2877276 AAAA
196 AAAA
2877280 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
2877345 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
2877410 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGG-GAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGAAAA
2877474 AAAA
196 AAAA
2877478 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
2877543 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
**
2877608 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGAAAA
2877673 AAAA
196 AAAA
2877677 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
2877742 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
2877807 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCT-GAGAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGA-AA
2877871 AAAAA
195 AAAAA
2877876 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
2877941 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
**
2878006 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGGAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGAAAA
2878071 AAAA
196 AAAA
2878075 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
* *
2878140 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGATTTTGGGA
* *
2878205 TTGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
130 TCGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTT
2878253 GGCCATATTG
Statistics
Matches: 1739, Mismatches: 25, Indels: 8
0.98 0.01 0.00
Matches are distributed among these distances:
198 197 0.11
199 1481 0.85
200 22 0.01
201 39 0.02
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (199 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGAAAA
AAAA
Found at i:2878397 original size:18 final size:18
Alignment explanation
Indices: 2878371--2878418 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 18
2878361 TTATATTCAC
*
2878371 ATACAAAAATATAAATCGT
1 ATACAAAATTAT-AATCGT
*
2878390 ATACAAAATTATAATCTT
1 ATACAAAATTATAATCGT
2878408 ATACAAAATTA
1 ATACAAAATTA
2878419 ACTCGACATT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 16 0.59
19 11 0.41
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.31
Consensus pattern (18 bp):
ATACAAAATTATAATCGT
Found at i:2882363 original size:19 final size:19
Alignment explanation
Indices: 2882308--2882354 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
2882298 ATCCGGTATC
2882308 ATTTTACCGGTTTTATCAT
1 ATTTTACCGGTTTTATCAT
*
2882327 TTTGTTACCGGTTTTATCAT
1 ATT-TTACCGGTTTTATCAT
2882347 ATTTTACC
1 ATTTTACC
2882355 TGTTATATCG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
ATTTTACCGGTTTTATCAT
Found at i:2888444 original size:22 final size:21
Alignment explanation
Indices: 2888419--2888459 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2888409 TACGTGTGCA
*
2888419 TGAGCAGTGCCCAACAATATGT
1 TGAGC-GTCCCCAACAATATGT
*
2888441 TGAGCTTCCCCAACAATAT
1 TGAGCGTCCCCAACAATAT
2888460 TGCATTCTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (21 bp):
TGAGCGTCCCCAACAATATGT
Found at i:2890686 original size:15 final size:16
Alignment explanation
Indices: 2890660--2890689 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2890650 TTTTTGAAAG
2890660 TTTTATAATTTTAAAA
1 TTTTATAATTTTAAAA
2890676 TTTTA-AATTTTAAA
1 TTTTATAATTTTAAA
2890690 GACGAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TTTTATAATTTTAAAA
Found at i:2891188 original size:2 final size:2
Alignment explanation
Indices: 2891183--2891211 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2891173 TTCTCTTAAT
2891183 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
