Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008706.1 Hibiscus syriacus cultivar Beakdansim tig00111746_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: 76580
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1470 original size:230 final size:228
Alignment explanation
Indices: 1023--1482 Score: 776
Period size: 230 Copynumber: 2.0 Consensus size: 228
1013 GGTGTTGAAG
*
1023 CTTAAGGACTAATCTTATAAATACCCTAAAGTTTAGAGACTAAATGAGAAATTTTCCCATTACCA
1 CTTAAGGACTAATCTTATAAATACCCTAAAGTTCAGAGACTAAATGAGAAATTTTCCCATTACCA
* *
1088 TATTTTCAACAAAATGAAGCTACAACTTTCGGTGTAAGCTTTCGGTGGAATTGGTGCATTCACAC
66 TATTTTCAACAAAATCAAGCTACAACTTTCGGTGTAAACTTTCGGTGGAATTGGTGCATTCACAC
*
1153 TAATTTTCAACACCATCCACTTGCATGGATTCAATTTCTTTGCCGTCGGTAGGGGACTCATAAAC
131 TAATTTTCAACACCATCCACTTGCATGGATTCAATTTCTTTGCCGTCGGTAGGGGACTCAGAAAC
1218 TATAATCCGAAAACCGATCCTCGAAACTTCAAT
196 TATAATCCGAAAACCGATCCTCGAAACTTCAAT
* * * *
1251 CTTAAGGATTAATCTTGTAAATACCCTAAAGTTCATAGACTAAATGAGTAATTTTCCCATTACCA
1 CTTAAGGACTAATCTTATAAATACCCTAAAGTTCAGAGACTAAATGAGAAATTTTCCCATTACCA
*
1316 TATTTTCAACAAAATCAAGCTGCAACTTTCGGTGTAATACTTTCGGTGGAATTCGGTGCATTCAC
66 TATTTTCAACAAAATCAAGCTACAACTTTCGGTGTAA-ACTTTCGGTGGAATT-GGTGCATTCAC
* **
1381 ACTAATTTTCAACACCATCCACTTGCATGGATTCAATTTCTTTGTCGTCGGTAGGGGACTTGGAA
129 ACTAATTTTCAACACCATCCACTTGCATGGATTCAATTTCTTTGCCGTCGGTAGGGGACTCAGAA
* *
1446 ACTATAATTCGAAAATCGATCCTCGAAACTTCAAT
194 ACTATAATCCGAAAACCGATCCTCGAAACTTCAAT
1481 CT
1 CT
1483 CGTCGATCCA
Statistics
Matches: 216, Mismatches: 14, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
228 95 0.44
229 14 0.06
230 107 0.50
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (228 bp):
CTTAAGGACTAATCTTATAAATACCCTAAAGTTCAGAGACTAAATGAGAAATTTTCCCATTACCA
TATTTTCAACAAAATCAAGCTACAACTTTCGGTGTAAACTTTCGGTGGAATTGGTGCATTCACAC
TAATTTTCAACACCATCCACTTGCATGGATTCAATTTCTTTGCCGTCGGTAGGGGACTCAGAAAC
TATAATCCGAAAACCGATCCTCGAAACTTCAAT
Found at i:8326 original size:18 final size:18
Alignment explanation
Indices: 8305--8346 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
8295 CAAAGAAAAA
8305 TGCAACGGCAACAACCAT
1 TGCAACGGCAACAACCAT
8323 TGCAACGGCAACAACCAT
1 TGCAACGGCAACAACCAT
8341 TGCAAC
1 TGCAAC
8347 AGCTGGGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.38, C:0.33, G:0.17, T:0.12
Consensus pattern (18 bp):
TGCAACGGCAACAACCAT
Found at i:11630 original size:18 final size:18
Alignment explanation
Indices: 11592--11631 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
11582 TTATCTTACC
*
11592 TTTATTTTTATATTTTTA
1 TTTATTTTTATATTTTGA
11610 TTTATTTTTA-ATCTTTGA
1 TTTATTTTTATAT-TTTGA
11628 TTTA
1 TTTA
11632 ATTCCTATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (18 bp):
TTTATTTTTATATTTTGA
Found at i:14999 original size:25 final size:25
Alignment explanation
Indices: 14971--15031 Score: 113
Period size: 25 Copynumber: 2.4 Consensus size: 25
14961 CATAAAACCA
14971 AAAGATGAAAGAGTTAAGAAGGATT
1 AAAGATGAAAGAGTTAAGAAGGATT
*
14996 AAAGATGAAAGAGTTAAGAATGATT
1 AAAGATGAAAGAGTTAAGAAGGATT
15021 AAAGATGAAAG
1 AAAGATGAAAG
15032 GTTTATAAGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.54, C:0.00, G:0.26, T:0.20
Consensus pattern (25 bp):
