Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004957.1 Hibiscus syriacus cultivar Beakdansim tig00011144_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: 65761
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:1599 original size:18 final size:18
Alignment explanation
Indices: 1572--1622 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
1562 ATCAACTCTT
*
1572 GTCAAAGTCAACGGGTAGG
1 GTCAAAGTCAACGGGT-CG
*
1591 GTC-AAGTCAATGGGTCG
1 GTCAAAGTCAACGGGTCG
1608 GTCAAAGTCAACGGG
1 GTCAAAGTCAACGGG
1623 ACAGATTGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 4 0.14
18 21 0.75
19 3 0.11
ACGTcount: A:0.29, C:0.18, G:0.35, T:0.18
Consensus pattern (18 bp):
GTCAAAGTCAACGGGTCG
Found at i:2797 original size:261 final size:265
Alignment explanation
Indices: 2435--2966 Score: 966
Period size: 261 Copynumber: 2.0 Consensus size: 265
2425 TTTCAGTTGA
*
2435 ATATTGGTAAATTATGGGGCTAGTCCCTAAACTTCCTAAACTTTTGAAATTAGCCCAAAATTTTT
1 ATATGGGTAAATTATGGGGCTAGTCCCTAAACTTCCTAAACTTTTGAAATTAGCCCAAAATTTTT
2500 AGAAACGTACAGTTTAGTCCTTACAAATCAATTAATTAATTTTAAATAAATTTCAAATAAATTTT
66 AGAAACGTACAGTTTAGTCCTTACAAATCAATTAATTAATTTTAAATAAATTTCAAATAAATTTT
*
2565 TGGGTGTGACATTTTTTGTTTGTGTGACAG-ATCGATGTGTAGGTCCATTGGG-TGTAATCGAGT
131 TGGGTGTGACATTTTTTGTGTGTGTGACAGAATCGATGTGTAGGTCCATTGGGATGTAATCGAGT
*
2628 CGGGAGTTTGAAAACGATAAATTTGAGCTTGTTTCAACCAAA-CAACTTTTAAGTTTGAATACGA
196 CGGGAGTTTGAAAACGATAAATTTGAGCTTGCTTCAACCAAACCAACTTTTAAG-TTGAATACGA
2692 TTTAAG
260 TTTAAG
2698 ATATGGGTAAATTATGGGGCTAGTCCCTAAAC-TCCTAAACTTTTGAAATTAGCCC-AAATTTTT
1 ATATGGGTAAATTATGGGGCTAGTCCCTAAACTTCCTAAACTTTTGAAATTAGCCCAAAATTTTT
*
2761 AGAAACGTATAGTTTAGTCCTTACAAATCAATTAATTAATTTTAAATAAATTTCAAATAAATTTT
66 AGAAACGTACAGTTTAGTCCTTACAAATCAATTAATTAATTTTAAATAAATTTCAAATAAATTTT
2826 TGGGTGTGACATTTTTTGTGTGTGTGACAGAATCGATGTGTAGGTCCATTGGGATGTAATCGAGT
131 TGGGTGTGACATTTTTTGTGTGTGTGACAGAATCGATGTGTAGGTCCATTGGGATGTAATCGAGT
2891 CGGGAGTTTGAAAACGATAAATTTGAGCTTGCTTCAACCAAATGCCAACTTTTAAGTTGAATACG
196 CGGGAGTTTGAAAACGATAAATTTGAGCTTGCTTCAACCAAA--CCAACTTTTAAGTTGAATACG
2956 ATTTAAG
259 ATTTAAG
2963 ATAT
1 ATAT
2967 AATTCAATTA
Statistics
Matches: 260, Mismatches: 4, Indels: 8
0.96 0.01 0.03
Matches are distributed among these distances:
261 101 0.39
262 45 0.17
263 83 0.32
265 20 0.08
266 11 0.04
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (265 bp):
ATATGGGTAAATTATGGGGCTAGTCCCTAAACTTCCTAAACTTTTGAAATTAGCCCAAAATTTTT
AGAAACGTACAGTTTAGTCCTTACAAATCAATTAATTAATTTTAAATAAATTTCAAATAAATTTT
TGGGTGTGACATTTTTTGTGTGTGTGACAGAATCGATGTGTAGGTCCATTGGGATGTAATCGAGT
CGGGAGTTTGAAAACGATAAATTTGAGCTTGCTTCAACCAAACCAACTTTTAAGTTGAATACGAT
TTAAG
Found at i:9045 original size:2 final size:2
Alignment explanation
Indices: 9038--9062 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9028 TTAAAAATTA
9038 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
