Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009242.1 Hibiscus syriacus cultivar Beakdansim tig00112873_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: 55318
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:449 original size:73 final size:73
Alignment explanation
Indices: 372--635 Score: 263
Period size: 73 Copynumber: 3.6 Consensus size: 73
362 CTACCTACCG
* *
372 GTTTGTTTAAATGTTACTAATAATGTAAATGATAAAA-AAAATAGCGTTACCTATTACGTTAAAA
1 GTTTGTTTAAAGGTTACTAATAATGTAAACGATAAAATAAAATAGCGTTACCTATTACGTTAAAA
436 TACTTATCA
66 TACTTA-CA
* ** *
445 GTTTGTTTAAAGATTACTAATAATGTAAA-GAGTAAAATAAAATAGACACTACATATTACGTTAA
1 GTTTGTTTAAAGGTTACTAATAATGTAAACGA-TAAAATAAAATAG-CGTTACCTATTACGTTAA
* *
509 ATTA-TCTACC
64 AATACT-TACA
* * *
519 GGTTGTTT-AAGGTTACT-ATAATGT-AACGGTAAAATAAAACAGGCGTTACCTATTACGTTAAA
1 GTTTGTTTAAAGGTTACTAATAATGTAAACGATAAAATAAAATA-GCGTTACCTATTACGTTAAA
* *
581 CTAAC-TACCG
65 AT-ACTTA-CA
* * * *
591 GTTTGTTTAAAGGTTAATTATAAGGTAAACGGTAAAATAAAATAG
1 GTTTGTTTAAAGGTTACTAATAATGTAAACGATAAAATAAAATAG
636 GTGCTACATA
Statistics
Matches: 159, Mismatches: 20, Indels: 23
0.79 0.10 0.11
Matches are distributed among these distances:
71 32 0.20
72 20 0.13
73 48 0.30
74 23 0.14
75 36 0.23
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (73 bp):
GTTTGTTTAAAGGTTACTAATAATGTAAACGATAAAATAAAATAGCGTTACCTATTACGTTAAAA
TACTTACA
Found at i:595 original size:146 final size:148
Alignment explanation
Indices: 325--656 Score: 406
Period size: 146 Copynumber: 2.2 Consensus size: 148
315 AAAACTTAAC
* * * *
325 CGGTTAAATAAAATAGACACTACTTATTATTGTTAAACTACCTACCGGTTTGTTTAAATGTTACT
1 CGGTAAAATAAAATAGACACTACATATTA-TGTTAAATTACCTACCGGTTTGTTTAAAGGTTACT
* * *
390 AATAATGTAAATGATAAAAAAAATAGCGTTACCTATTACGTTAAAATACTTATCAGTTTGTTTAA
65 AATAATGTAAACGATAAAAAAAACAGCGTTACCTATTACGTTAAAATACTTACCAGTTTGTTTAA
* *
455 AGATTACTAATAATGTAAA
130 AGATTAATAATAAGGTAAA
* *
474 -GAGTAAAATAAAATAGACACTACATATTACGTTAAATTATCTACCGG-TTGTTT-AAGGTTACT
1 CG-GTAAAATAAAATAGACACTACATATTATGTTAAATTACCTACCGGTTTGTTTAAAGGTTACT
* * *
536 -ATAATGT-AACGGTAAAATAAAACAGGCGTTACCTATTACGTTAAACTAAC-TACCGGTTTGTT
65 AATAATGTAAACGATAAAA-AAAACA-GCGTTACCTATTACGTTAAAAT-ACTTACCAGTTTGTT
* *
598 TAAAGGTTAATTATAAGGTAAA
127 TAAAGATTAATAATAAGGTAAA
***
620 CGGTAAAATAAAATAGGTGCTACATATTATGTTAAAT
1 CGGTAAAATAAAATAGACACTACATATTATGTTAAAT
657 AGGCGCTACA
Statistics
Matches: 158, Mismatches: 20, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
144 8 0.05
145 12 0.08
146 88 0.56
147 9 0.06
148 16 0.10
149 25 0.16
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34
Consensus pattern (148 bp):
CGGTAAAATAAAATAGACACTACATATTATGTTAAATTACCTACCGGTTTGTTTAAAGGTTACTA
ATAATGTAAACGATAAAAAAAACAGCGTTACCTATTACGTTAAAATACTTACCAGTTTGTTTAAA
GATTAATAATAAGGTAAA
Found at i:654 original size:75 final size:75
Alignment explanation
Indices: 325--655 Score: 309
Period size: 75 Copynumber: 4.5 Consensus size: 75