2891212 TTTGACAGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2892780 original size:15 final size:15
Alignment explanation
Indices: 2892756--2892799 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
2892746 GTTTTTTTAA
*
2892756 GATTATGTTCGGGTC
1 GATTAGGTTCGGGTC
*
2892771 GATTGGGTTCGGGTC
1 GATTAGGTTCGGGTC
*
2892786 GATTAGGTTTGGGT
1 GATTAGGTTCGGGT
2892800 TTAGGGTGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.11, C:0.09, G:0.41, T:0.39
Consensus pattern (15 bp):
GATTAGGTTCGGGTC
Found at i:2897250 original size:22 final size:24
Alignment explanation
Indices: 2897195--2897250 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 24
2897185 TAAAAATCCT
*
2897195 AAAAGATAATTCCTAAGAAATTGC
1 AAAAGATAATTCCTAAGAAATTAC
*
2897219 -AAAGAAAATTCCT-A-AAATTAC
1 AAAAGATAATTCCTAAGAAATTAC
2897240 AAAAGATAATT
1 AAAAGATAATT
2897251 GCAAAGGATA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 6 0.21
22 10 0.36
23 12 0.43
ACGTcount: A:0.55, C:0.11, G:0.09, T:0.25
Consensus pattern (24 bp):
AAAAGATAATTCCTAAGAAATTAC
Found at i:2897877 original size:48 final size:48
Alignment explanation
Indices: 2897834--2897926 Score: 136
Period size: 48 Copynumber: 1.9 Consensus size: 48
2897824 AGGTCGAGTT
*
2897834 ATTTCAGGTTT-AGGTTTTATTCGGGTCTATAGTAAGTCTGGTCGGATC
1 ATTTCAGGTTTCA-ATTTTATTCGGGTCTATAGTAAGTCTGGTCGGATC
*
2897882 ATTTCGGGTTTCAATTTTATTCGGGTCTATAGTAAGT-TGGATCGG
1 ATTTCAGGTTTCAATTTTATTCGGGTCTATAGTAAGTCTGG-TCGG
2897927 TTCGGGTATC
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
47 3 0.07
48 37 0.90
49 1 0.02
ACGTcount: A:0.19, C:0.12, G:0.27, T:0.42
Consensus pattern (48 bp):
ATTTCAGGTTTCAATTTTATTCGGGTCTATAGTAAGTCTGGTCGGATC
Found at i:2898032 original size:19 final size:19
Alignment explanation
Indices: 2897988--2898033 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
2897978 TTTTGGTTTG
*
2897988 GGTCAACTTTGAATCTTCA
1 GGTCAATTTTGAATCTTCA
* *
2898007 GGTCAATTTTGAGTCTTTA
1 GGTCAATTTTGAATCTTCA
2898026 GGTCAATT
1 GGTCAATT
2898034 CAAGTTGAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (19 bp):
GGTCAATTTTGAATCTTCA
Found at i:2898211 original size:53 final size:53
Alignment explanation
Indices: 2898153--2898259 Score: 214
Period size: 53 Copynumber: 2.0 Consensus size: 53
2898143 TTCAAATTCA
2898153 ATAATCATTTACGAATTATAATTTATCTCAAACTCGACTTATAAGATATATTG
1 ATAATCATTTACGAATTATAATTTATCTCAAACTCGACTTATAAGATATATTG
2898206 ATAATCATTTACGAATTATAATTTATCTCAAACTCGACTTATAAGATATATTG
1 ATAATCATTTACGAATTATAATTTATCTCAAACTCGACTTATAAGATATATTG
2898259 A
1 A
2898260 AGTTTGTGAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.39
Consensus pattern (53 bp):
ATAATCATTTACGAATTATAATTTATCTCAAACTCGACTTATAAGATATATTG
Found at i:2901241 original size:17 final size:17
Alignment explanation
Indices: 2901210--2901243 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2901200 TAGGACTTTA
* *
2901210 TTTATTTTGATTTTTCT
1 TTTATTTTAACTTTTCT
2901227 TTTATTTTAACTTTTCT
1 TTTATTTTAACTTTTCT
2901244 AATTTGATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.09, G:0.03, T:0.74
Consensus pattern (17 bp):
TTTATTTTAACTTTTCT
Found at i:2904458 original size:2 final size:2
Alignment explanation
Indices: 2904451--2904479 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2904441 ACTTATATGC
2904451 AT AT 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 AT AT A
2904480 ATTTCATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2904981 original size:54 final size:53
Alignment explanation
Indices: 2904923--2905050 Score: 134