9063 AATTAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:14788 original size:6 final size:6
Alignment explanation
Indices: 14764--14828 Score: 93
Period size: 6 Copynumber: 11.3 Consensus size: 6
14754 TGGAGCTTGG
14764 AGGAGA A-GAGA A-GATGA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA
1 AGGAGA AGGAGA AGGA-GA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA
14811 AGGAGA A-GAGA A-GAGA AG
1 AGGAGA AGGAGA AGGAGA AG
14829 AAAAAGACAA
Statistics
Matches: 56, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
5 17 0.30
6 37 0.66
7 2 0.04
ACGTcount: A:0.52, C:0.00, G:0.46, T:0.02
Consensus pattern (6 bp):
AGGAGA
Found at i:15938 original size:41 final size:41
Alignment explanation
Indices: 15890--15975 Score: 138
Period size: 41 Copynumber: 2.1 Consensus size: 41
15880 TTACTGACTT
*
15890 ATTGAAGGCTAATAACAAAGGGTCGATATCGATACTCTTTC
1 ATTGAAGGCTAATAACAAAGGGTCGATATCAATACTCTTTC
* *
15931 ATTGAAGGTTGATAACAAAGGGTCGATATCAATACTCTTTC
1 ATTGAAGGCTAATAACAAAGGGTCGATATCAATACTCTTTC
15972 -TTGA
1 ATTGA
15976 GTATCGATAC
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
40 4 0.10
41 38 0.90
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (41 bp):
ATTGAAGGCTAATAACAAAGGGTCGATATCAATACTCTTTC
Found at i:16475 original size:18 final size:18
Alignment explanation
Indices: 16452--16493 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
16442 AACATCAAAA
16452 ACATGCAATCTACCATGG
1 ACATGCAATCTACCATGG
16470 ACATGCAATCTACCATGG
1 ACATGCAATCTACCATGG
16488 ACATGC
1 ACATGC
16494 TTCATAACTT
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:0.33, C:0.29, G:0.17, T:0.21
Consensus pattern (18 bp):
ACATGCAATCTACCATGG
Found at i:18405 original size:24 final size:24
Alignment explanation
Indices: 18373--18434 Score: 115
Period size: 24 Copynumber: 2.6 Consensus size: 24
18363 ATACCGTCCA
18373 AGGAGTATCGATACTACTATATAT
1 AGGAGTATCGATACTACTATATAT
18397 AGGAGTATCGATACTACTATATAT
1 AGGAGTATCGATACTACTATATAT
*
18421 AGTAGTATCGATAC
1 AGGAGTATCGATAC
18435 CAGACCGTTG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (24 bp):
AGGAGTATCGATACTACTATATAT
Found at i:18522 original size:20 final size:20
Alignment explanation
Indices: 18497--18556 Score: 102
Period size: 20 Copynumber: 3.0 Consensus size: 20
18487 ACCAAAGGAG
18497 TAGTATCGGTACTACATAGA
1 TAGTATCGGTACTACATAGA
*
18517 TAGTATCGGTACTACATAGG
1 TAGTATCGGTACTACATAGA
18537 TAGTATCGGTACTACTATAG
1 TAGTATCGGTACTAC-ATAG
18557 TGTATGGTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
20 34 0.89
21 4 0.11
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.32
Consensus pattern (20 bp):
TAGTATCGGTACTACATAGA
Found at i:20700 original size:2 final size:2
Alignment explanation
Indices: 20693--20728 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
20683 ATGGAAAACA
20693 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20729 TCAAAATAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21271 original size:20 final size:20
