Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000080.1 Hibiscus syriacus cultivar Beakdansim tig00000144_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: 60479
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:292 original size:2 final size:2
Alignment explanation
Indices: 285--317 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
275 TATCCATAAT
285 TA TA 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 TA TA T
318 TATTTTTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:720 original size:14 final size:14
Alignment explanation
Indices: 701--767 Score: 98
Period size: 14 Copynumber: 4.8 Consensus size: 14
691 GGTAATATGC
701 TCGTTTATGTTCGT
1 TCGTTTATGTTCGT
*
715 TCGTTTATATTCGT
1 TCGTTTATGTTCGT
*
729 TCATTTATGTTCGT
1 TCGTTTATGTTCGT
*
743 TCGTTTATGTGCGT
1 TCGTTTATGTTCGT
*
757 TCATTTATGTT
1 TCGTTTATGTT
768 TAGCTCAATC
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 46 1.00
ACGTcount: A:0.12, C:0.13, G:0.18, T:0.57
Consensus pattern (14 bp):
TCGTTTATGTTCGT
Found at i:740 original size:28 final size:28
Alignment explanation
Indices: 704--767 Score: 110
Period size: 28 Copynumber: 2.3 Consensus size: 28
694 AATATGCTCG
*
704 TTTATGTTCGTTCGTTTATATTCGTTCA
1 TTTATGTTCGTTCGTTTATATGCGTTCA
*
732 TTTATGTTCGTTCGTTTATGTGCGTTCA
1 TTTATGTTCGTTCGTTTATATGCGTTCA
760 TTTATGTT
1 TTTATGTT
768 TAGCTCAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.12, C:0.12, G:0.17, T:0.58
Consensus pattern (28 bp):
TTTATGTTCGTTCGTTTATATGCGTTCA
Found at i:979 original size:47 final size:47
Alignment explanation
Indices: 910--1005 Score: 174
Period size: 47 Copynumber: 2.0 Consensus size: 47
900 AAAAATCTAT
910 TTCATTTATGTTCGTTTACGTTCATTTATTGTGTTCGTTTACGTTCG
1 TTCATTTATGTTCGTTTACGTTCATTTATTGTGTTCGTTTACGTTCG
* *
957 TTCATTTGTGTTCGTTTACGTTCATTTATTGTGTTCGTTTATGTTCG
1 TTCATTTATGTTCGTTTACGTTCATTTATTGTGTTCGTTTACGTTCG
1004 TT
1 TT
1006 TACATCCGTT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.11, C:0.14, G:0.18, T:0.57
Consensus pattern (47 bp):
TTCATTTATGTTCGTTTACGTTCATTTATTGTGTTCGTTTACGTTCG
Found at i:1046 original size:24 final size:24
Alignment explanation
Indices: 910--1045 Score: 136
Period size: 23 Copynumber: 5.8 Consensus size: 24
900 AAAAATCTAT
* *
910 TTCATTTATGTTCGTTTACGTTCA
1 TTCATTTGTGTTCGTTTACGTTCG
*
934 TTTA-TTGTGTTCGTTTACGTTCG
1 TTCATTTGTGTTCGTTTACGTTCG
*
957 TTCATTTGTGTTCGTTTACGTTCA
1 TTCATTTGTGTTCGTTTACGTTCG
* *
981 TTTA-TTGTGTTCGTTTATGTTCG
1 TTCATTTGTGTTCGTTTACGTTCG
** *
1004 TTTACATCCGT-TTC-TTTATGTTCG
1 -TT-CATTTGTGTTCGTTTACGTTCG
*
1028 TTCATTTGTATTCGTTTA
1 TTCATTTGTGTTCGTTTA
1046 TCATTTAAAT
Statistics
Matches: 93, Mismatches: 13, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
22 5 0.05
23 42 0.45
24 40 0.43
25 4 0.04
26 2 0.02
ACGTcount: A:0.12, C:0.15, G:0.16, T:0.57
Consensus pattern (24 bp):
TTCATTTGTGTTCGTTTACGTTCG
Found at i:1269 original size:34 final size:32
Alignment explanation
Indices: 1189--1268 Score: 121
Period size: 32 Copynumber: 2.6 Consensus size: 32
1179 TATATAGAAA
*
1189 TCTTG-AT-AAAGAGAGAATGGTGGCTAGGAG
1 TCTTGAATAAAAGAGAGAATGGTGGCCAGGAG
1219 TCTTGAATAAAAGAGAGAATGG-GGCCAGGGAG
1 TCTTGAATAAAAGAGAGAATGGTGGCCA-GGAG
1251 TCTTGAATAAAAGAGAGA
1 TCTTGAATAAAAGAGAGA
1269 GTTGGAAATC
Statistics
Matches: 46, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
30 5 0.11
31 6 0.13
32 35 0.76
ACGTcount: A:0.39, C:0.07, G:0.34, T:0.20
Consensus pattern (32 bp):
TCTTGAATAAAAGAGAGAATGGTGGCCAGGAG
Found at i:9664 original size:5 final size:5
Alignment explanation
Indices: 9654--9696 Score: 59
Period size: 5 Copynumber: 8.6 Consensus size: 5
9644 TGGGGTTGGC
* * *
9654 CTCTT CTCTT CTCTT CTCTT CTCTT CGCTT CTCAT CTCAT CTC
1 CTCTT CTCTT CTCTT CTCTT CTCTT CTCTT CTCTT CTCTT CTC