Period size: 51 Copynumber: 2.4 Consensus size: 53
2904913 GTCCTTCAGA
** **
2904923 GAGTATAGAACTCGAACATCTTCTTCTTACGGGTTCGTTCACTCTTTATCCAGG
1 GAGTATAGAACTCGAACATCTTCTT-AAACGGGTTCACTCACTCTTTATCCAGG
* * * * *
2904977 GAGTATGGAACTCGAACGTC-T-TTAAACGGGTTCACTCCCTCTTTTTTCAGG
1 GAGTATAGAACTCGAACATCTTCTTAAACGGGTTCACTCACTCTTTATCCAGG
* *
2905028 GAGAATAGAACTCGAATATCTTC
1 GAGTATAGAACTCGAACATCTTC
2905051 AACAATCGTG
Statistics
Matches: 59, Mismatches: 13, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
51 37 0.63
52 3 0.05
53 1 0.02
54 18 0.31
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.33
Consensus pattern (53 bp):
GAGTATAGAACTCGAACATCTTCTTAAACGGGTTCACTCACTCTTTATCCAGG
Found at i:2905173 original size:108 final size:108
Alignment explanation
Indices: 2905045--2905375 Score: 470
Period size: 108 Copynumber: 3.1 Consensus size: 108
2905035 GAACTCGAAT
* * * *
2905045 ATCTTCAACAATCG-TGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTGAAC
1 ATCTTCATCAATCGCT-TCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC
*
2905109 AATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACCCACA
65 AATTGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACCCACA
* *
2905153 ATCTTCATCAATCGCTTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACGATCTTCAACG
1 ATCTTCATCAATCGCTTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACA
* *
2905218 ATTGTGTCTGCCCCCTATATCTTCAGAGAGTATAAGACCCACA
66 ATTGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACCCACA
* * * *
2905261 ATCTTCATCAATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGAC-C-CACAATCTTCATCA
1 ATCTTCATCAATCGCTTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACA
* * *
2905324 ATTGCGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACA
66 ATTGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGAC-C-CACA
2905369 ATCTTCA
1 ATCTTCA
2905376 ATAATTGTTG
Statistics
Matches: 200, Mismatches: 20, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
106 44 0.22
107 2 0.01
108 153 0.76
109 1 0.00
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (108 bp):
ATCTTCATCAATCGCTTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACA
ATTGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACCCACA
Found at i:2905179 original size:53 final size:55
Alignment explanation
Indices: 2905037--2905376 Score: 426
Period size: 53 Copynumber: 6.3 Consensus size: 55
2905027 GGAGAATAGA
* * *
2905037 ACTCGAA-TATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAG
1 ACTCGAACAATCTTCAACAATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* *
2905091 ACTCGAACAATCTTGAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* *
2905146 AC-C-CACAATCTTCATCAATCGCT-TCTGCCCCCTATTTCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCG-TGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * * *
2905199 ACTCGAACGATCTTCAACGATTGTGTCTGCCCCCTATATCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * * *
2905254 AC-C-CACAATCTTCATCAATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * * * * *
2905307 AC-C-CACAATCTTCATCAATTGCGTCTGCTCCCTATTTCTTCAGAGAGTATGAG
1 ACTCGAACAATCTTCAACAATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
2905360 ACTCGAACAATCTTCAA
1 ACTCGAACAATCTTCAA
2905377 TAATTGTTGG
Statistics
Matches: 256, Mismatches: 23, Indels: 13
0.88 0.08 0.04
Matches are distributed among these distances:
53 143 0.56
54 13 0.05
55 100 0.39
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (55 bp):
ACTCGAACAATCTTCAACAATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
