Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002641.1 Hibiscus syriacus cultivar Beakdansim tig00005386_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: 51517
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:394 original size:19 final size:22
Alignment explanation
Indices: 360--404 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
350 TTTTTTCACT
360 AAAAAAAGGTAGAAAAAT-CAA
1 AAAAAAAGGTAGAAAAATACAA
381 AAAAAAAGG-A-AAAAATACAA
1 AAAAAAAGGTAGAAAAATACAA
401 AAAA
1 AAAA
405 TCAAAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 6 0.26
20 8 0.35
21 9 0.39
ACGTcount: A:0.78, C:0.04, G:0.11, T:0.07
Consensus pattern (22 bp):
AAAAAAAGGTAGAAAAATACAA
Found at i:5488 original size:42 final size:43
Alignment explanation
Indices: 5383--5650 Score: 339
Period size: 42 Copynumber: 6.2 Consensus size: 43
5373 TTCTCTTACC
* *
5383 TTTAGTGGCATTTTTTTACCACAAACACCGCTAATGCTATTGGT
1 TTTAGTGGCA-TTTTTTACCACAAACGCCGCTAACGCTATTGGT
* * *
5427 TTTAGTGGCA-TTTTCACCACAAATG-CGCTAACGCTATTGAT
1 TTTAGTGGCATTTTTTACCACAAACGCCGCTAACGCTATTGGT
5468 TTTAGTGGCATTTTTTACCACAAACGCCGCTAACGCTATTGGT
1 TTTAGTGGCATTTTTTACCACAAACGCCGCTAACGCTATTGGT
* *
5511 TTTAGTGGC-TTTTTTACCACAAACGCCGTTAATGCTATTGGT
1 TTTAGTGGCATTTTTTACCACAAACGCCGCTAACGCTATTGGT
**
5553 TTTAGTGGC-TTTTTTGGCACAAACGCCGCTAATGCTATGCTATTGGT
1 TTTAGTGGCATTTTTTACCACAAACGCCGCTAA--C---GCTATTGGT
* * *
5600 TTTAGTGGCATTTTTT-GCATAAACGCCGCTAATGCTATTGGT
1 TTTAGTGGCATTTTTTACCACAAACGCCGCTAACGCTATTGGT
5642 TTTAGTGGC
1 TTTAGTGGC
5651 GTTTGTAATA
Statistics
Matches: 200, Mismatches: 16, Indels: 18
0.85 0.07 0.08
Matches are distributed among these distances:
41 24 0.12
42 103 0.51
43 24 0.12
44 10 0.05
47 33 0.17
48 6 0.03
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (43 bp):
TTTAGTGGCATTTTTTACCACAAACGCCGCTAACGCTATTGGT
Found at i:22265 original size:80 final size:79
Alignment explanation
Indices: 22132--22339 Score: 299
Period size: 80 Copynumber: 2.6 Consensus size: 79
22122 TATAAGTCCT
* * *
22132 TACGGACCTAAGGATATCTTGGGTAGGCCCGAAGGCATATCCTTAGGCTGGTTCCCTTTGCTGTG
1 TACGGACCTAAGGATATCTTGGGTAGGCCC-AAGGTATATCCTTAGGTTGGTTCCCTTAGCTGTG
22197 TGCATAAGGTAACCC
65 TGCATAAGGTAACCC
* *
22212 TACGGACCTAAGGATATCTTGGGTAGGCCCAAAGGTATATCCTTAGGTTGGTTCTCTTAGGTGTG
1 TACGGACCTAAGGATATCTTGGGTAGGCCC-AAGGTATATCCTTAGGTTGGTTCCCTTAGCTGTG
*
22277 TGCTTAAGGTAACCC
65 TGCATAAGGTAACCC
* * * *
22292 TACGGATCTAAGGATGTCCTTGGGTAGACCCAAGGTACATCCTTAGGT
1 TACGGACCTAAGGATAT-CTTGGGTAGGCCCAAGGTATATCCTTAGGT
22340 AGGCTCCCCT
Statistics
Matches: 116, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
80 104 0.90
81 12 0.10
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (79 bp):
TACGGACCTAAGGATATCTTGGGTAGGCCCAAGGTATATCCTTAGGTTGGTTCCCTTAGCTGTGT
GCATAAGGTAACCC
Found at i:25777 original size:22 final size:22
Alignment explanation
Indices: 25734--25777 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
25724 ATTTACTTTA
25734 AATAATTCGTTAGTTTATGTTC
1 AATAATTCGTTAGTTTATGTTC
* *
25756 AATAATTTGTTCGTTTATGTTC
1 AATAATTCGTTAGTTTATGTTC
25778 GGGAATACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.25, C:0.09, G:0.14, T:0.52
Consensus pattern (22 bp):
AATAATTCGTTAGTTTATGTTC
Found at i:25836 original size:14 final size:14