315 AAAACTTAAC
* * * * * * *
325 CGGTTAAATAAAATAGACACTACTTATTATTGTTAAACTACCTACCGGTTTGTTTAAATGTTACT
1 CGGTAAAATAAAATAGGCACTACATATTA-CGTTAAACTAACTACCGGTTTGTTTAAAGGTTAAT
390 AATAATGTAAA
65 AATAATGTAAA
* * ** * * * * * *
401 TGATAAAA-AAAATA-GCGTTACCTATTACGTTAAAAT-ACTTATCAGTTTGTTTAAAGATTACT
1 CGGTAAAATAAAATAGGCACTACATATTACGTTAAACTAAC-TACCGGTTTGTTTAAAGGTTAAT
463 AATAATGTAAA
65 AATAATGTAAA
* * * *
474 -GAGTAAAATAAAATAGACACTACATATTACGTTAAATTATCTACCGG-TTGTTT-AAGGTTACT
1 CG-GTAAAATAAAATAGGCACTACATATTACGTTAAACTAACTACCGGTTTGTTTAAAGGTTAAT
536 -ATAATGT-AA
65 AATAATGTAAA
* ** * *
545 CGGTAAAATAAAACAGGCGTTACCTATTACGTTAAACTAACTACCGGTTTGTTTAAAGGTTAATT
1 CGGTAAAATAAAATAGGCACTACATATTACGTTAAACTAACTACCGGTTTGTTTAAAGGTTAATA
*
610 ATAAGGTAAA
66 ATAATGTAAA
** *
620 CGGTAAAATAAAATAGGTGCTACATATTATGTTAAA
1 CGGTAAAATAAAATAGGCACTACATATTACGTTAAA
656 TAGGCGCTAC
Statistics
Matches: 207, Mismatches: 38, Indels: 21
0.78 0.14 0.08
Matches are distributed among these distances:
71 40 0.19
72 16 0.08
73 58 0.28
74 27 0.13
75 60 0.29
76 6 0.03
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34
Consensus pattern (75 bp):
CGGTAAAATAAAATAGGCACTACATATTACGTTAAACTAACTACCGGTTTGTTTAAAGGTTAATA
ATAATGTAAA
Found at i:656 original size:23 final size:23
Alignment explanation
Indices: 630--692 Score: 85
Period size: 21 Copynumber: 2.8 Consensus size: 23
620 CGGTAAAATA
*
630 AAATAGGTGCTACATATTATGTT
1 AAATAGGCGCTACATATTATGTT
653 AAATAGGCGCTACATA-T-TGTT
1 AAATAGGCGCTACATATTATGTT
* *
674 AAATAAGCGCTACCTATTA
1 AAATAGGCGCTACATATTA
693 CATTAAACTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 18 0.51
22 2 0.06
23 15 0.43
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (23 bp):
AAATAGGCGCTACATATTATGTT
Found at i:775 original size:22 final size:23
Alignment explanation
Indices: 749--796 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
739 CGGTAAAATA
*
749 AAATAAGCG-TACCTATTACTTT
1 AAATAAGCGCTACCTATTACGTT
771 AAATAAGCGCTACCTATTACGTT
1 AAATAAGCGCTACCTATTACGTT
794 AAA
1 AAA
797 CTAGCTACCG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 9 0.38
23 15 0.62
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (23 bp):
AAATAAGCGCTACCTATTACGTT
Found at i:901 original size:115 final size:120
Alignment explanation
Indices: 749--1032 Score: 391
Period size: 115 Copynumber: 2.4 Consensus size: 120
739 CGGTAAAATA
* * * *
749 AAATAAGC-GTACCTATTACTTTAAATAAGCGCTACCTATTACGTTAAACTAGCTACCGATTTGT
1 AAATAAGCACTACCTATTACATTAAATAAGCACTACCTATTACGTTAAACTAACTACCGATTTGT
* *
813 TTAAAGGTTAATAATAATG-AAATGGTTAAATAAAATAGACGC-A-TATTATG-T
66 TTAAAGGTTAATAATAATGTAAATGGTAAAATAAAATAGACGCTACTATTACGTT
* * * *
864 AAATAGGTACTACCTATTACATT-AATAACCACTACCTATTATGTTAAACTAACTACCGATTTGT
1 AAATAAGCACTACCTATTACATTAAATAAGCACTACCTATTACGTTAAACTAACTACCGATTTGT
928 TTAAAGGTTAATAATAATGTAAATGGTAAAATAAAATAGACGCTACCTATTACGTT
66 TTAAAGGTTAATAATAATGTAAATGGTAAAATAAAATAGACGCTA-CTATTACGTT