9697 ATCAGTTTGG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.05, C:0.42, G:0.02, T:0.51
Consensus pattern (5 bp):
CTCTT
Found at i:14764 original size:24 final size:24
Alignment explanation
Indices: 14719--14764 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
14709 TAGATTTTGG
* *
14719 TGGAGGATATAGATTTTTCGGACC
1 TGGAGGATATAGAATTTCCGGACC
*
14743 TGGAGGATATATAATTTCCGGA
1 TGGAGGATATAGAATTTCCGGA
14765 ATAGGTCAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.28, C:0.11, G:0.28, T:0.33
Consensus pattern (24 bp):
TGGAGGATATAGAATTTCCGGACC
Found at i:17893 original size:20 final size:20
Alignment explanation
Indices: 17868--17905 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
17858 AACACGCTGG
*
17868 GCATCCGAGGCCATCCGAAA
1 GCATCCGAGACCATCCGAAA
17888 GCATCCGAGACCATCCGA
1 GCATCCGAGACCATCCGA
17906 CCGAGGCCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.37, G:0.24, T:0.11
Consensus pattern (20 bp):
GCATCCGAGACCATCCGAAA
Found at i:17942 original size:23 final size:23
Alignment explanation
Indices: 17907--17958 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
17897 ACCATCCGAC
* *
17907 CGAGGCCATCCGAACGAGCTATG
1 CGAGGGCAACCGAACGAGCTATG
*
17930 CGAGGGCAACCGAGCGAGCTATG
1 CGAGGGCAACCGAACGAGCTATG
17953 CGAGGG
1 CGAGGG
17959 AATCGAGGGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.25, C:0.27, G:0.38, T:0.10
Consensus pattern (23 bp):
CGAGGGCAACCGAACGAGCTATG
Found at i:18053 original size:33 final size:33
Alignment explanation
Indices: 18012--18086 Score: 105
Period size: 33 Copynumber: 2.3 Consensus size: 33
18002 GCGACCTACC
*
18012 CTCGCTCGGTCACCCTCGGATTCCCTCGCATAG
1 CTCGCTCGGTCACCCTCGGATGCCCTCGCATAG
** *
18045 CTCGCTCGGTTGCCCTTGGATGCCCTCGCATAG
1 CTCGCTCGGTCACCCTCGGATGCCCTCGCATAG
*
18078 CTCGGTCGG
1 CTCGCTCGG
18087 ATGGCCTCGG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.09, C:0.39, G:0.27, T:0.25
Consensus pattern (33 bp):
CTCGCTCGGTCACCCTCGGATGCCCTCGCATAG
Found at i:18098 original size:10 final size:10
Alignment explanation
Indices: 18083--18139 Score: 73
Period size: 10 Copynumber: 5.7 Consensus size: 10
18073 CATAGCTCGG
18083 TCGGATGGCC
1 TCGGATGGCC
18093 TCGGAT-GCTC
1 TCGGATGGC-C
18103 TCGGATGGCC
1 TCGGATGGCC
*
18113 TCGGAT-GCTT
1 TCGGATGGC-C
18123 TCGGATGGCC
1 TCGGATGGCC
18133 TCGGATG
1 TCGGATG
18140 CCCAACGTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
9 4 0.10
10 33 0.80
11 4 0.10
ACGTcount: A:0.11, C:0.26, G:0.37, T:0.26
Consensus pattern (10 bp):
TCGGATGGCC
Found at i:18099 original size:33 final size:33
Alignment explanation
Indices: 18024--18105 Score: 110
Period size: 33 Copynumber: 2.5 Consensus size: 33
18014 CGCTCGGTCA
* *
18024 CCCTCGGATTCCCTCGCATAGCTCGCTCGGTTG
1 CCCTCGGATGCCCTCGCATAGCTCGCTCGGATG
* *
18057 CCCTTGGATGCCCTCGCATAGCTCGGTCGGATG
1 CCCTCGGATGCCCTCGCATAGCTCGCTCGGATG
* *
18090 GCCTCGGATGCTCTCG
1 CCCTCGGATGCCCTCG
18106 GATGGCCTCG
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.10, C:0.37, G:0.28, T:0.26
Consensus pattern (33 bp):
CCCTCGGATGCCCTCGCATAGCTCGCTCGGATG
Found at i:18108 original size:20 final size:20
Alignment explanation
Indices: 18083--18140 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
18073 CATAGCTCGG
18083 TCGGATGGCCTCGGATGCTC
1 TCGGATGGCCTCGGATGCTC
*
18103 TCGGATGGCCTCGGATGCTT
1 TCGGATGGCCTCGGATGCTC
18123 TCGGATGGCCTCGGATGC
1 TCGGATGGCCTCGGATGC
18141 CCAACGTTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.10, C:0.28, G:0.36, T:0.26
Consensus pattern (20 bp):
TCGGATGGCCTCGGATGCTC
Found at i:18195 original size:29 final size:29
Alignment explanation
Indices: 18152--18209 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
18142 CAACGTTATT
18152 GTAGGTCACCGGGAAGACATGGCGACCTA