Alignment explanation
Indices: 25819--25848 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
25809 ATTAAATTTA
*
25819 TATTTATGTTCTTT
1 TATTTATATTCTTT
25833 TATTTATATTCTTT
1 TATTTATATTCTTT
25847 TA
1 TA
25849 AGAAATTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.20, C:0.07, G:0.03, T:0.70
Consensus pattern (14 bp):
TATTTATATTCTTT
Found at i:25924 original size:26 final size:26
Alignment explanation
Indices: 25890--25940 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
25880 ATTTTATGTT
* *
25890 TGTTCGTTTATGTACGTTTGTGTTTA
1 TGTTCGTTTACGTACCTTTGTGTTTA
* *
25916 TGTTTGTTTACGTTCCTTTGTGTTT
1 TGTTCGTTTACGTACCTTTGTGTTT
25941 GATTATCATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.08, C:0.10, G:0.22, T:0.61
Consensus pattern (26 bp):
TGTTCGTTTACGTACCTTTGTGTTTA
Found at i:26341 original size:37 final size:37
Alignment explanation
Indices: 26285--26388 Score: 136
Period size: 37 Copynumber: 2.8 Consensus size: 37
26275 CTTTTCGTCC
* *
26285 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
1 TACTAAGATTCAAACTCCTAAAAATAGGATAGAATTA
* *
26322 TGCTAAGATTCAAACTCCTAAAAATAGGATAGAGTTA
1 TACTAAGATTCAAACTCCTAAAAATAGGATAGAATTA
** * *
26359 TACTATTATTTAAACTCCTAAAGATAGGAT
1 TACTAAGATTCAAACTCCTAAAAATAGGAT
26389 CCACAAGCAT
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.31
Consensus pattern (37 bp):
TACTAAGATTCAAACTCCTAAAAATAGGATAGAATTA
Found at i:26855 original size:22 final size:23
Alignment explanation
Indices: 26807--26855 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
26797 ATATGTATAT
*
26807 ATTTAATTATATTTTATTTTTTT
1 ATTTAATTATATTTTATTTTTTC
26830 ATTT-ATTATAATTTT-TTTTTTC
1 ATTTAATTAT-ATTTTATTTTTTC
26852 ATTT
1 ATTT
26856 TTCTTTGCGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 15 0.62
23 9 0.38
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (23 bp):
ATTTAATTATATTTTATTTTTTC
Found at i:26938 original size:21 final size:21
Alignment explanation
Indices: 26912--26961 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
26902 TATTATATTA
26912 TTATTTTTTATCTATGTTTAC
1 TTATTTTTTATCTATGTTTAC
* * * *
26933 TTATTTATTATGTTTTTTTAC
1 TTATTTTTTATCTATGTTTAC
26954 TATATTTT
1 T-TATTTT
26962 CCTAACGTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.20, C:0.06, G:0.04, T:0.70
Consensus pattern (21 bp):
TTATTTTTTATCTATGTTTAC
Found at i:26962 original size:104 final size:99
Alignment explanation
Indices: 26781--27025 Score: 217
Period size: 104 Copynumber: 2.4 Consensus size: 99
26771 ATTTAACCCT
* * * * *
26781 TATTATTTATATGTATATATGTATATATTTAATTATATTTTATTTTTTTATTTATTATAATTTTT
1 TATTA-TTATAT-TATATATAT-TATA-TT-ATTATTTTTTATTTGTTTACTTATTATAATGTTT
* * ** *
26846 TTTTTCATTTTTCTTTGCGTTATAT-TATATTATT-TTTC
61 TTTTACATTTTTCCTAACGTTATATATATA-TATTCTTAC
*
26884 TATTATTATATATATATATATTATATTATTATTTTTTATCTATGTTTACTTATTTATTATGTTTT
1 TATTATTATAT-TATATATATTATATTATTATTTTTTAT-T-TGTTTACTTA-TTATAATGTTTT
26949 TTTACTATATTTTCCTAACGTTATATATATATATTCTTAC
62 TTTAC-AT-TTTTCCTAACGTTATATATATATATTCTTAC
* * *
26989 T-TTATTTTATTTTATATTTTTATGATTATTATTTTTT
1 TATTATTATATTATATA-TATTAT-ATTATTATTTTTT
27026 TAGTTAATAT
Statistics
Matches: 118, Mismatches: 15, Indels: 16
0.79 0.10 0.11
Matches are distributed among these distances:
99 11 0.09
100 3 0.03
101 12 0.10
102 28 0.24
103 12 0.10
104 31 0.26
105 21 0.18
ACGTcount: A:0.27, C:0.05, G:0.03, T:0.65
Consensus pattern (99 bp):
TATTATTATATTATATATATTATATTATTATTTTTTATTTGTTTACTTATTATAATGTTTTTTTA
CATTTTTCCTAACGTTATATATATATATTCTTAC
Found at i:27122 original size:57 final size:53
Alignment explanation
Indices: 26998--27122 Score: 119
Period size: 54 Copynumber: 2.3 Consensus size: 53
26988 CTTTATTTTA
* **
26998 TTTTATATTTTTATGATTATTATTTTTTTAGTTAATATTATATGTATATTTAT
1 TTTTATATTTTTATGATTATTATTTATTTAGTTAATATTATATGTATATACAT
* **
27051 TTTTCAT-TTATTTATTATTATTATTACTATTTAGTATTTTATTATAT-TATACATACAT
1 TTTT-ATATT-TTTATGATTATTATT--TATTTAGT-TAATATTATATGTAT--ATACAT
27109 TTTTATATTTTTAT
1 TTTTATATTTTTAT
27123 ATATATATAT
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
53 6 0.10
54 16 0.28
56 10 0.17
57 16 0.28
58 10 0.17
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (53 bp):
TTTTATATTTTTATGATTATTATTTATTTAGTTAATATTATATGTATATACAT
Found at i:27148 original size:27 final size:27
Alignment explanation
Indices: 27080--27154 Score: 71
Period size: 28 Copynumber: 2.7 Consensus size: 27
27070 ATTATTACTA
*
27080 TTTAGTATTTTATTATATTATACATACAT
1 TTTATTATTTTA-TATA-TATACATACAT
* *
27109 TTT-TATATTTTTATATATATATATATAT
1 TTTAT-TA-TTTTATATATATACATACAT
*
27137 TTTATTATTTTATTTATA
1 TTTATTATTTTATATATA
27155 CTATTTATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
27 10 0.26
28 14 0.36
29 10 0.26
30 5 0.13
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (27 bp):
TTTATTATTTTATATATATACATACAT
Found at i:27177 original size:49 final size:48
Alignment explanation
Indices: 27055--27177 Score: 124
Period size: 49 Copynumber: 2.4 Consensus size: 48
27045 ATTTATTTTT
*
27055 CATTTATTTATTATTATTATTACTATTTAGTATTTTATTATATTATACATA
1 CATTTATTTATT-TTATTA-TA-TATATAGTATTTTATTATATTATACATA
* **
27106 CATTT-TTATATTTTTATATATATATATA-TATTTTATTATTTTATTTATA
1 CATTTATT-TA-TTTTAT-TATATATATAGTATTTTATTATATTATACATA
27155 CTATTTATTTATTTTCATTATAT
1 C-ATTTATTTATTTT-ATTATAT
27178 TTTTAGTTTC
Statistics
Matches: 62, Mismatches: 4, Indels: 14
0.77 0.05 0.17
Matches are distributed among these distances:
49 28 0.45
50 15 0.24
51 15 0.24
52 4 0.06
ACGTcount: A:0.32, C:0.05, G:0.01, T:0.63
Consensus pattern (48 bp):
CATTTATTTATTTTATTATATATATAGTATTTTATTATATTATACATA
Found at i:27298 original size:19 final size:19
Alignment explanation
Indices: 27271--27326 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
27261 TTTTATCTTC
27271 ATTTATTTTATTTTATTCA
1 ATTTATTTTATTTTATTCA
* * *
27290 ATTTCTTTTTTTTTCATCCA
1 ATTTATTTTATTTT-ATTCA
27310 A-TTATTTTATGTTTATT
1 ATTTATTTTAT-TTTATT
27327 ATTATTGGTT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
19 21 0.72
20 8 0.28
ACGTcount: A:0.21, C:0.09, G:0.02, T:0.68
Consensus pattern (19 bp):
ATTTATTTTATTTTATTCA
Found at i:27412 original size:21 final size:21
Alignment explanation
Indices: 27374--27413 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
27364 GTTTTGTTAC
* *
27374 TTTCTTTTATATTATTATTAT
1 TTTCTTTTAAAATATTATTAT
*
27395 TTTCTTTTAAAATCTTATT
1 TTTCTTTTAAAATATTATT
27414 TTTAAGGGTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.07, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTCTTTTAAAATATTATTAT
Found at i:31720 original size:16 final size:17
Alignment explanation
Indices: 31699--31784 Score: 70
Period size: 19 Copynumber: 4.8 Consensus size: 17
31689 ATTCAATCAG
31699 AACAAAAAGAAAA-AAA
1 AACAAAAAGAAAACAAA
*
31715 AACAAAAAAGAAAAGAAGCA
1 AAC-AAAAAGAAAACAA--A
31735 AA-AAAGAAGAAAACAAA
1 AACAAA-AAGAAAACAAA
31752 AGA-AAAAAGAAAGAACAAA
1 A-ACAAAAAG-AA-AACAAA
31771 AATCAAAAAGAAAA
1 AA-CAAAAAGAAAA
31785 AAGGACAAAG
Statistics
Matches: 59, Mismatches: 1, Indels: 18
0.76 0.01 0.23
Matches are distributed among these distances:
16 3 0.05
17 15 0.25
18 14 0.24
19 18 0.31
20 9 0.15
ACGTcount: A:0.80, C:0.07, G:0.12, T:0.01
Consensus pattern (17 bp):
AACAAAAAGAAAACAAA
Found at i:31747 original size:24 final size:22
Alignment explanation
Indices: 31703--31786 Score: 69
Period size: 24 Copynumber: 3.5 Consensus size: 22
31693 AATCAGAACA
*
31703 AAAAGAAAAAAAAACAAAAAAG
1 AAAAGAAAAAAAAACAAAAAAC
* *
31725 AAAAGAAGCAAAAAAGAAGAAAAC
1 AAAAGAA-AAAAAAACAA-AAAAC
*
31749 AAAAGAAAAAAGAAAGAACAAAAATC
1 AAAAG--AAAA-AAA-AACAAAAAAC
31775 AAAAAGAAAAAA
1 -AAAAGAAAAAA
31787 GGACAAAGGA
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
22 7 0.14
23 8 0.16
24 11 0.22
25 5 0.10
26 9 0.18
27 9 0.18
ACGTcount: A:0.81, C:0.06, G:0.12, T:0.01
Consensus pattern (22 bp):
AAAAGAAAAAAAAACAAAAAAC
Found at i:31758 original size:36 final size:34
Alignment explanation
Indices: 31705--31772 Score: 100
Period size: 36 Copynumber: 1.9 Consensus size: 34
31695 TCAGAACAAA
31705 AAGAAAAAAAAACAAAAAAGAAAAGAAGCAAAAAAG
1 AAGAAAAAAAAACAAAAAAG-AAAGAA-CAAAAAAG
* *
31741 AAGAAAACAAAAGAAAAAAGAAAGAACAAAAA
1 AAGAAAAAAAAACAAAAAAGAAAGAACAAAAA
31773 TCAAAAAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 6 0.20
35 6 0.20
36 18 0.60
ACGTcount: A:0.81, C:0.06, G:0.13, T:0.00
Consensus pattern (34 bp):
AAGAAAAAAAAACAAAAAAGAAAGAACAAAAAAG
Found at i:31759 original size:20 final size:19
Alignment explanation
Indices: 31734--31786 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
31724 GAAAAGAAGC
31734 AAAAAAGAAGAAAACAAAAG
1 AAAAAAGAA-AAAACAAAAG
*
31754 AAAAAAGAAAGAACAAAA-
1 AAAAAAGAAAAAACAAAAG
31772 ATCAAAAAGAAAAAA
1 A--AAAAAGAAAAAA
31787 GGACAAAGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 1 0.03
19 8 0.28
20 20 0.69
ACGTcount: A:0.81, C:0.06, G:0.11, T:0.02
Consensus pattern (19 bp):
AAAAAAGAAAAAACAAAAG
Found at i:31765 original size:21 final size:20
Alignment explanation
Indices: 31704--31783 Score: 62
Period size: 20 Copynumber: 4.2 Consensus size: 20
31694 ATCAGAACAA
*
31704 AAAG-AAAAAAA-AACAAA-
1 AAAGAAAAAAAAGAAAAAAG
*
31721 AAAG-AAAAGAAGCAAAAAAG
1 AAAGAAAAAAAAG-AAAAAAG
31741 -AAGAAAACAAAAGAAAAAAG
1 AAAGAAAA-AAAAGAAAAAAG
* **
31761 AAAGAACAAAAATCAAAAAG
1 AAAGAAAAAAAAGAAAAAAG
31781 AAA
1 AAA
31784 AAAGGACAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
17 10 0.20
19 8 0.16
20 23 0.45
21 10 0.20
ACGTcount: A:0.80, C:0.06, G:0.12, T:0.01
Consensus pattern (20 bp):
AAAGAAAAAAAAGAAAAAAG
Found at i:31784 original size:13 final size:13
Alignment explanation
Indices: 31711--31786 Score: 64
Period size: 13 Copynumber: 5.5 Consensus size: 13
31701 CAAAAAGAAA
31711 AAAAAACAAAAAAG
1 AAAAAAC-AAAAAG