* ** *
984 AAATAAGCGCTATTTATTACGTTAAATAAGCACTACCTATTACGTTAAA
1 AAATAAGCACTACCTATTACATTAAATAAGCACTACCTATTACGTTAAA
1033 TAAGCGCTAC
Statistics
Matches: 144, Mismatches: 18, Indels: 8
0.85 0.11 0.05
Matches are distributed among these distances:
115 62 0.43
116 34 0.24
117 1 0.01
119 6 0.04
120 18 0.12
121 23 0.16
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.33
Consensus pattern (120 bp):
AAATAAGCACTACCTATTACATTAAATAAGCACTACCTATTACGTTAAACTAACTACCGATTTGT
TTAAAGGTTAATAATAATGTAAATGGTAAAATAAAATAGACGCTACTATTACGTT
Found at i:941 original size:212 final size:217
Alignment explanation
Indices: 565--1009 Score: 591
Period size: 212 Copynumber: 2.1 Consensus size: 217
555 AAACAGGCGT
* *
565 TACCTATTACGTTAAACTAACTACCGGTTTGTTTAAAGGTTAATTATAAGGTAAACGGTAAAATA
1 TACCTATTACGTTAAACTAACTACCGATTTGTTTAAAGGTTAATAATAAGGTAAACGGTAAAATA
* * * * *
630 AAATAGGTGCTACATATTATGTTAAATAGGCGCTACATATTGTTAAATAAGCGCTACCTATTACA
66 AAATAGGTACTACATATTATGTTAAATAGGCACTACATATTATTAAATAACCACTACCTATTACA
* * *
695 TTAAACTAGCTACCTATTTGTTTAAAGATTAATAATGATGTAAACGGTAAAATAAAATA-A-GCG
131 TTAAACTAACTACCGATTTGTTTAAAGATTAATAATAATGTAAACGGTAAAATAAAATAGACGC-
*
758 TACCTATTACTTTAAATAAGCGC
195 TACCTATTACGTTAAATAAGCGC
* * * *
781 TACCTATTACGTTAAACTAGCTACCGATTTGTTTAAAGGTTAATAATAATG-AAATGGTTAAATA
1 TACCTATTACGTTAAACTAACTACCGATTTGTTTAAAGGTTAATAATAAGGTAAACGGTAAAATA
* * *
845 AAATA-G-AC-GCATATTATG-TAAATAGGTACTACCTATTACATT-AATAACCACTACCTATTA
66 AAATAGGTACTACATATTATGTTAAATAGGCACTACATATT--ATTAAATAACCACTACCTATTA
** * *
905 TGTTAAACTAACTACCGATTTGTTTAAAGGTTAATAATAATGTAAATGGTAAAATAAAATAGACG
129 CATTAAACTAACTACCGATTTGTTTAAAGATTAATAATAATGTAAACGGTAAAATAAAATAGACG
970 CTACCTATTACGTTAAATAAGCGC
194 CTACCTATTACGTTAAATAAGCGC
**
994 TATTTATTACGTTAAA
1 TACCTATTACGTTAAA
1010 TAAGCACTAC
Statistics
Matches: 201, Mismatches: 24, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
211 16 0.08
212 79 0.39
213 40 0.20
214 3 0.01
215 16 0.08
216 47 0.23
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (217 bp):
TACCTATTACGTTAAACTAACTACCGATTTGTTTAAAGGTTAATAATAAGGTAAACGGTAAAATA
AAATAGGTACTACATATTATGTTAAATAGGCACTACATATTATTAAATAACCACTACCTATTACA
TTAAACTAACTACCGATTTGTTTAAAGATTAATAATAATGTAAACGGTAAAATAAAATAGACGCT
ACCTATTACGTTAAATAAGCGC
Found at i:987 original size:23 final size:23
Alignment explanation
Indices: 968--1055 Score: 140
Period size: 23 Copynumber: 3.8 Consensus size: 23
958 ATAAAATAGA
968 CGCTACCTATTACGTTAAATAAG
1 CGCTACCTATTACGTTAAATAAG
**
991 CGCTATTTATTACGTTAAATAAG
1 CGCTACCTATTACGTTAAATAAG
*
1014 CACTACCTATTACGTTAAATAAG
1 CGCTACCTATTACGTTAAATAAG
*
1037 CGCTACATATTACGTTAAA
1 CGCTACCTATTACGTTAAA
1056 CTAACTACCG
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 58 1.00
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.33
Consensus pattern (23 bp):
CGCTACCTATTACGTTAAATAAG
Found at i:3194 original size:20 final size:20
Alignment explanation