Alignment explanation
Indices: 21246--21319 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
21236 TCGATAAGAA
*
21246 TAGTATCGATACTAGGCTAG
1 TAGTATCGATACTAAGCTAG
* *
21266 TAGTATCGATACCAAGCAAGAG
1 TAGTATCGATACTAAGC--TAG
* *
21288 TAGTATCGATGCTATG-TGAG
1 TAGTATCGATACTAAGCT-AG
21308 TAGTATCGATAC
1 TAGTATCGATAC
21320 CAAGTGCACA
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
20 28 0.65
22 15 0.35
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.28
Consensus pattern (20 bp):
TAGTATCGATACTAAGCTAG
Found at i:21274 original size:42 final size:42
Alignment explanation
Indices: 21241--21323 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 42
21231 GATACTCGAT
21241 AAGAATAGTATCGATACTAGGCT-AGTAGTATCGATACCAAGC
1 AAGAATAGTATCGATACTAGG-TGAGTAGTATCGATACCAAGC
* * *
21283 AAGAGTAGTATCGATGCTATGTGAGTAGTATCGATACCAAG
1 AAGAATAGTATCGATACTAGGTGAGTAGTATCGATACCAAG
21324 TGCACAAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 1 0.03
42 36 0.97
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.25
Consensus pattern (42 bp):
AAGAATAGTATCGATACTAGGTGAGTAGTATCGATACCAAGC
Found at i:27110 original size:20 final size:21
Alignment explanation
Indices: 27085--27125 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
27075 AACCAAAGGA
27085 GTAGTATCGGTACTAC-ATAG
1 GTAGTATCGGTACTACTATAG
27105 GTAGTATCGGTACTACTATAG
1 GTAGTATCGGTACTACTATAG
27126 TGTATAGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (21 bp):
GTAGTATCGGTACTACTATAG
Found at i:37961 original size:17 final size:17
Alignment explanation
Indices: 37939--37974 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
37929 ATGGATGAGG
37939 GTCATAATGTGCAATGA
1 GTCATAATGTGCAATGA
37956 GTCATAATGTGCAATGA
1 GTCATAATGTGCAATGA
37973 GT
1 GT
37975 GCTGCAACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.31
Consensus pattern (17 bp):
GTCATAATGTGCAATGA
Found at i:38773 original size:24 final size:24
Alignment explanation
Indices: 38745--38806 Score: 97
Period size: 24 Copynumber: 2.6 Consensus size: 24
38735 TGTTCATTTA
* *
38745 CGTTCGTTAATGTTCGTTTACTTT
1 CGTTCATTTATGTTCGTTTACTTT
*
38769 TGTTCATTTATGTTCGTTTACTTT
1 CGTTCATTTATGTTCGTTTACTTT
38793 CGTTCATTTATGTT
1 CGTTCATTTATGTT
38807 TAGTTTAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.13, C:0.15, G:0.15, T:0.58
Consensus pattern (24 bp):
CGTTCATTTATGTTCGTTTACTTT
Found at i:44073 original size:31 final size:30
Alignment explanation
Indices: 44016--44082 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 30
44006 TTTTATAGTA
*
44016 TTTAGATAAATTTATTAATAAATTTATTATCT
1 TTTA-ATAAATTTAATAATAAATTTA-TATCT
* *
44048 TTTAATAAATTTAATAAGT-ATTTTATATTT
1 TTTAATAAATTTAATAA-TAAATTTATATCT
44078 TTTAA
1 TTTAA
44083 ACTTTATTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
30 9 0.29
31 17 0.55