1 GTAGGTCACCGGGAAGACATGGCGACCTA
* * *
18181 GTAGGTCGCCTGGAAGGCATGGCGACCTA
1 GTAGGTCACCGGGAAGACATGGCGACCTA
18210 CGGCCAACAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.24, C:0.24, G:0.36, T:0.16
Consensus pattern (29 bp):
GTAGGTCACCGGGAAGACATGGCGACCTA
Found at i:19403 original size:3 final size:3
Alignment explanation
Indices: 19395--19431 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
19385 TTAATGATTT
19395 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
19432 TAGGAGCTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:21367 original size:38 final size:38
Alignment explanation
Indices: 21316--21394 Score: 158
Period size: 38 Copynumber: 2.1 Consensus size: 38
21306 ATCCCAAATG
21316 CAAATATCCCTCAAATATTTAAAAATAAAACAATCAAA
1 CAAATATCCCTCAAATATTTAAAAATAAAACAATCAAA
21354 CAAATATCCCTCAAATATTTAAAAATAAAACAATCAAA
1 CAAATATCCCTCAAATATTTAAAAATAAAACAATCAAA
21392 CAA
1 CAA
21395 GCATGAATAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.58, C:0.19, G:0.00, T:0.23
Consensus pattern (38 bp):
CAAATATCCCTCAAATATTTAAAAATAAAACAATCAAA
Found at i:21956 original size:20 final size:21
Alignment explanation
Indices: 21931--21975 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 21
21921 TAATAAAATT
21931 TATACACAAAT-TTTAATATA
1 TATACACAAATATTTAATATA
21951 TATACACAAATAATTTAATATA
1 TATACACAAAT-ATTTAATATA
21973 TAT
1 TAT
21976 TTTACCAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 11 0.48
22 12 0.52
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (21 bp):
TATACACAAATATTTAATATA
Found at i:22135 original size:36 final size:35
Alignment explanation
Indices: 22059--22325 Score: 203
Period size: 36 Copynumber: 7.8 Consensus size: 35
22049 ATTTTTCAAT
* * * * *
22059 CTAAAATATGATTACAACTTAAAACAAGTTTCAGC
1 CTAAAATATGGTTGCAACCTAAAACAAGTTCCAAC
22094 CTAAAATATGGTTGCAACCTAAAAACAAGTTCCAAC
1 CTAAAATATGGTTGCAACCT-AAAACAAGTTCCAAC
* * * ** *
22130 TTAAAATAT-G-TG-TATCTTGAACAAATTCCAAC
1 CTAAAATATGGTTGCAACCTAAAACAAGTTCCAAC
* * * *
22162 CTAAAATATGGTTACAACCTAAAAACATGATCTAAC
1 CTAAAATATGGTTGCAACCT-AAAACAAGTTCCAAC
* * *
22198 TTAAAATATGG--G-TATCTAAAACAAGTTCCAAC
1 CTAAAATATGGTTGCAACCTAAAACAAGTTCCAAC
* * *
22230 TTAAAATATGATTGTAACCTGAAAACAAGTTCCAAC
1 CTAAAATATGGTTGCAACCT-AAAACAAGTTCCAAC
* *
22266 CTAAAATATGG--G-TATCTAAAAC-AGTTCCAAC
1 CTAAAATATGGTTGCAACCTAAAACAAGTTCCAAC
* *
22297 CCAAAATATGGTCGCAACCTAAAAACAAG
1 CTAAAATATGGTTGCAACCT-AAAACAAG
22326 CATGTTCTTG
Statistics
Matches: 180, Mismatches: 38, Indels: 27
0.73 0.16 0.11
Matches are distributed among these distances:
31 19 0.11
32 47 0.26
33 11 0.06
34 8 0.04
35 29 0.16
36 66 0.37
ACGTcount: A:0.45, C:0.19, G:0.11, T:0.26
Consensus pattern (35 bp):
CTAAAATATGGTTGCAACCTAAAACAAGTTCCAAC
Found at i:22159 original size:32 final size:32
Alignment explanation
Indices: 22117--22307 Score: 123
Period size: 32 Copynumber: 5.8 Consensus size: 32
22107 GCAACCTAAA
*
22117 AACAAGTTCCAACTTAAAATATGTGTATCTTG
1 AACAAGTTCCAACTTAAAATATGGGTATCTTG
* * * * **
22149 AACAAATTCCAACCTAAAATATGGTTACAACCTAAA
1 AACAAGTTCCAACTTAAAATATGGGT---ATCT-TG
* * * **
22185 AACATGATCTAACTTAAAATATGGGTATCTAA
1 AACAAGTTCCAACTTAAAATATGGGTATCTTG
* * *
22217 AACAAGTTCCAACTTAAAATATGATTGTAACCTG
1 AACAAGTTCCAACTTAAAATATG--GGTATCTTG
* **
22251 AAAACAAGTTCCAACCTAAAATATGGGTATCTAA
1 --AACAAGTTCCAACTTAAAATATGGGTATCTTG
**
22285 AAC-AGTTCCAACCCAAAATATGG
1 AACAAGTTCCAACTTAAAATATGG
22308 TCGCAACCTA
Statistics
Matches: 122, Mismatches: 29, Indels: 17
0.73 0.17 0.10
Matches are distributed among these distances:
31 19 0.16
32 47 0.39
33 3 0.02
34 8 0.07
35 3 0.02
36 42 0.34
ACGTcount: A:0.44, C:0.18, G:0.11, T:0.27
Consensus pattern (32 bp):
AACAAGTTCCAACTTAAAATATGGGTATCTTG
Found at i:22172 original size:68 final size:68