Found at i:2905312 original size:161 final size:163
Alignment explanation
Indices: 2905037--2905376 Score: 506
Period size: 161 Copynumber: 2.1 Consensus size: 163
2905027 GGAGAATAGA
* * * *
2905037 ACTCGAA-TATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAA
1 ACTCGAACAATCTTCAACAATCGTGTCTGCCCCCTATATCTTCAGAGAGTATAAGACTCGAACAA
* * *
2905101 TCTTGAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATC
66 TCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATC
*
2905166 GCTTCTGCCCCCTATTTCTTCAGAGAGTATAAG
131 GCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * * *
2905199 ACTCGAACGATCTTCAACGATTGTGTCTGCCCCCTATATCTTCAGAGAGTATAAGAC-C-CACAA
1 ACTCGAACAATCTTCAACAATCGTGTCTGCCCCCTATATCTTCAGAGAGTATAAGACTCGAACAA
* * *
2905262 TCTTCATCAATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATT
66 TCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATC
* *
2905327 GCGTCTGCTCCCTATTTCTTCAGAGAGTATGAG
131 GCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
2905360 ACTCGAACAATCTTCAA
1 ACTCGAACAATCTTCAA
2905377 TAATTGTTGG
Statistics
Matches: 160, Mismatches: 17, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
161 109 0.68
162 8 0.05
163 43 0.27
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (163 bp):
ACTCGAACAATCTTCAACAATCGTGTCTGCCCCCTATATCTTCAGAGAGTATAAGACTCGAACAA
TCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATC
GCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
Found at i:2905886 original size:13 final size:13
Alignment explanation
Indices: 2905868--2905914 Score: 94
Period size: 13 Copynumber: 3.6 Consensus size: 13
2905858 ATGCTTGTAA
2905868 AAGGGAAATTAAG
1 AAGGGAAATTAAG
2905881 AAGGGAAATTAAG
1 AAGGGAAATTAAG
2905894 AAGGGAAATTAAG
1 AAGGGAAATTAAG
2905907 AAGGGAAA
1 AAGGGAAA
2905915 ATATCTCTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 34 1.00
ACGTcount: A:0.55, C:0.00, G:0.32, T:0.13
Consensus pattern (13 bp):
AAGGGAAATTAAG
Found at i:2906303 original size:7 final size:7
Alignment explanation
Indices: 2906293--2906326 Score: 50
Period size: 7 Copynumber: 4.6 Consensus size: 7
2906283 TTTTCCATTT
2906293 TTTTTTA
1 TTTTTTA
2906300 TTTTTTTA
1 -TTTTTTA
2906308 TTTTTTA
1 TTTTTTA
2906315 TTTTTTCA
1 TTTTTT-A
2906323 TTTT
1 TTTT
2906327 CACTCATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 13 0.52
8 12 0.48
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTTTA
Found at i:2906303 original size:8 final size:8
Alignment explanation
Indices: 2906292--2906326 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
2906282 TTTTTCCATT
2906292 TTTTTTTA
1 TTTTTTTA
2906300 TTTTTTTA
1 TTTTTTTA
2906308 -TTTTTTA
1 TTTTTTTA
*
2906315 TTTTTTCA
1 TTTTTTTA
2906323 TTTT
1 TTTT
2906327 CACTCATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
7 7 0.28
8 18 0.72
ACGTcount: A:0.11, C:0.03, G:0.00, T:0.86
Consensus pattern (8 bp):
TTTTTTTA
Found at i:2906311 original size:15 final size:15
Alignment explanation
Indices: 2906293--2906326 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
2906283 TTTTCCATTT
*
2906293 TTTTTTATTTTTTTA
1 TTTTTTATTTTTTCA
2906308 TTTTTTATTTTTTCA
1 TTTTTTATTTTTTCA
2906323 TTTT
1 TTTT
2906327 CACTCATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTTTTATTTTTTCA
Found at i:2909852 original size:8 final size:8
Alignment explanation
Indices: 2909839--2909866 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
2909829 AAAAGAAGAT
2909839 ATATATAC
1 ATATATAC
2909847 ATATATAC
1 ATATATAC
2909855 ATATATAC
1 ATATATAC
2909863 ATAT
1 ATAT