32 5 0.16
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.55
Consensus pattern (30 bp):
TTTAATAAATTTAATAATAAATTTATATCT
Found at i:44850 original size:19 final size:21
Alignment explanation
Indices: 44809--44858 Score: 70
Period size: 19 Copynumber: 2.5 Consensus size: 21
44799 TAAAGTTTAA
44809 AAAATTA-TAAAATACTTATT
1 AAAATTATTAAAATACTTATT
*
44829 AAATTTATTAAAATA-TTA-T
1 AAAATTATTAAAATACTTATT
44848 AAAATTATTAA
1 AAAATTATTAA
44859 TAAATATATC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 11 0.41
20 9 0.33
21 7 0.26
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
AAAATTATTAAAATACTTATT
Found at i:44874 original size:31 final size:31
Alignment explanation
Indices: 44805--44872 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
44795 TCAATAAAGT
* * *
44805 TTAAAAAATTATAAAA-TACTTATTAAATTTA
1 TTAAAATATTATAAAATTA-TTAATAAATATA
44836 TTAAAATATTATAAAATTATTAATAAATATA
1 TTAAAATATTATAAAATTATTAATAAATATA
44867 TCTAAA
1 T-TAAA
44873 TACTCTAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 26 0.81
32 6 0.19
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (31 bp):
TTAAAATATTATAAAATTATTAATAAATATA
Found at i:45337 original size:22 final size:24
Alignment explanation
Indices: 45290--45338 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 24
45280 CATACGAACT
45290 ATTTACATAAAATAATAACTTTTA
1 ATTTACATAAAATAATAACTTTTA
* *
45314 ATTTA-ATAAAA-ATTAATTTTTA
1 ATTTACATAAAATAATAACTTTTA
45336 ATT
1 ATT
45339 AGATTAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 12 0.52
23 6 0.26
24 5 0.22
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (24 bp):
ATTTACATAAAATAATAACTTTTA
Found at i:51348 original size:24 final size:24
Alignment explanation
Indices: 51321--51411 Score: 87
Period size: 24 Copynumber: 3.8 Consensus size: 24
51311 AAATGGAGAT
*
51321 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAAAACAGAATCCAG
* * * *
51345 ATCATATATCAGAACAAAATCCAG
1 ATCAGAAATCAAAACAGAATCCAG
* *
51369 ATCA-AAATCAGAACAGAATCCAT
1 ATCAGAAATCAAAACAGAATCCAG
*
51392 ATCATG-TATCAAAACAGAAT
1 ATCA-GAAATCAAAACAGAAT
51412 TTAAATCGAA
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
23 20 0.36
24 35 0.64
ACGTcount: A:0.52, C:0.19, G:0.10, T:0.20
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATCCAG
Found at i:55671 original size:48 final size:48
Alignment explanation
Indices: 55567--55675 Score: 121
Period size: 48 Copynumber: 2.3 Consensus size: 48
55557 AAATGGATAT
* * * * *
55567 ATCGGAAATCAAAACAGAATTCAGATCAGATATCAGAATAGAATACAT
1 ATCGGAAATCAGAACAAAATCCAGATCAGATATCAGAACAGAATACAA
* * * *
55615 ATCAGAAATCAGAACAAAATCCATG-TCAGTTATCAGAACATAATTCAA
1 ATCGGAAATCAGAACAAAATCCA-GATCAGATATCAGAACAGAATACAA
55663 ATCGGAAATCAGA
1 ATCGGAAATCAGA
55676 TAAAACATTC
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
48 49 0.98
49 1 0.02
ACGTcount: A:0.49, C:0.17, G:0.14, T:0.21