Alignment explanation
Indices: 22078--22325 Score: 336
Period size: 68 Copynumber: 3.7 Consensus size: 68
22068 GATTACAACT
* * *
22078 TAAAACAAGTTTCAGCCTAAAATATGGTTGCAACCTAAAAACAAGTTCCAACTTAAAATATGTGT
1 TAAAACAAGTTCCAACCTAAAATATGGTTGCAACCTAAAAACAAGTTCCAACTTAAAATATGGGT
22143 ATC
66 ATC
** * * * * *
22146 TTGAACAAATTCCAACCTAAAATATGGTTACAACCTAAAAACATGATCTAACTTAAAATATGGGT
1 TAAAACAAGTTCCAACCTAAAATATGGTTGCAACCTAAAAACAAGTTCCAACTTAAAATATGGGT
22211 ATC
66 ATC
* * * * *
22214 TAAAACAAGTTCCAACTTAAAATATGATTGTAACCTGAAAACAAGTTCCAACCTAAAATATGGGT
1 TAAAACAAGTTCCAACCTAAAATATGGTTGCAACCTAAAAACAAGTTCCAACTTAAAATATGGGT
22279 ATC
66 ATC
* *
22282 TAAAAC-AGTTCCAACCCAAAATATGGTCGCAACCTAAAAACAAG
1 TAAAACAAGTTCCAACCTAAAATATGGTTGCAACCTAAAAACAAG
22326 CATGTTCTTG
Statistics
Matches: 152, Mismatches: 28, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
67 32 0.21
68 120 0.79
ACGTcount: A:0.44, C:0.19, G:0.11, T:0.25
Consensus pattern (68 bp):
TAAAACAAGTTCCAACCTAAAATATGGTTGCAACCTAAAAACAAGTTCCAACTTAAAATATGGGT
ATC
Found at i:22534 original size:51 final size:50
Alignment explanation
Indices: 22447--22560 Score: 147
Period size: 51 Copynumber: 2.2 Consensus size: 50
22437 TACTTTTTAC
* *
22447 TATTTTTTATTCATACTTACACCGGTGTAAGTATGTGCTAATTATTATAT
1 TATTTTTTATTCATACTTACACCGATATAAGTATGTGCTAATTATTATAT
* * * *
22497 TATTTTTTATTCATACTTATTACCTATATAAGTATGTGTTAATTGTTATAT
1 TATTTTTTATTCATACTTA-CACCGATATAAGTATGTGCTAATTATTATAT
*
22548 TTTTATTTTATTC
1 TATT-TTTTATTC
22561 TAAATGTATG
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
50 19 0.35
51 28 0.51
52 8 0.15
ACGTcount: A:0.27, C:0.10, G:0.09, T:0.54
Consensus pattern (50 bp):
TATTTTTTATTCATACTTACACCGATATAAGTATGTGCTAATTATTATAT
Found at i:28461 original size:24 final size:24
Alignment explanation
Indices: 28434--28514 Score: 75
Period size: 24 Copynumber: 3.5 Consensus size: 24
28424 ACACTTAACA
28434 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATGCATCCCTTTGAAT
* *
28458 GTGCATCGATTCAT-CATGTTG-A-
1 GTGCATCGATGCATCCCT-TTGAAT
*
28480 -TGCACCGATGCA-CGCC-TTGAAT
1 GTGCATCGATGCATC-CCTTTGAAT
28502 GTGCATCGATGCA
1 GTGCATCGATGCA
28515 CATGGTCATG
Statistics
Matches: 45, Mismatches: 6, Indels: 13
0.70 0.09 0.20
Matches are distributed among these distances:
20 3 0.07
21 11 0.24
22 1 0.02
23 14 0.31
24 16 0.36
ACGTcount: A:0.22, C:0.25, G:0.23, T:0.30
Consensus pattern (24 bp):
GTGCATCGATGCATCCCTTTGAAT
Found at i:28500 original size:44 final size:44
Alignment explanation
Indices: 28435--28537 Score: 138
Period size: 44 Copynumber: 2.3 Consensus size: 44
28425 CACTTAACAG
* * *
28435 TGCATCGATGCATCCCTTTGAATGTGCATCGATTCATCATGTTGA
1 TGCATCGATGCATCCCTTTGAATGTGCATCGATGCA-CATGGTCA
*
28480 TGCACCGATGCA-CGCC-TTGAATGTGCATCGATGCACATGGTCA
1 TGCATCGATGCATC-CCTTTGAATGTGCATCGATGCACATGGTCA
28523 TGCATCGATGCATCC
1 TGCATCGATGCATCC
28538 GTCGGGTTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
43 18 0.35
44 20 0.39
45 13 0.25
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.29
Consensus pattern (44 bp):
TGCATCGATGCATCCCTTTGAATGTGCATCGATGCACATGGTCA
Found at i:30088 original size:21 final size:21
Alignment explanation
Indices: 30046--30089 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
30036 ACTCCGGGAG
* *
30046 CTAGTTCCTCACGAGCTGCTC
1 CTAGCTCCTCACGAGCTCCTC
* *
30067 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCACGAGCTCCTC
30088 CT
1 CT
30090 CCTCCAGCTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.43, G:0.16, T:0.32
Consensus pattern (21 bp):
CTAGCTCCTCACGAGCTCCTC
Found at i:32334 original size:54 final size:53
Alignment explanation
Indices: 32155--32418 Score: 395
Period size: 53 Copynumber: 5.0 Consensus size: 53
32145 TTTGTATCAT
* * * *