Indices: 3158--3195 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3148 ATCATATTCC
**
3158 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
3178 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
3196 GTGAACCAAA
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:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:10276 original size:29 final size:29
Alignment explanation
Indices: 10240--10303 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
10230 TGAAAGTTAT
10240 AATTTAAGGATAAAATTAAAATAATTAAA
1 AATTTAAGGATAAAATTAAAATAATTAAA
* * * *
10269 AATTTAAGGATTAATTTAAAATAATTCAT
1 AATTTAAGGATAAAATTAAAATAATTAAA
10298 AATTTA
1 AATTTA
10304 GGGAATATGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.38
Consensus pattern (29 bp):
AATTTAAGGATAAAATTAAAATAATTAAA
Found at i:17006 original size:2 final size:2
Alignment explanation
Indices: 16999--17027 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
16989 TCTGTATCCC
16999 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17028 GAAAACTTTA
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:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19266 original size:69 final size:69
Alignment explanation
Indices: 19180--19318 Score: 260
Period size: 69 Copynumber: 2.0 Consensus size: 69
19170 TGGGGAGTGA
* *
19180 TGAAGCCTTGGATTCAGTTTGTTTATCAGCCTCAACAGTCCAACTGTAAACTACCATGCCAAGGA
1 TGAAGCCTTGGATTCAGTTTGTTTATAAGCCTCAACAGCCCAACTGTAAACTACCATGCCAAGGA
19245 TCGC
66 TCGC
19249 TGAAGCCTTGGATTCAGTTTGTTTATAAGCCTCAACAGCCCAACTGTAAACTACCATGCCAAGGA
1 TGAAGCCTTGGATTCAGTTTGTTTATAAGCCTCAACAGCCCAACTGTAAACTACCATGCCAAGGA
19314 TCGC
66 TCGC
19318 T
1 T
19319 ATCGCCATCC
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (69 bp):
TGAAGCCTTGGATTCAGTTTGTTTATAAGCCTCAACAGCCCAACTGTAAACTACCATGCCAAGGA
TCGC
Found at i:20673 original size:41 final size:41
Alignment explanation
Indices: 20626--20866 Score: 208
Period size: 41 Copynumber: 6.0 Consensus size: 41
20616 GGGTTAGGTT
*
20626 TGAAATCTAAATCACAACGACAATGACAGAGCTGGAATAAA
1 TGAAATCTAAATCACAACGACAATGACAGAGCTGGAATATA
* * *
20667 TGAAATCTATATCACAACGACAATGACAGAGCTGGAATGTG
1 TGAAATCTAAATCACAACGACAATGACAGAGCTGGAATATA
* * * * *
20708 TAAAATATATATCATAACGACAACGACAGAGCTGGAATATA
1 TGAAATCTAAATCACAACGACAATGACAGAGCTGGAATATA
* * *
20749 TGAAATC----T---AACGACAACGACAGAGCAGGAATGTA
1 TGAAATCTAAATCACAACGACAATGACAGAGCTGGAATATA
* * * * * * *
20783 TAAAATATATACCATAACGAAAACGACAGAGCTGGAATATA
1 TGAAATCTAAATCACAACGACAATGACAGAGCTGGAATATA
* * * * *
20824 TGAAATCTATATCAATAACAACAACGACAGATCTGGAATATA
1 TGAAATCTAAATC-ACAACGACAATGACAGAGCTGGAATATA
20866 T
1 T
20867 ATCGTGTATA
Statistics
Matches: 166, Mismatches: 26, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
34 29 0.17
37 1 0.01
41 110 0.66
42 26 0.16
ACGTcount: A:0.46, C:0.16, G:0.17, T:0.20
Consensus pattern (41 bp):
TGAAATCTAAATCACAACGACAATGACAGAGCTGGAATATA