31725 AAAAGAAGCAAAAAAG
1 AAAA-AA-C-AAAAAG
31741 AAGAAAAC-AAAAG
1 AA-AAAACAAAAAG
* *
31754 AAAAAAGAAAGAAC
1 AAAAAACAAA-AAG
*
31768 AAAAATCAAAAAG
1 AAAAAACAAAAAG
31781 AAAAAA
1 AAAAAA
31787 GGACAAAGGA
Statistics
Matches: 51, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
12 4 0.08
13 16 0.31
14 14 0.27
15 3 0.06
16 12 0.24
17 2 0.04
ACGTcount: A:0.80, C:0.07, G:0.12, T:0.01
Consensus pattern (13 bp):
AAAAAACAAAAAG
Found at i:31785 original size:7 final size:7
Alignment explanation
Indices: 31711--31787 Score: 59
Period size: 7 Copynumber: 11.0 Consensus size: 7
31701 CAAAAAGAAA
*
31711 AAAAAAC
1 AAAAAAG
31718 AAAAAAG
1 AAAAAAG
31725 AAAAGAAG
1 AAAA-AAG
31733 CAAAAAAG
1 -AAAAAAG
*
31741 AAGAAA-
1 AAAAAAG
*
31747 ACAAAAG
1 AAAAAAG
31754 AAAAAAG
1 AAAAAAG
*
31761 AAAGAA-
1 AAAAAAG
* *
31767 CAAAAAT
1 AAAAAAG
*
31774 CAAAAAG
1 AAAAAAG
31781 AAAAAAG
1 AAAAAAG
31788 GACAAAGGAC
Statistics
Matches: 56, Mismatches: 10, Indels: 8
0.76 0.14 0.11
Matches are distributed among these distances:
6 8 0.14
7 38 0.68
8 6 0.11
9 4 0.07
ACGTcount: A:0.79, C:0.06, G:0.13, T:0.01
Consensus pattern (7 bp):
AAAAAAG
Found at i:31793 original size:16 final size:14
Alignment explanation
Indices: 31699--31786 Score: 58
Period size: 16 Copynumber: 6.1 Consensus size: 14
31689 ATTCAATCAG
31699 AACAAAAAGAAAAAAA
1 AACAAAAAG--AAAAA
31715 AACAAAAAAGAAAAGA
1 AAC-AAAAAGAAAA-A
* *
31731 AGCAAAAAAGAAGAA
1 AAC-AAAAAGAAAAA
31746 AAC-AAAAG--AAA
1 AACAAAAAGAAAAA
*
31757 AA-AGAAAGAACAAA
1 AACAAAAAGAA-AAA
31771 AATCAAAAAGAAAAA
1 AA-CAAAAAGAAAAA
31786 A
1 A
31787 GGACAAAGGA
Statistics
Matches: 58, Mismatches: 6, Indels: 17
0.72 0.07 0.21
Matches are distributed among these distances:
11 8 0.14
13 5 0.09
14 5 0.09
15 11 0.19
16 23 0.40
17 6 0.10
ACGTcount: A:0.81, C:0.07, G:0.11, T:0.01
Consensus pattern (14 bp):
AACAAAAAGAAAAA
Found at i:32472 original size:22 final size:22
Alignment explanation
Indices: 32400--32475 Score: 125
Period size: 22 Copynumber: 3.5 Consensus size: 22
32390 CTACCCCATT
* *
32400 AAACCATTGAGCATCAAATACC
1 AAACCTTTGAGCATCAAATGCC
*
32422 AAACCTATGAGCATCAAATGCC
1 AAACCTTTGAGCATCAAATGCC
32444 AAACCTTTGAGCATCAAATGCC
1 AAACCTTTGAGCATCAAATGCC
32466 AAACCTTTGA
1 AAACCTTTGA
32476 CCAAACATAA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.41, C:0.26, G:0.12, T:0.21
Consensus pattern (22 bp):
AAACCTTTGAGCATCAAATGCC
Found at i:32695 original size:24 final size:24
Alignment explanation
Indices: 32667--32729 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
32657 GGGGCAATAT
32667 TTTCAAAACTTTTAATTAAACATC
1 TTTCAAAACTTTTAATTAAACATC
* *
32691 TTTCAAAACTCTTGATTAAACATC
1 TTTCAAAACTTTTAATTAAACATC
*
32715 TTTCGAAACTCTTTA
1 TTTCAAAACT-TTTA
32730 TTGATATTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
24 31 0.94
25 2 0.06
ACGTcount: A:0.37, C:0.19, G:0.03, T:0.41
Consensus pattern (24 bp):
TTTCAAAACTTTTAATTAAACATC
Found at i:34368 original size:106 final size:106
Alignment explanation
Indices: 33309--34367 Score: 1715
Period size: 106 Copynumber: 10.0 Consensus size: 106
33299 GTCCCATTCA
* * * *
33309 AGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAATAACTTCTCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