32155 CACTATGTATGCATCCATGATATTCATAATGAGTTTGTGAATTATCATTTCGG
1 CACTATGTGTGCATCCATGGTATTCATAATGAGTTTGTGAATTACCATTTCGA
* * *
32208 CACTATG-CTGCATTCATGGTATTCATGATGAGTTTGTGAATTACCATTTCGA
1 CACTATGTGTGCATCCATGGTATTCATAATGAGTTTGTGAATTACCATTTCGA
*
32260 CACTATGTGTGCATCCATGGTATTCATAATGAGTTTGTGAAATTACCATTTCGG
1 CACTATGTGTGCATCCATGGTATTCATAATGAGTTTGTG-AATTACCATTTCGA
* * *
32314 CACCATGTGTGAATCTATGGTATTCATAATGAGTTTGTGAATTACCATTTCGA
1 CACTATGTGTGCATCCATGGTATTCATAATGAGTTTGTGAATTACCATTTCGA
* *
32367 CACTATGTGTGTATCCATGGTATTCATAATGAGTTTGTGAATTTCCATTTCG
1 CACTATGTGTGCATCCATGGTATTCATAATGAGTTTGTGAATTACCATTTCG
32419 TTACTTTAAT
Statistics
Matches: 191, Mismatches: 18, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
52 46 0.24
53 96 0.50
54 49 0.26
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (53 bp):
CACTATGTGTGCATCCATGGTATTCATAATGAGTTTGTGAATTACCATTTCGA
Found at i:32369 original size:107 final size:105
Alignment explanation
Indices: 32155--32418 Score: 413
Period size: 107 Copynumber: 2.5 Consensus size: 105
32145 TTTGTATCAT
* * * * *
32155 CACTATGTATGCATCCATGATATTCATAATGAGTTTGTGAATTATCATTTCGGCACTATGCTGCA
1 CACTATGTGTGCATCCATGGTATTCATAATGAGTTTGTGAATTACCATTTCGGCACCATGCTGAA
*
32220 TTCATGGTATTCATGATGAGTTTGTGAATTACCATTTCGA
66 TTCATGGTATTCATAATGAGTTTGTGAATTACCATTTCGA
*
32260 CACTATGTGTGCATCCATGGTATTCATAATGAGTTTGTGAAATTACCATTTCGGCACCATGTGTG
1 CACTATGTGTGCATCCATGGTATTCATAATGAGTTTGTG-AATTACCATTTCGGCACCATG-CTG
32325 AA-TCTATGGTATTCATAATGAGTTTGTGAATTACCATTTCGA
64 AATTC-ATGGTATTCATAATGAGTTTGTGAATTACCATTTCGA
* *
32367 CACTATGTGTGTATCCATGGTATTCATAATGAGTTTGTGAATTTCCATTTCG
1 CACTATGTGTGCATCCATGGTATTCATAATGAGTTTGTGAATTACCATTTCG
32419 TTACTTTAAT
Statistics
Matches: 147, Mismatches: 9, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
105 37 0.25
106 33 0.22
107 77 0.52
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (105 bp):
CACTATGTGTGCATCCATGGTATTCATAATGAGTTTGTGAATTACCATTTCGGCACCATGCTGAA
TTCATGGTATTCATAATGAGTTTGTGAATTACCATTTCGA
Found at i:32944 original size:20 final size:21
Alignment explanation
Indices: 32919--32970 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
32909 TTTTCCCAAT
32919 TCGCAATGCGAATAAGT-AAA
1 TCGCAATGCGAATAAGTAAAA
* **
32939 TCGCAACGCGAATTGGTAAAA
1 TCGCAATGCGAATAAGTAAAA
32960 TCGCAATGCGA
1 TCGCAATGCGA
32971 TACTGACTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 14 0.52
21 13 0.48
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.19
Consensus pattern (21 bp):
TCGCAATGCGAATAAGTAAAA
Found at i:32984 original size:20 final size:20
Alignment explanation
Indices: 32959--33053 Score: 102
Period size: 20 Copynumber: 4.7 Consensus size: 20
32949 AATTGGTAAA
*
32959 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
32979 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
33000 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
33020 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
* *
33040 TTCGCAACGAGATA
1 ATCGCAACGCGATA
33054 ATACAGAATC
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 2 0.03
20 44 0.70
21 15 0.24
22 2 0.03
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:33801 original size:24 final size:24
Alignment explanation
Indices: 33774--33827 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
33764 GTATTCGAAA
*
33774 TTTGATCTTGGTCAATACTCAGAC
1 TTTGATATTGGTCAATACTCAGAC
* *
33798 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACTCAGAC
33822 TTTGAT
1 TTTGAT
33828 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.15, G:0.19, T:0.43
Consensus pattern (24 bp):
TTTGATATTGGTCAATACTCAGAC
Found at i:34019 original size:12 final size:12
Alignment explanation
Indices: 34002--34026 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
33992 ATATAATCCC