AAAGATGAAAGAGTTAAGAAGGATT
Found at i:15492 original size:18 final size:19
Alignment explanation
Indices: 15456--15493 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
15446 ATGCAAGGGG
15456 GTATCGATACCTAAAGGGTA
1 GTATCGATACC-AAAGGGTA
15476 GTATCGATACC-AAGGGTA
1 GTATCGATACCAAAGGGTA
15494 CAGATACCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
20 11 0.61
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (19 bp):
GTATCGATACCAAAGGGTA
Found at i:16266 original size:21 final size:20
Alignment explanation
Indices: 16237--16299 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 20
16227 GTCGAGAGAT
16237 TATATGAGGTCCTTCGGAACA
1 TATATGAGGTCCTTC-GAACA
* *
16258 TATACGAGGTCTTTCGAGACA
1 TATATGAGGTCCTTCGA-ACA
*
16279 TACATGAGGTCCTTCAGAACA
1 TATATGAGGTCCTTC-GAACA
16300 AATTTTATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 2 0.06
21 31 0.89
22 2 0.06
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (20 bp):
TATATGAGGTCCTTCGAACA
Found at i:16498 original size:15 final size:15
Alignment explanation
Indices: 16478--16506 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
16468 TGGCCGACCG
16478 AACCGAATTAACCAT
1 AACCGAATTAACCAT
16493 AACCGAATTAACCA
1 AACCGAATTAACCA
16507 AACTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.28, G:0.07, T:0.17
Consensus pattern (15 bp):
AACCGAATTAACCAT
Found at i:16955 original size:183 final size:184
Alignment explanation
Indices: 16634--17019 Score: 611
Period size: 183 Copynumber: 2.1 Consensus size: 184
16624 TTTTCTAATT
* *
16634 TATATAA-A-ATTAAATATTTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATAAATAAT
1 TATATAATATATTTAATATTTTTTAATTCAAAAAAAGTTTACAATTAATTTAAATAATAAATAAT
**
16697 TATAAAATAAAAATTTTAGATAAAATTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
66 TATAAAATAAAAAAATTAGATAAAATTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
* *
16762 AGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTT-AGCCCATATGTTA
131 AGATCTTAAATTATTAATTGGGTTTTAAATGATTTGGG-TTGAACCCATATGTTA
*
16816 TATATAATATATTTAATATTTTTTAATT-AAAAAACAGTTTACAATTAATTTAAATAATATATAA
1 TATATAATATATTTAATATTTTTTAATTCAAAAAA-AGTTTACAATTAATTTAAATAATAAATAA
* *
16880 TTATAAAATAAAAAAATTATAT-AATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
65 TTATAAAATAAAAAAATTAGATAAAATTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
* *
16944 TGGATCTTAAATTATTAATTGGGTTTTTAATGATTTGGGTTGAACCCATATGTTA
130 TAGATCTTAAATTATTAATTGGGTTTTAAATGATTTGGGTTGAACCCATATGTTA
*
16999 TATATAATATATTTAAAATTT
1 TATATAATATATTTAATATTT
17020 AAAATTTAAT
Statistics
Matches: 188, Mismatches: 12, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
182 9 0.05
183 116 0.62
184 63 0.34
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (184 bp):
TATATAATATATTTAATATTTTTTAATTCAAAAAAAGTTTACAATTAATTTAAATAATAAATAAT
TATAAAATAAAAAAATTAGATAAAATTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
AGATCTTAAATTATTAATTGGGTTTTAAATGATTTGGGTTGAACCCATATGTTA
Found at i:24913 original size:30 final size:32
Alignment explanation
Indices: 24878--24940 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
24868 AAATTTCGTC
* *
24878 ACTAAAT-ATTTT-TTATAATTTTTTACTGTG