33374 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* *
33415 AGACAACGCAAGTTAAACTTCACGGCGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
* *
33480 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCG
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
33521 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
33586 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* *
33627 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
33692 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* *
33733 AGACAACGCAAGTTCAACTTCACGACAAATGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
* * *
33798 CAGAGCCAATTTCAACTTCACATCGAAGGATATTAGACTCG
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
*
33839 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
** * *
33904 TGGAGCCAATTTCAACTCCACAGCGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* *
33945 AGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
*
34010 CAGAGCCAATTTCAACTTCACAAAGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
*
34051 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTTGTTGTCAACAAACAACTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
* *
34116 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCG
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* * * *
34157 AGACAACGCAAGTTCAACTTCACGACAAAGGGACCGCTAGTTGTCAACAAACAATTTCCTAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
* * *
34222 CGGAGCCAATTTCAACTTCACAACAAAGGATATTGGACTCG
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* ** * *
34263 AGACAACACAAGTTCAACTTCAAAACGAAGGGA-CGACTGGTTGTCAACAAACAATTTCCCGATT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAACAAACAACTTCCCAATT
* * * * *
34327 CCATAGCAAATTTCAACTTCACGACGGAGGATATTGGACTC
65 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
34368 GGAACAATGC
Statistics
Matches: 887, Mismatches: 65, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
105 2 0.00
106 885 1.00
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (106 bp):
AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
Found at i:35207 original size:37 final size:37
Alignment explanation
Indices: 35124--35221 Score: 124
Period size: 37 Copynumber: 2.6 Consensus size: 37
35114 GTCCTAGTAA
* * *
35124 GATTCAAACTCCTAAAAATATGATAGAATTTTGCTAG
1 GATTCAAACTCCTAAAAATAGGATAGAATTATACTAG
* *
35161 GATTCAAACTCCTAAAAATAGGATAGAGTTATACTAT
1 GATTCAAACTCCTAAAAATAGGATAGAATTATACTAG
* * *
35198 TATTTAAACTCCTAAAGATAGGAT
1 GATTCAAACTCCTAAAAATAGGAT
35222 CCACAAGCAT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 53 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (37 bp):
GATTCAAACTCCTAAAAATAGGATAGAATTATACTAG
Found at i:35260 original size:13 final size:13
Alignment explanation
Indices: 35242--35276 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
35232 TATAAATAGT
35242 TATTGTAACTCAC
1 TATTGTAACTCAC
35255 TATTGTAACTCAC
1 TATTGTAACTCAC
35268 TATTGTAAC
1 TATTGTAAC
35277 ACATTCGGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.40
Consensus pattern (13 bp):
TATTGTAACTCAC
Found at i:35733 original size:19 final size:18
Alignment explanation
Indices: 35709--35776 Score: 59
Period size: 19 Copynumber: 3.7 Consensus size: 18
35699 CTTTGCGTTA