34002 GAAGAAGAAAAA
1 GAAGAAGAAAAA
34014 GAAGAAGAAAAA
1 GAAGAAGAAAAA
34026 G
1 G
34027 TCTCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:36340 original size:19 final size:19
Alignment explanation
Indices: 36318--36382 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 19
36308 GGAAATTACT
36318 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
36337 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
36351 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
36370 ATCGCAACGCGAA
1 ATCGCAATGCGAA
36383 TTTAATTTCG
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
14 9 0.25
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 21 0.58
ACGTcount: A:0.43, C:0.20, G:0.25, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:36341 original size:39 final size:33
Alignment explanation
Indices: 36318--36380 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
36308 GGAAATTACT
*
36318 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGCGGGA
36351 ATCGCAATGCGAAATGAAAATCGCAACGCG
1 ATCGCAATGCGAAATGAAAATCGCAACGCG
36381 AATTTAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.41, C:0.21, G:0.25, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGCGGGA
Found at i:36410 original size:14 final size:14
Alignment explanation
Indices: 36393--36449 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
36383 TTTAATTTCG
36393 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
* *
36407 CGTTGTGATTTTCATTTT
1 CGTTGCGA--TTC--TCT
36425 GCGTTGCGATTCTCT
1 -CGTTGCGATTCTCT
36440 CGTTGCGATT
1 CGTTGCGATT
36450 TTCATTTCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 17 0.50
15 2 0.06
16 3 0.09
17 3 0.09
18 2 0.06
19 7 0.21
ACGTcount: A:0.09, C:0.21, G:0.23, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:36434 original size:33 final size:33
Alignment explanation
Indices: 36378--36467 Score: 135
Period size: 33 Copynumber: 2.7 Consensus size: 33
36368 AAATCGCAAC
* *
36378 GCGAATTTAATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
* *
36411 GTGATTTTCATTTTGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
*
36444 GCGATTTTCATTTCGCATTGCGAT
1 GCGATTTTCATTTCGCGTTGCGAT
36468 AGTACTTTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.13, C:0.20, G:0.21, T:0.46
Consensus pattern (33 bp):
GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
Found at i:36435 original size:19 final size:19
Alignment explanation
Indices: 36407--36467 Score: 51
Period size: 19 Copynumber: 3.5 Consensus size: 19
36397 GCGATTCTCT
*
36407 CGTTGTGATTTTCATTTTG
1 CGTTGCGATTTTCATTTTG
*
36426 CGTTGCGA--TTC--TCT-
1 CGTTGCGATTTTCATTTTG
*
36440 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTTG
*
36459 CATTGCGAT
1 CGTTGCGAT
36468 AGTACTTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 10
0.68 0.11 0.21
Matches are distributed among these distances:
14 8 0.25
15 2 0.06
16 3 0.09
17 3 0.09
18 1 0.03
19 15 0.47
ACGTcount: A:0.11, C:0.20, G:0.21, T:0.48
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTTG
Found at i:36593 original size:14 final size:14
Alignment explanation
Indices: 36574--36610 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
36564 CATCAATTAA
36574 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
36588 ACAAATCACCTTTT
1 ACAAATCAACTTTT
36602 ACAAATCAA
1 ACAAATCAA
36611 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:38482 original size:91 final size:90
Alignment explanation
Indices: 38304--38488 Score: 282
Period size: 91 Copynumber: 2.0 Consensus size: 90
38294 ATTTCAAACT
*
38304 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
38369 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
* *