2909867 GGGAGAATCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (8 bp):
ATATATAC
Found at i:2919612 original size:2 final size:2
Alignment explanation
Indices: 2919605--2919635 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2919595 ACTTATATGC
2919605 AT AT AT 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 AT AT AT A
2919636 ATTTCATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2921402 original size:133 final size:133
Alignment explanation
Indices: 2921245--2921511 Score: 525
Period size: 133 Copynumber: 2.0 Consensus size: 133
2921235 AAGAAAAGCT
2921245 TCACCCTTCTAATCAAATTACGTTTCTTATGTTCTCTAATTATCTCTTAATTAATTTGTGTCATA
1 TCACCCTTCTAATCAAATTACGTTTCTTATGTTCTCTAATTATCTCTTAATTAATTTGTGTCATA
2921310 TTAAATTCGAGTCAAACTCTAACAATATTGAACATCATAAATCAATCATTGTTAATAAATAAAAT
66 TTAAATTCGAGTCAAACTCTAACAATATTGAACATCATAAATCAATCATTGTTAATAAATAAAAT
2921375 GAA
131 GAA
2921378 TCACCCTTCTAATCAAATTACGTTTCTTATGTTCTCTAATTATCTCTTAATTAATTTGTGTCATA
1 TCACCCTTCTAATCAAATTACGTTTCTTATGTTCTCTAATTATCTCTTAATTAATTTGTGTCATA
*
2921443 TTGAATTCGAGTCAAACTCTAACAATATTGAACATCATAAATCAATCATTGTTAATAAATAAAAT
66 TTAAATTCGAGTCAAACTCTAACAATATTGAACATCATAAATCAATCATTGTTAATAAATAAAAT
2921508 GAA
131 GAA
2921511 T
1 T
2921512 ATATCCATAT
Statistics
Matches: 133, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
133 133 1.00
ACGTcount: A:0.37, C:0.16, G:0.07, T:0.39
Consensus pattern (133 bp):
TCACCCTTCTAATCAAATTACGTTTCTTATGTTCTCTAATTATCTCTTAATTAATTTGTGTCATA
TTAAATTCGAGTCAAACTCTAACAATATTGAACATCATAAATCAATCATTGTTAATAAATAAAAT
GAA
Found at i:2926451 original size:31 final size:31
Alignment explanation
Indices: 2926413--2926471 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
2926403 AAACCCAAGA
2926413 AGTTCCTAGTGAGAAGGACATATTGAATGAG
1 AGTTCCTAGTGAGAAGGACATATTGAATGAG
2926444 AGTTCCTAGTGAGAAGGACATATTGAAT
1 AGTTCCTAGTGAGAAGGACATATTGAAT
2926472 TCACCGAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.36, C:0.10, G:0.27, T:0.27
Consensus pattern (31 bp):
AGTTCCTAGTGAGAAGGACATATTGAATGAG
Found at i:2935238 original size:15 final size:15
Alignment explanation
Indices: 2935218--2935253 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
2935208 GGTTGTGCTT
2935218 TTTTTTTTCATTTAA
1 TTTTTTTTCATTTAA
*
2935233 TTTTTTTTCATTTTA
1 TTTTTTTTCATTTAA
2935248 TTTTTT
1 TTTTTT
2935254 ATGTAAATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.14, C:0.06, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTTTTTTCATTTAA
Found at i:2936800 original size:13 final size:12
Alignment explanation
Indices: 2936784--2936830 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
2936774 TCTTTTATAG
2936784 TTCTCTTCTAAT
1 TTCTCTTCTAAT
*
2936796 CTTCTCTTTTAA-
1 -TTCTCTTCTAAT
*
2936808 TTCTCTTCCTATT
1 TTCTCTT-CTAAT
2936821 TTCTCTTCTA
1 TTCTCTTCTA
2936831 CTTTATTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 7 0.24
12 5 0.17
13 17 0.59
ACGTcount: A:0.13, C:0.28, G:0.00, T:0.60
Consensus pattern (12 bp):
TTCTCTTCTAAT
Found at i:2940184 original size:16 final size:17
Alignment explanation
Indices: 2940134--2940185 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 17
2940124 AAAATAATTA
2940134 AATTTGAAAGTTAGAGT
1 AATTTGAAAGTTAGAGT
*
2940151 GA-TT-AAA-TTAGGAGT
1 AATTTGAAAGTTA-GAGT
2940166 AATTTGAAAGTTA-AGT
1 AATTTGAAAGTTAGAGT
2940182 AATT
1 AATT
2940186 AAATTAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 3 0.10
15 8 0.28
16 11 0.38
17 4 0.14
18 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.21, T:0.37
Consensus pattern (17 bp):
AATTTGAAAGTTAGAGT
Done.