Found at i:20762 original size:34 final size:34
Alignment explanation
Indices: 20722--20832 Score: 123
Period size: 34 Copynumber: 3.1 Consensus size: 34
20712 ATATATATCA
20722 TAACGACAACGACAGAGCTGGAATATATGAAATC
1 TAACGACAACGACAGAGCTGGAATATATGAAATC
* **
20756 TAACGACAACGACAGAGCAGGAATGTATAAAATATATACC
1 TAACGACAACGACAGAGCTGGAA--TATATGA-A-AT--C
*
20796 ATAACGAAAACGACAGAGCTGGAATATATGAAATC
1 -TAACGACAACGACAGAGCTGGAATATATGAAATC
20831 TA
1 TA
20833 TATCAATAAC
Statistics
Matches: 63, Mismatches: 7, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
34 24 0.38
35 1 0.02
36 5 0.08
37 3 0.05
38 3 0.05
39 5 0.08
40 1 0.02
41 21 0.33
ACGTcount: A:0.47, C:0.16, G:0.19, T:0.18
Consensus pattern (34 bp):
TAACGACAACGACAGAGCTGGAATATATGAAATC
Found at i:20772 original size:116 final size:117
Alignment explanation
Indices: 20641--20866 Score: 301
Period size: 116 Copynumber: 1.9 Consensus size: 117
20631 TCTAAATCAC
* * * * * * * *
20641 AACGACAATGACAGAGCTGGAATAAATGAAATCTATATCACAACGACAATGACAGAGCTGGAATG
1 AACGACAACGACAGAGCAGGAATAAATAAAATATATACCACAACGAAAACGACAGAGCTGGAATA
* *
20706 TGTAAAATATATATC-ATAACGACAACGACAGAGCTGGAATATATGAAATCT
66 TATAAAATATATATCAATAACAACAACGACAGAGCTGGAATATATGAAATCT
** *
20757 AACGACAACGACAGAGCAGGAATGTATAAAATATATACCATAACGAAAACGACAGAGCTGGAATA
1 AACGACAACGACAGAGCAGGAATAAATAAAATATATACCACAACGAAAACGACAGAGCTGGAATA
* * *
20822 TATGAAATCTATATCAATAACAACAACGACAGATCTGGAATATAT
66 TATAAAATATATATCAATAACAACAACGACAGAGCTGGAATATAT
20867 ATCGTGTATA
Statistics
Matches: 93, Mismatches: 16, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
116 66 0.71
117 27 0.29
ACGTcount: A:0.46, C:0.16, G:0.18, T:0.20
Consensus pattern (117 bp):
AACGACAACGACAGAGCAGGAATAAATAAAATATATACCACAACGAAAACGACAGAGCTGGAATA
TATAAAATATATATCAATAACAACAACGACAGAGCTGGAATATATGAAATCT
Found at i:20808 original size:75 final size:75
Alignment explanation
Indices: 20682--20832 Score: 257
Period size: 75 Copynumber: 2.0 Consensus size: 75
20672 TCTATATCAC
* * * * *
20682 AACGACAATGACAGAGCTGGAATGTGTAAAATATATATCATAACGACAACGACAGAGCTGGAATA
1 AACGACAACGACAGAGCAGGAATGTATAAAATATATACCATAACGAAAACGACAGAGCTGGAATA
20747 TATGAAATCT
66 TATGAAATCT
20757 AACGACAACGACAGAGCAGGAATGTATAAAATATATACCATAACGAAAACGACAGAGCTGGAATA
1 AACGACAACGACAGAGCAGGAATGTATAAAATATATACCATAACGAAAACGACAGAGCTGGAATA
20822 TATGAAATCT
66 TATGAAATCT
20832 A
1 A
20833 TATCAATAAC
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 71 1.00
ACGTcount: A:0.46, C:0.15, G:0.19, T:0.19
Consensus pattern (75 bp):
AACGACAACGACAGAGCAGGAATGTATAAAATATATACCATAACGAAAACGACAGAGCTGGAATA
TATGAAATCT
Found at i:40622 original size:56 final size:56
Alignment explanation
Indices: 40543--40726 Score: 217
Period size: 56 Copynumber: 3.3 Consensus size: 56
40533 TAGGGGTCTC
** * *
40543 AAATCGAATATATCTATCAGTTGTTGCCATTAGTAAGTATAAAAATAGAGGC-CCCG
1 AAATCGAATATATCTATCAGTTGTTGCCATTAACAAGCATAAAAATAG-GACTCCCG
* *