Consensus pattern (48 bp):
ATCGGAAATCAGAACAAAATCCAGATCAGATATCAGAACAGAATACAA
Found at i:55673 original size:24 final size:24
Alignment explanation
Indices: 55565--55675 Score: 96
Period size: 24 Copynumber: 4.6 Consensus size: 24
55555 GTAAATGGAT
* *
55565 ATATCGGAAATCAAAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
* * * *
55589 AGATCAGATATCAGAATAGAATAC
1 ATATCAGAAATCAGAACAGAATTC
* *
55613 ATATCAGAAATCAGAACAAAATCC
1 ATATCAGAAATCAGAACAGAATTC
* ** *
55637 ATGTCAGTTATCAGAACATAATTC
1 ATATCAGAAATCAGAACAGAATTC
* *
55661 AAATCGGAAATCAGA
1 ATATCAGAAATCAGA
55676 TAAAACATTC
Statistics
Matches: 66, Mismatches: 21, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 66 1.00
ACGTcount: A:0.49, C:0.16, G:0.14, T:0.22
Consensus pattern (24 bp):
ATATCAGAAATCAGAACAGAATTC
Found at i:57709 original size:18 final size:19
Alignment explanation
Indices: 57682--57718 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
57672 GGGTTAACGA
57682 TCAACAGTCAAC-GGTCGG
1 TCAACAGTCAACGGGTCGG
*
57700 TCAACGGTCAACGGGTCGG
1 TCAACAGTCAACGGGTCGG
57719 ATATGGTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.24, C:0.27, G:0.32, T:0.16
Consensus pattern (19 bp):
TCAACAGTCAACGGGTCGG
Found at i:57774 original size:19 final size:19
Alignment explanation
Indices: 57750--57797 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
57740 TCAGGTTAGT
57750 TGGTTCAGACTGGTTCAGC
1 TGGTTCAGACTGGTTCAGC
57769 TGGTTCAGACTGGTTCAGC
1 TGGTTCAGACTGGTTCAGC
* *
57788 CGGTTTAGAC
1 TGGTTCAGAC
57798 CGGTCTGGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.17, C:0.21, G:0.31, T:0.31
Consensus pattern (19 bp):
TGGTTCAGACTGGTTCAGC
Found at i:57792 original size:9 final size:10
Alignment explanation
Indices: 57750--57786 Score: 67
Period size: 10 Copynumber: 3.8 Consensus size: 10
57740 TCAGGTTAGT
57750 TGGTTCAGAC
1 TGGTTCAGAC
57760 TGGTTCAG-C
1 TGGTTCAGAC
57769 TGGTTCAGAC
1 TGGTTCAGAC
57779 TGGTTCAG
1 TGGTTCAG
57787 CCGGTTTAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 9 0.35
10 17 0.65
ACGTcount: A:0.16, C:0.19, G:0.32, T:0.32
Consensus pattern (10 bp):
TGGTTCAGAC
Found at i:58517 original size:58 final size:58
Alignment explanation
Indices: 58449--58576 Score: 238
Period size: 58 Copynumber: 2.2 Consensus size: 58
58439 TGGTCTGGCA
* *
58449 ACTTTGTAATTTTACAATTTAATCCTCAATTTCTTCTAAAATACCATTTAAAATCAAT
1 ACTTTATAATTTTACAATTTAATCCTCAATTTCTTCCAAAATACCATTTAAAATCAAT
58507 ACTTTATAATTTTACAATTTAATCCTCAATTTCTTCCAAAATACCATTTAAAATCAAT
1 ACTTTATAATTTTACAATTTAATCCTCAATTTCTTCCAAAATACCATTTAAAATCAAT
58565 ACTTTATAATTT
1 ACTTTATAATTT
58577 CTAAAATCGA
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 68 1.00
ACGTcount: A:0.38, C:0.17, G:0.01, T:0.44
Consensus pattern (58 bp):
ACTTTATAATTTTACAATTTAATCCTCAATTTCTTCCAAAATACCATTTAAAATCAAT
Found at i:58555 original size:29 final size:29
Alignment explanation
Indices: 58465--58557 Score: 84