1 ACTAAATAATTTTGTTACAATTTGTTACTGTG
*
24908 ACTAAATAATTTTGTTACAATTTGTTATTGTG
1 ACTAAATAATTTTGTTACAATTTGTTACTGTG
24940 A
1 A
24941 AAGAATATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 7 0.25
31 5 0.18
32 16 0.57
ACGTcount: A:0.32, C:0.06, G:0.10, T:0.52
Consensus pattern (32 bp):
ACTAAATAATTTTGTTACAATTTGTTACTGTG
Found at i:31460 original size:29 final size:31
Alignment explanation
Indices: 31392--31467 Score: 90
Period size: 29 Copynumber: 2.6 Consensus size: 31
31382 AAACCTGAGT
31392 ATGTTTTATTTA-TTTTAATTTGGCCATGCA
1 ATGTTTTATTTATTTTTAATTTGGCCATGCA
* *
31422 AT-TTTAATTTATTTTTAATTTAGTCC-T-C-
1 ATGTTTTATTTATTTTTAATTT-GGCCATGCA
31450 ATGTTTTATTTATTTTTA
1 ATGTTTTATTTATTTTTA
31468 TTAATTGTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
28 2 0.05
29 23 0.57
30 12 0.30
31 3 0.08
ACGTcount: A:0.24, C:0.08, G:0.08, T:0.61
Consensus pattern (31 bp):
ATGTTTTATTTATTTTTAATTTGGCCATGCA
Found at i:31586 original size:6 final size:6
Alignment explanation
Indices: 31575--31605 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
31565 GTTTTAGTCC
31575 TATTTT TATTTT TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT TATTTT T
31606 GCATGTTGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:37589 original size:18 final size:18
Alignment explanation
Indices: 37568--37608 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
37558 ATAATAAAGA
* *
37568 AAAAAATAGAAAAATAGG
1 AAAAAAGAGAAAAAGAGG
37586 AAAAAAGAGAAAAAGAGG
1 AAAAAAGAGAAAAAGAGG
37604 AAAAA
1 AAAAA
37609 GAAAAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.05
Consensus pattern (18 bp):
AAAAAAGAGAAAAAGAGG
Found at i:37616 original size:9 final size:9
Alignment explanation
Indices: 37541--37625 Score: 55
Period size: 9 Copynumber: 9.1 Consensus size: 9
37531 ACATAAAATG
37541 AAAAAGAAAA
1 AAAAAG-AAA
*
37551 AAGAAAGATA
1 AA-AAAGAAA
*
37561 ATAAAGAAA
1 AAAAAGAAA
37570 AAAATAGAAA
1 AAAA-AGAAA
* *
37580 AATAGGAAA
1 AAAAAGAAA
*
37589 AAAGAGAAA
1 AAAAAGAAA
* *
37598 AAGAGGAAA
1 AAAAAGAAA
37607 AAGAAA-AAA
1 AA-AAAGAAA
*
37616 AAAGAGAAA
1 AAAAAGAAA
37625 A
1 A
37626 TAAATCAAAT
Statistics
Matches: 56, Mismatches: 15, Indels: 9
0.70 0.19 0.11
Matches are distributed among these distances:
8 2 0.04
9 36 0.64
10 14 0.25
11 4 0.07
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.05
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:37617 original size:18 final size:18
Alignment explanation
Indices: 37577--37616 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
37567 AAAAAAATAG
* *
37577 AAAAATAGGAAAAAAGAG
1 AAAAAGAGGAAAAAAGAA
37595 AAAAAGAGG-AAAAAGAA
1 AAAAAGAGGAAAAAAGAA
37612 AAAAA
1 AAAAA
37617 AAGAGAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.03
Consensus pattern (18 bp):
AAAAAGAGGAAAAAAGAA
Found at i:40199 original size:31 final size:31
Alignment explanation
Indices: 40129--40251 Score: 133
Period size: 31 Copynumber: 4.0 Consensus size: 31
40119 GTCGAGGGTT
*
40129 TACCTATGTTCTACGGAACATATGGACAGAA
1 TACCTATGTTCTACGGAACATATGGACAGTA
* *
40160 TTACCTATG-TCTTTCGGGACATATGGACAGTA
1 -TACCTATGTTC-TACGGAACATATGGACAGTA
* *
40192 TACCTATGTTCTAAGGAACATATGGACAGTT
1 TACCTATGTTCTACGGAACATATGGACAGTA