35709 TATTATATTATTTTTCTAT
1 TATTAT-TTATTTTTCTAT
* * *
35728 TATTATATATATATTATAT
1 TATTATTTAT-TTTTCTAT
35747 TATTATTT-TTTTATCTAT
1 TATTATTTATTTT-TCTAT
35765 GT-TTATTTATTT
1 -TATTATTTATTT
35777 ACTATGTTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
17 2 0.05
18 14 0.36
19 23 0.59
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.68
Consensus pattern (18 bp):
TATTATTTATTTTTCTAT
Found at i:35753 original size:11 final size:11
Alignment explanation
Indices: 35709--35753 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
35699 CTTTGCGTTA
35709 TATTATATTAT
1 TATTATATTAT
* *
35720 TTTTCTATTAT
1 TATTATATTAT
35731 TA-TATA-TA-
1 TATTATATTAT
35739 TATTATATTAT
1 TATTATATTAT
35750 TATT
1 TATT
35754 TTTTTATCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
8 2 0.07
9 6 0.22
10 5 0.19
11 14 0.52
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (11 bp):
TATTATATTAT
Found at i:35772 original size:18 final size:17
Alignment explanation
Indices: 35749--35789 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
35739 TATTATATTA
35749 TTATTTTTTTATCTATGT
1 TTATTTTTTTA-CTATGT
*
35767 TTATTTATTTACTATGT
1 TTATTTTTTTACTATGT
35784 TT-TTTT
1 TTATTTT
35790 ACTATATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 3 0.14
17 8 0.38
18 10 0.48
ACGTcount: A:0.17, C:0.05, G:0.05, T:0.73
Consensus pattern (17 bp):
TTATTTTTTTACTATGT
Found at i:35783 original size:17 final size:18
Alignment explanation
Indices: 35749--35790 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
35739 TATTATATTA
*
35749 TTATTTTTTTATCTATGT
1 TTATTTATTTATCTATGT
35767 TTATTTATTTA-CTATGT
1 TTATTTATTTATCTATGT
*
35784 TTTTTTA
1 TTATTTA
35791 CTATATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.19, C:0.05, G:0.05, T:0.71
Consensus pattern (18 bp):
TTATTTATTTATCTATGT
Found at i:35967 original size:2 final size:2
Alignment explanation
Indices: 35954--35984 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
35944 CATACATTTT
*
35954 TA TA TT 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 T
35985 TATTATTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:36005 original size:17 final size:17
Alignment explanation
Indices: 35956--36014 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
35946 TACATTTTTA
* *
35956 TATTTATATATA-TATA
1 TATTTATTTATACTATT
* * *
35972 TATATATATATATTA-T
1 TATTTATTTATACTATT
35988 TATTTTATTTATACTATT
1 TA-TTTATTTATACTATT
36006 TATTTATTT
1 TATTTATTT
36015 TCATTATAGT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
16 13 0.37
17 19 0.54
18 3 0.09
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.63
Consensus pattern (17 bp):
TATTTATTTATACTATT
Found at i:36015 original size:22 final size:22
Alignment explanation
Indices: 35987--36036 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
35977 ATATATATTA
35987 TTATTTT-ATTTATACTATTTA-T
1 TTATTTTCA-TTATACT-TTTAGT
*
36009 TTATTTTCATTATAGTTTTAGT
1 TTATTTTCATTATACTTTTAGT
36031 TTATTT
1 TTATTT
36037 GCTCTTATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 4 0.16
22 20 0.80
23 1 0.04
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.68
Consensus pattern (22 bp):
TTATTTTCATTATACTTTTAGT
Found at i:36140 original size:19 final size:19