38397 TTCAACTAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGTA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
*
38461 GTATTGGCAGCAACCGAATAAATTTAC
64 GAATTGGCAGCAACCGAATAAATTTAC
38488 T
1 T
38489 AAGCAATATA
Statistics
Matches: 86, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
91 41 0.48
93 18 0.21
95 27 0.31
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.23
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:40204 original size:20 final size:19
Alignment explanation
Indices: 40173--40251 Score: 86
Period size: 20 Copynumber: 4.1 Consensus size: 19
40163 TCTTTTGGTT
*
40173 GAAATGAAAATCGCAACGA
1 GAAATGACAATCGCAACGA
* *
40192 GATAATGAGAATCGCAACGCG
1 GA-AATGACAATCGCAACG-A
* *
40213 GAAATGACTATCGCAACGC
1 GAAATGACAATCGCAACGA
*
40232 GAAATGACTATCGCAACGA
1 GAAATGACAATCGCAACGA
40251 G
1 G
40252 CGAATCGCAA
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
19 21 0.40
20 29 0.56
21 2 0.04
ACGTcount: A:0.42, C:0.20, G:0.24, T:0.14
Consensus pattern (19 bp):
GAAATGACAATCGCAACGA
Found at i:40237 original size:19 final size:19
Alignment explanation
Indices: 40182--40249 Score: 91
Period size: 20 Copynumber: 3.5 Consensus size: 19
40172 TGAAATGAAA
* **
40182 ATCGCAACGAGATAATGAGA
1 ATCGCAACGCGA-AATGACT
40202 ATCGCAACGCGGAAATGACT
1 ATCGCAACGC-GAAATGACT
40222 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
40241 ATCGCAACG
1 ATCGCAACG
40250 AGCGAATCGC
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
19 18 0.41
20 24 0.55
21 2 0.05
ACGTcount: A:0.38, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:40278 original size:19 final size:19
Alignment explanation
Indices: 40173--40285 Score: 92
Period size: 19 Copynumber: 6.1 Consensus size: 19
40163 TCTTTTGGTT
*
40173 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
40192 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
40212 GGAAATGACTATCGCAACGC
1 -GAAATGAAAATCGCAACGC
**
40232 GAAATGACTATCGCAA--C
1 GAAATGAAAATCGCAACGC
**
40249 G--A-GCGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
40265 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
40284 GA
1 GA
40286 TTTTGGTTTC
Statistics
Matches: 77, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
14 8 0.10
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 31 0.40
20 30 0.39
21 2 0.03
ACGTcount: A:0.42, C:0.21, G:0.24, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:40314 original size:19 final size:19
Alignment explanation
Indices: 40281--40325 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
40271 AAAATCGCAA
*
40281 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
40300 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
40319 TGCGATT
1 TGCGATT
40326 CTCTCGTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.09, C:0.16, G:0.27, T:0.49
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:40902 original size:20 final size:20
Alignment explanation
Indices: 40877--40929 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
40867 GCGCTATGTA
40877 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
40897 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
40917 TATCTCGTTGCGA
1 AATCGCGTTGCGA
40930 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:40963 original size:20 final size:20
Alignment explanation
Indices: 40938--40991 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
40928 GATTTTGTAT
40938 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
40958 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
40978 TATCGCATTGCGAT
1 TATCGCATTGCGAT
40992 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:40976 original size:61 final size:61
Alignment explanation
Indices: 40878--40994 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
40868 CGCTATGTAA
* * * * *