* * * *
40223 TACCTAGGTTCTTCAG-ACCTATGGACAGT
1 TACCTATGTTCTACGGAACATATGGACAGT
40252 TGCCGAGGTT
Statistics
Matches: 77, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
30 12 0.16
31 38 0.49
32 27 0.35
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (31 bp):
TACCTATGTTCTACGGAACATATGGACAGTA
Found at i:43188 original size:233 final size:231
Alignment explanation
Indices: 42738--43532 Score: 1019
Period size: 233 Copynumber: 3.4 Consensus size: 231
42728 GTAAGAAAGA
* * *
42738 TCATCTATAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACATTCGAGCAAG
1 TCATCTATAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTTGAGCAGG
* * *
42803 ATGTTTTCACACGTCTCTTGAAAAATGAGAAAGATTTCTCATTTAAATCTGAAAATT-AAATTTT
66 ATGTTTTCACATGTTTTTTGAAAAATGAGAAAGATTTCTCATTTAAATCTGAAAATTGAAA---T
* * * * * *
42867 TTTTGAAAAGTAAGTAAAGTTTCTTACCTAGTAAACTATTCTCGAATTTGGTAAATCCTTTGGGC
128 TTTTGAAAAGTAAGGAAGGTTTTTTACCTAGTAAACTATT-TCCAAATTGGTAATTCCTTT-GGC
* * *
42932 CATCAGT--GTCTTTCAAACATGATGTTTAAATCATTCGAG
191 CATCAGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGAG
* * * *
42971 TCATCTGTAAGTCTTTCGAGCAAGATGGTAAGTCTTTCGGGCCATCCATAAGACCTTTGTGCAGG
1 TCATCTATAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTTGAGCAGG
* * * *
43036 ATGTTTTCACATGTTTTTTGAAAAATAAGAAAGGTTTTTCATCTAAATCTGAAAATTGAAATTTT
66 ATGTTTTCACATGTTTTTTGAAAAATGAGAAAGATTTCTCATTTAAATCTGAAAATTGAAATTTT
*
43101 TGAAAAGTAAGGAAGGTTTTTTAACTAGTAAACTATTTCCAAAATTGGTAATTCCTTTAGGCCAT
131 TGAAAAGTAAGGAAGGTTTTTTACCTAGTAAACTATTTCC-AAATTGGTAATTCCTTT-GGCCAT
* *
43166 CAGTAAGCCTTTTGAGCATGATGTTTAAATCCTTC-AGG
194 CAGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGA-G
*
43204 TCATCTGA-AAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTTGGGCAG
1 TCATCT-ATAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTTGAGCAG
* * *
43268 GATGTTTTCACATGTTTTTCGAAAAATGAGAAAGAATTCTCATTTAAATCTGGAAATTGAAA-TT
65 GATGTTTTCACATGTTTTTTGAAAAATGAGAAAGATTTCTCATTTAAATCTGAAAATTGAAATTT
* * *
43332 TTGAAAAAGTAAGGAAGGTTTTTT-CCTAGTAAACTATTTCCGAGTTGGTAATTCCTTTGGACAA
130 TTG-AAAAGTAAGGAAGGTTTTTTACCTAGTAAACTATTTCCAAATTGGTAATTCCTTTGG-CCA
** *
43396 TCAGTAAGTCTTTCGAGCATGATGCCTAAATCCTTCGGG
193 TCAGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGAG
* *** * * *
43435 TCATCTATAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGTCCATCCATAAGTTATTAGGGTAGG
1 TCATCTATAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTTGAGCAGG
* * *
43500 ATATTTTCGCATGATTTTTCGAAAAATGAGAAA
66 ATGTTTTCACATG-TTTTTTGAAAAATGAGAAA
43533 ATAATTTCCA
Statistics
Matches: 496, Mismatches: 55, Indels: 23
0.86 0.10 0.04
Matches are distributed among these distances:
230 5 0.01
231 180 0.36
232 41 0.08
233 267 0.54
234 3 0.01
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.34
Consensus pattern (231 bp):
TCATCTATAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTTGAGCAGG
ATGTTTTCACATGTTTTTTGAAAAATGAGAAAGATTTCTCATTTAAATCTGAAAATTGAAATTTT
TGAAAAGTAAGGAAGGTTTTTTACCTAGTAAACTATTTCCAAATTGGTAATTCCTTTGGCCATCA
GTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGAG
Found at i:43486 original size:41 final size:42
Alignment explanation
Indices: 43400--43487 Score: 117