40599 AAATCGAATATATCAATCCGTTGTTGCCATTAACAAGCATAAAAATAGGACTCCCG
1 AAATCGAATATATCTATCAGTTGTTGCCATTAACAAGCATAAAAATAGGACTCCCG
* * * * **
40655 AAATCGAGTATATCTATCAGTTGTTGCTATTAAAAATCATAAAAATAGGGGTCCCG
1 AAATCGAATATATCTATCAGTTGTTGCCATTAACAAGCATAAAAATAGGACTCCCG
* **
40711 GAATTAAATATATCTA
1 AAATCGAATATATCTA
40727 GAAAATAGAG
Statistics
Matches: 109, Mismatches: 18, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
55 2 0.02
56 107 0.98
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (56 bp):
AAATCGAATATATCTATCAGTTGTTGCCATTAACAAGCATAAAAATAGGACTCCCG
Found at i:42253 original size:3 final size:3
Alignment explanation
Indices: 42245--42270 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
42235 ACCATTGCTT
42245 GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
42271 TTGCAAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:49542 original size:48 final size:51
Alignment explanation
Indices: 49449--49602 Score: 161
Period size: 51 Copynumber: 3.1 Consensus size: 51
49439 GGCTGGCTTG
* * * * * * *
49449 GCTCCGAACTTCTCTCAGCTATTCCAATTTCTTTTCTTGACTCAGCAACCT
1 GCTCCAAACATCTCCCAGATATTCCAACTTCTTTTCTTGATTCAGCAGCCT
* *
49500 GTTCC-AA-A-CTCCCAGATATTCCAACTTCTTTTCTTGATTCAGCGGCCT
1 GCTCCAAACATCTCCCAGATATTCCAACTTCTTTTCTTGATTCAGCAGCCT
* * * * *
49548 GCTCCAAACATCTCCCAGTTGTTCCAGCTTCCTTCCTTGATTCAGCAGCCT
1 GCTCCAAACATCTCCCAGATATTCCAACTTCTTTTCTTGATTCAGCAGCCT
49599 GCTC
1 GCTC
49603 AACCTCAGAT
Statistics
Matches: 85, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
48 38 0.45
49 2 0.02
50 3 0.04
51 42 0.49
ACGTcount: A:0.19, C:0.34, G:0.12, T:0.34
Consensus pattern (51 bp):
GCTCCAAACATCTCCCAGATATTCCAACTTCTTTTCTTGATTCAGCAGCCT
Found at i:54857 original size:31 final size:30
Alignment explanation
Indices: 54821--54885 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 30
54811 TTTATATAAA
54821 TTTTTAGTACTTAAACTATCAGTTTTTATCC
1 TTTTTAGTACTTAAACTATCAG-TTTTATCC
* *
54852 TTTTTAGTCCTTAAACTATCAGTTTTGTCC
1 TTTTTAGTACTTAAACTATCAGTTTTATCC
54882 TTTT
1 TTTT
54886 AGTCCTTTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 11 0.34
31 21 0.66
ACGTcount: A:0.22, C:0.17, G:0.08, T:0.54
Consensus pattern (30 bp):
TTTTTAGTACTTAAACTATCAGTTTTATCC
Found at i:55235 original size:18 final size:18
Alignment explanation
Indices: 55214--55250 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
55204 GTAATTGGAG
55214 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
55232 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
55250 T
1 T
55251 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:55258 original size:24 final size:24
Alignment explanation
Indices: 55206--55252 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
55196 TTTCATATGT
* *
55206 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
55230 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
55253 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Done.