Alignment explanation
Indices: 36113--36168 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
36103 TTTTATCTTC
36113 ATTTATTTTATTTTATTCA
1 ATTTATTTTATTTTATTCA
* * *
36132 ATTTCTTTTTTTTTCATCCA
1 ATTTATTTTATTTT-ATTCA
36152 A-TTATTTTATGTTTATT
1 ATTTATTTTAT-TTTATT
36169 ATTATTGGTT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
19 21 0.72
20 8 0.28
ACGTcount: A:0.21, C:0.09, G:0.02, T:0.68
Consensus pattern (19 bp):
ATTTATTTTATTTTATTCA
Found at i:43320 original size:19 final size:21
Alignment explanation
Indices: 43282--43321 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
43272 CACGAGATAC
*
43282 ATATTTCACATCACTTGAAAA
1 ATATTTCACATCAATTGAAAA
43303 ATATTTC-C-TCAATTGAAAA
1 ATATTTCACATCAATTGAAAA
43322 CCCATAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 1 0.06
21 7 0.39
ACGTcount: A:0.42, C:0.17, G:0.05, T:0.35
Consensus pattern (21 bp):
ATATTTCACATCAATTGAAAA
Found at i:43873 original size:45 final size:45
Alignment explanation
Indices: 43818--44099 Score: 424
Period size: 45 Copynumber: 6.3 Consensus size: 45
43808 ATTATTCATT
*
43818 ATTTCCATTTATGACATCTTTTCATGCCTTTAATGCACCGTTATGC
1 ATTT-CATTTATGACATCCTTTCATGCCTTTAATGCACCGTTATGC
* * * *
43864 ATTTTATTTATGACATCCTTTCATGCATTTTATGCACCATTATGC
1 ATTTCATTTATGACATCCTTTCATGCCTTTAATGCACCGTTATGC
*
43909 ATTTCATTTATGACAT-CTTTTATGCCTTTAATGCACCGTTATGC
1 ATTTCATTTATGACATCCTTTCATGCCTTTAATGCACCGTTATGC
* *
43953 ATTTCATTTATGGCATCAC-TTCATGCCTTTAAAGCACCGTTATGC
1 ATTTCATTTATGACATC-CTTTCATGCCTTTAATGCACCGTTATGC
43998 ATTTCATTTATGACATCCTTTCATGCCTTTAATGCACCGTTATGC
1 ATTTCATTTATGACATCCTTTCATGCCTTTAATGCACCGTTATGC
* * *
44043 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCATTATGA
1 ATTTCATTTATGACATCCTTTCATGCCTTTAATGCACCGTTATGC
*
44088 ATTTCATGTATG
1 ATTTCATTTATG
44100 TAATAAAAAA
Statistics
Matches: 214, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
44 40 0.19
45 169 0.79
46 5 0.02
ACGTcount: A:0.23, C:0.22, G:0.11, T:0.43
Consensus pattern (45 bp):
ATTTCATTTATGACATCCTTTCATGCCTTTAATGCACCGTTATGC
Found at i:44041 original size:134 final size:135
Alignment explanation
Indices: 43818--44099 Score: 431
Period size: 134 Copynumber: 2.1 Consensus size: 135
43808 ATTATTCATT
** * *
43818 ATTTCCATTTATGACATCTTTTCATGCCTTTAATGCACCGTTATGCATTTTATTTATGACATCCT
1 ATTT-CATTTATGACATCACTTCATGCCTTTAAAGCACCGTTATGCATTTCATTTATGACATCCT
* * *
43883 TTCATGCATTTTATGCACCATTATGCATTTCATTTATGACAT-CTTTTATGCCTTTAATGCACCG
65 TTCATGCATTTAATGCACCATTATGCATTTCATTTATGACATCCTTTCATGCCTTTAATGCACCA
*
43947 TTATGC
130 TTATGA
*
43953 ATTTCATTTATGGCATCACTTCATGCCTTTAAAGCACCGTTATGCATTTCATTTATGACATCCTT
1 ATTTCATTTATGACATCACTTCATGCCTTTAAAGCACCGTTATGCATTTCATTTATGACATCCTT
* * *
44018 TCATGCCTTTAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCAT
66 TCATGCATTTAATGCACCATTATGCATTTCATTTATGACATCCTTTCATGCCTTTAATGCACCAT
44083 TATGA
131 TATGA
*
44088 ATTTCATGTATG
1 ATTTCATTTATG
44100 TAATAAAAAA
Statistics
Matches: 133, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
134 93 0.70
135 40 0.30
ACGTcount: A:0.23, C:0.22, G:0.11, T:0.43
Consensus pattern (135 bp):
ATTTCATTTATGACATCACTTCATGCCTTTAAAGCACCGTTATGCATTTCATTTATGACATCCTT
TCATGCATTTAATGCACCATTATGCATTTCATTTATGACATCCTTTCATGCCTTTAATGCACCAT
TATGA
Done.