Period size: 41 Copynumber: 2.1 Consensus size: 42
43390 GGACAATCAG
* * *
43400 TAAGTCTTTCGAGCATGATGCCTAAATCCTTCGGGTCATCTA
1 TAAGTCTTTCGAGCAAGATGCATAAATCCTTCGGGTCATCCA
*
43442 TAAGTCTTTCGAGCAAGATG-ATAAGTCCTTC-GGTCCATCCA
1 TAAGTCTTTCGAGCAAGATGCATAAATCCTTCGGGT-CATCCA
43483 TAAGT
1 TAAGT
43488 TATTAGGGTA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
40 3 0.07
41 19 0.46
42 19 0.46
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (42 bp):
TAAGTCTTTCGAGCAAGATGCATAAATCCTTCGGGTCATCCA
Found at i:44103 original size:134 final size:131
Alignment explanation
Indices: 43815--44141 Score: 487
Period size: 134 Copynumber: 2.5 Consensus size: 131
43805 CGAATCGAAG
* *
43815 TCGATTCAATCTTCCCTGAGTGACAGTGAAATGAATCAAC-ACCCCATATCTGAT-TTCCCTCAA
1 TCGATTCAATCTTCCCTGAGTGACAGTGAAATGAATCAACGTCCCCAGATCTGATATTCCCTCAA
* * * *
43878 GAGAAGCGAACATATCCCTCTCTTCTAAGATTTGATATTCTCTGAGTAACAATGAACAAGTCTGC
66 GAGAAACGAACATATCCCTCTCTTCCAAGATTTGATATTCCCTGAGTAACAATGAACAAGTCTAC
43943 C
131 C
* * * *
43944 TCGATTCAATCTTCCTTGAGTGACAGCGAAATGAATCAACGTCCCTAGATCTGATATTCCCTCCA
1 TCGATTCAATCTTCCCTGAGTGACAGTGAAATGAATCAACGTCCCCAGATCTGATATTCCCTCAA
* *
44009 GAAGAAACGAAATATATCCCTCTCTTCCAAGATTTGATATTCCCTGAGTAACATTTGAACAAGTC
66 G-AGAAACG-AACATATCCCTCTCTTCCAAGATTTGATATTCCCTGAGTAACA-ATGAACAAGTC
44074 TACC
128 TACC
* *
44078 TCGATTCAATCTTCCCTGAGTGACAGTGGAATGGATCAACGTCCCCAGATCTGATATTCCCTCA
1 TCGATTCAATCTTCCCTGAGTGACAGTGAAATGAATCAACGTCCCCAGATCTGATATTCCCTCA
44142 TCATATTCCA
Statistics
Matches: 175, Mismatches: 18, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
129 38 0.22
130 11 0.06
131 9 0.05
132 6 0.03
133 40 0.23
134 71 0.41
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (131 bp):
TCGATTCAATCTTCCCTGAGTGACAGTGAAATGAATCAACGTCCCCAGATCTGATATTCCCTCAA
GAGAAACGAACATATCCCTCTCTTCCAAGATTTGATATTCCCTGAGTAACAATGAACAAGTCTAC
C
Found at i:49714 original size:5 final size:5
Alignment explanation
Indices: 49704--49756 Score: 52
Period size: 5 Copynumber: 9.8 Consensus size: 5
49694 AACGGTCAAC
* *
49704 GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG
49753 GGTC
1 GGTC
49757 AGACCGGTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
5 32 0.80
7 8 0.20
ACGTcount: A:0.08, C:0.23, G:0.51, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:49719 original size:17 final size:17
Alignment explanation
Indices: 49697--49757 Score: 77
Period size: 17 Copynumber: 3.3 Consensus size: 17
49687 AACGGTCAAC
49697 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
49714 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAA----C-GGTCGGGTCG
49736 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
49753 GGTCA
1 GGTCA
49758 GACCGGTCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
17 21 0.54
18 1 0.03
21 1 0.03
22 16 0.41
ACGTcount: A:0.11, C:0.23, G:0.48, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:49732 original size:22 final size:22
Alignment explanation
Indices: 49690--49756 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
49680 GAAAGTCAAC
*
49690 GGTCAACGGTCAACGGTCGGGTCG
1 GGTCAACGGTC--GGGTCGGGTCG
49714 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