40878 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
40939 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
40995 CCCAATTCGC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:41010 original size:61 final size:61
Alignment explanation
Indices: 40878--41012 Score: 155
Period size: 61 Copynumber: 2.2 Consensus size: 61
40868 CGCTATGTAA
* * * * * ** *
40878 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * *
40939 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
41001 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
41013 TTACTTATTC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
61 59 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:41102 original size:21 final size:21
Alignment explanation
Indices: 41062--41102 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
41052 ACTGTAGACC
** *
41062 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAACT
41083 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATGCAAC
41103 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAACT
Found at i:41880 original size:18 final size:18
Alignment explanation
Indices: 41837--41883 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
41827 GAAAGATAGG
*
41837 AGGAGAAAACTTATTTGA
1 AGGAGAACACTTATTTGA
41855 AGGAGAACACTTATTTGA
1 AGGAGAACACTTATTTGA
41873 AGGAGAACACT
1 AGGAGAACACT
41884 GGAGAAGAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.43, C:0.11, G:0.23, T:0.23
Consensus pattern (18 bp):
AGGAGAACACTTATTTGA
Found at i:53718 original size:35 final size:35
Alignment explanation
Indices: 53677--53786 Score: 184
Period size: 35 Copynumber: 3.1 Consensus size: 35
53667 TTCATGTTCG
* *
53677 AAATTCCAAAACACTTCAATTACATTCTAAACCCC
1 AAATTCCAAAATACTTCAATTATATTCTAAACCCC
*
53712 AAATTCCAAAATACTTTAATTATATTCTAAACCCC
1 AAATTCCAAAATACTTCAATTATATTCTAAACCCC
*
53747 AAATTCCAAAATACTTCAATTATATTCTAAACCCT
1 AAATTCCAAAATACTTCAATTATATTCTAAACCCC
53782 AAATT
1 AAATT
53787 AAAGTATTTT
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 70 1.00
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.32
Consensus pattern (35 bp):
AAATTCCAAAATACTTCAATTATATTCTAAACCCC
Found at i:53857 original size:35 final size:35
Alignment explanation
Indices: 53782--53858 Score: 91
Period size: 35 Copynumber: 2.2 Consensus size: 35
53772 TCTAAACCCT
* *
53782 AAATTAAAGTATTTTAGAATTTAGGGTTTAAAATG
1 AAATTGAAGTATTTTAGAATTTAGGGTTTAAAATA
* * * * *
53817 TAATTGAATTATTTTGGAATTTGGGGTTTAGAATA
1 AAATTGAAGTATTTTAGAATTTAGGGTTTAAAATA
53852 AAATTGA
1 AAATTGA
53859 GGATTGTGTT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.39, C:0.00, G:0.19, T:0.42
Consensus pattern (35 bp):
AAATTGAAGTATTTTAGAATTTAGGGTTTAAAATA
Found at i:55317 original size:24 final size:23
Alignment explanation
Indices: 55293--55378 Score: 79
Period size: 23 Copynumber: 3.7 Consensus size: 23
55283 TCATATAAAT
55293 TTGCACCGAAGTGCCACGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
* *
55316 TT-TATCCCGAA-TGACAGCGTAGAGA
1 TTGCA--CCGAAGTGCCA-CGTAGA-A
55341 -TGCACCGAAGTGCCACGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
* *
55363 TTGTACCGTAGTGCCA
1 TTGCACCGAAGTGCCA
55379 TATAATATGT
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
22 2 0.04
23 30 0.60
24 16 0.32
25 2 0.04
ACGTcount: A:0.29, C:0.24, G:0.26, T:0.21
Consensus pattern (23 bp):
TTGCACCGAAGTGCCACGTAGAA
Found at i:58336 original size:22 final size:21
Alignment explanation
Indices: 58306--58349 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 21
58296 CTCTAAGCTG
58306 AAAACTCTTTCGGCTTAAGGC
1 AAAACTCTTTCGGCTTAAGGC
58327 AAAACGTCTTTCGGCTTAAGGC
1 AAAAC-TCTTTCGGCTTAAGGC
58349 A
1 A
58350 TCCGCTACCC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (21 bp):
AAAACTCTTTCGGCTTAAGGC
Done.