49736 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
49757 AGACCGGTCA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
22 31 0.74
24 11 0.26
ACGTcount: A:0.12, C:0.24, G:0.46, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:49771 original size:9 final size:9
Alignment explanation
Indices: 49753--49860 Score: 108
Period size: 9 Copynumber: 11.3 Consensus size: 9
49743 GGTCGGGTCG
*
49753 GGTCAGACC
1 GGTCAAACC
49762 GGTCAAACC
1 GGTCAAACC
*
49771 GGTTCAGACC
1 GG-TCAAACC
49781 GGTCAAACC
1 GGTCAAACC
*
49790 GGTTCGAACC
1 GG-TCAAACC
*
49800 GGTTGAAACC
1 GG-TCAAACC
49810 GGTCAAACC
1 GGTCAAACC
49819 GGTCAAACC
1 GGTCAAACC
49828 GGTCAGAACC
1 GGTCA-AACC
*
49838 GGTTGAAAACC
1 GG-T-CAAACC
*
49849 GGTTAAACC
1 GGTCAAACC
49858 GGT
1 GGT
49861 TTCCAGCAGC
Statistics
Matches: 85, Mismatches: 9, Indels: 10
0.82 0.09 0.10
Matches are distributed among these distances:
9 46 0.54
10 31 0.36
11 7 0.08
12 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.28, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:49777 original size:19 final size:18
Alignment explanation
Indices: 49753--49840 Score: 106
Period size: 19 Copynumber: 4.7 Consensus size: 18
49743 GGTCGGGTCG
49753 GGTCAGACCGGTCAAACC
1 GGTCAGACCGGTCAAACC
49771 GGTTCAGACCGGTCAAACC
1 GG-TCAGACCGGTCAAACC
*
49790 GGTTC-GAACCGGTTGAAACC
1 GG-TCAG-ACCGG-TCAAACC
*
49810 GGTCAAACCGGTCAAACC
1 GGTCAGACCGGTCAAACC
49828 GGTCAGAACCGGT
1 GGTCAG-ACCGGT
49841 TGAAAACCGG
Statistics
Matches: 61, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
18 14 0.23
19 39 0.64
20 8 0.13
ACGTcount: A:0.27, C:0.30, G:0.28, T:0.15
Consensus pattern (18 bp):
GGTCAGACCGGTCAAACC
Found at i:49801 original size:38 final size:37
Alignment explanation
Indices: 49753--49860 Score: 121
Period size: 38 Copynumber: 2.8 Consensus size: 37
49743 GGTCGGGTCG
*
49753 GGTCAG-ACCGGTCAAACCGGTTCAGACCGGTCAAACC
1 GGTCAGAACCGGTCAAACCGG-TCAAACCGGTCAAACC
*
49790 GGTTC-GAACCGGTTGAAACCGGTCAAACCGGTCAAACC
1 GG-TCAGAACCGG-TCAAACCGGTCAAACCGGTCAAACC
* *
49828 GGTCAGAACCGGTTGAAAACCGGTTAAACCGGT
1 GGTCAGAACCGG-T-CAAACCGGTCAAACCGGT
49861 TTCCAGCAGC
Statistics
Matches: 62, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
37 5 0.08
38 33 0.53
39 24 0.39
ACGTcount: A:0.29, C:0.28, G:0.28, T:0.16
Consensus pattern (37 bp):
GGTCAGAACCGGTCAAACCGGTCAAACCGGTCAAACC
Found at i:57050 original size:5 final size:5
Alignment explanation
Indices: 57040--57092 Score: 52
Period size: 5 Copynumber: 9.8 Consensus size: 5
57030 AACGGTCAAC
* *
57040 GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG
57089 GGTC
1 GGTC
57093 AGACCGGTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
5 32 0.80
7 8 0.20
ACGTcount: A:0.08, C:0.23, G:0.51, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:57055 original size:17 final size:17
Alignment explanation
Indices: 57033--57093 Score: 77
Period size: 17 Copynumber: 3.3 Consensus size: 17
57023 AACGGTCAAC
57033 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
57050 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAA----C-GGTCGGGTCG
57072 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
57089 GGTCA
1 GGTCA
57094 GACCGGTCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
17 21 0.54
18 1 0.03
21 1 0.03
22 16 0.41
ACGTcount: A:0.11, C:0.23, G:0.48, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:57068 original size:22 final size:22
Alignment explanation
Indices: 57026--57092 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
57016 GAAAGTCAAC
*
57026 GGTCAACGGTCAACGGTCGGGTCG
1 GGTCAACGGTC--GGGTCGGGTCG
57050 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
57072 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
57093 AGACCGGTCA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
22 31 0.74
24 11 0.26
ACGTcount: A:0.12, C:0.24, G:0.46, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:57113 original size:19 final size:19
Alignment explanation
Indices: 57091--57188 Score: 101
Period size: 19 Copynumber: 5.1 Consensus size: 19
57081 TCGGGTCGGG
57091 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
57110 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
57129 TC-GAACCGGTTGAAACCGG-
1 TCAG-ACCGG-TCAAACCGGT
*
57148 TCAAACCGGTCAGAACCGGT
1 TCAGACCGGTCA-AACCGGT
* * *
57168 TGAAAACCGGTTAAACCGGT
1 T-CAGACCGGTCAAACCGGT
57188 T
1 T
57189 TCCAGCAGCC
Statistics
Matches: 68, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
18 3 0.04
19 39 0.57
20 17 0.25
21 9 0.13
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.17
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:57119 original size:10 final size:9
Alignment explanation
Indices: 57089--57187 Score: 90
Period size: 9 Copynumber: 10.3 Consensus size: 9
57079 GGTCGGGTCG
*
57089 GGTCAGACC
1 GGTCAAACC
57098 GGTCAAACC
1 GGTCAAACC
*
57107 GGTTCAGACC
1 GG-TCAAACC
57117 GGTCAAACC
1 GGTCAAACC
*
57126 GGTTCGAACC
1 GG-TCAAACC
*
57136 GGTTGAAACC
1 GG-TCAAACC
57146 GGTCAAACC
1 GGTCAAACC
57155 GGTCAGAACC
1 GGTCA-AACC
*
57165 GGTTGAAAACC
1 GG-T-CAAACC
*
57176 GGTTAAACC
1 GGTCAAACC
57185 GGT
1 GGT
57188 TTCCAGCAGC
Statistics
Matches: 76, Mismatches: 9, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
9 37 0.49
10 31 0.41
11 7 0.09
12 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.28, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:57146 original size:29 final size:28
Alignment explanation
Indices: 57090--57187 Score: 124
Period size: 29 Copynumber: 3.4 Consensus size: 28
57080 GTCGGGTCGG
* * *
57090 GTCAGACCGGTCAAACCGGTTCAGACCG
1 GTCAAACCGGTCAAACCGGTTGAAACCG
*
57118 GTCAAACCGGTTCGAACCGGTTGAAACCG
1 GTCAAACCGG-TCAAACCGGTTGAAACCG
57147 GTCAAACCGGTCAGAACCGGTTGAAAACCG
1 GTCAAACCGGTCA-AACCGGTTG-AAACCG
*
57177 GTTAAACCGGT
1 GTCAAACCGGT
57188 TTCCAGCAGC
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
28 11 0.18
29 34 0.56
30 16 0.26
ACGTcount: A:0.29, C:0.28, G:0.28, T:0.16
Consensus pattern (28 bp):
GTCAAACCGGTCAAACCGGTTGAAACCG
Found at i:76403 original size:11 final size:11
Alignment explanation
Indices: 76387--76414 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
76377 GAGTAAGAAT
76387 AATTATGGAAA
1 AATTATGGAAA
76398 AATTATGGAAA
1 AATTATGGAAA
76409 AATTAT
1 AATTAT
76415 ATATGGGTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.14, T:0.32
Consensus pattern (11 bp):
AATTATGGAAA
Done.