Period size: 29 Copynumber: 3.2 Consensus size: 29
58455 TAATTTTACA
58465 ATTTAATCCTCAATTTCTTCTAAAATACC
1 ATTTAATCCTCAATTTCTTCTAAAATACC
** * * *
58494 ATTTAA-AATCAA-TACTT-TATAATTTTACA
1 ATTTAATCCTCAATTTCTTCTA-AA--ATACC
*
58523 ATTTAATCCTCAATTTCTTCCAAAATACC
1 ATTTAATCCTCAATTTCTTCTAAAATACC
58552 ATTTAA
1 ATTTAA
58558 AATCAATACT
Statistics
Matches: 47, Mismatches: 11, Indels: 12
0.67 0.16 0.17
Matches are distributed among these distances:
26 2 0.04
27 6 0.13
28 4 0.09
29 24 0.51
30 4 0.09
31 6 0.13
32 1 0.02
ACGTcount: A:0.39, C:0.19, G:0.00, T:0.42
Consensus pattern (29 bp):
ATTTAATCCTCAATTTCTTCTAAAATACC
Found at i:61269 original size:35 final size:35
Alignment explanation
Indices: 61194--61278 Score: 102
Period size: 35 Copynumber: 2.4 Consensus size: 35
61184 TTTAAAAGTT
*
61194 ATGTTACTTCACCAAAGGATTCCTTTTCAAGAGTC
1 ATGTTGCTTCACCAAAGGATTCCTTTTCAAGAGTC
* * *
61229 GTGTTGTTTCACCAAATGATTCC-TTTCAA-ATGGTC
1 ATGTTGCTTCACCAAAGGATTCCTTTTCAAGA--GTC
61264 ATGTTGCTTCACCAA
1 ATGTTGCTTCACCAA
61279 GAAGTAAATC
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
33 1 0.02
34 6 0.14
35 35 0.83
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.36
Consensus pattern (35 bp):
ATGTTGCTTCACCAAAGGATTCCTTTTCAAGAGTC
Found at i:63663 original size:38 final size:38
Alignment explanation
Indices: 63636--63721 Score: 140
Period size: 38 Copynumber: 2.3 Consensus size: 38
63626 GATGCAATTA
63636 GTATCGATACTGAAGTGGGTATC-ATACTAAGAGAAAAG
1 GTATCGATACTGAAGTGGGTATCAATACT-AGAGAAAAG
63674 GTATCGATACTGAAGTGGGTATCAATACTA-AGAGAAAG
1 GTATCGATACTGAAGTGGGTATCAATACTAGAGA-AAAG
63712 GTATCGATAC
1 GTATCGATAC
63722 CATGGATTCC
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
37 3 0.07
38 38 0.83
39 5 0.11
ACGTcount: A:0.38, C:0.12, G:0.26, T:0.24
Consensus pattern (38 bp):
GTATCGATACTGAAGTGGGTATCAATACTAGAGAAAAG
Found at i:63678 original size:20 final size:20
Alignment explanation
Indices: 63653--63721 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
63643 TACTGAAGTG
63653 GGTATC-ATACTAAGAGAAAA
1 GGTATCGATACTAAGAG-AAA
*
63673 GGTATCGATACTGAAGTG---
1 GGTATCGATACT-AAGAGAAA
*
63691 GGTATCAATACTAAGAGAAA
1 GGTATCGATACTAAGAGAAA
63711 GGTATCGATAC
1 GGTATCGATAC
63722 CATGGATTCC
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
17 4 0.10
18 11 0.28
20 16 0.40
21 5 0.12
22 4 0.10
ACGTcount: A:0.41, C:0.12, G:0.25, T:0.23
Consensus pattern (20 bp):
GGTATCGATACTAAGAGAAA
Found at i:63696 original size:18 final size:18
Alignment explanation
Indices: 63636--63702 Score: 66
Period size: 18 Copynumber: 3.6 Consensus size: 18
63626 GATGCAATTA
63636 GTATCGATACTGAAGTGG
1 GTATCGATACTGAAGTGG
*
63654 GTATC-ATACT-AAGAGAAAAG
1 GTATCGATACTGAAGTG----G
63674 GTATCGATACTGAAGTGG
1 GTATCGATACTGAAGTGG
*
63692 GTATCAATACT
1 GTATCGATACT
63703 AAGAGAAAGG
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
16 4 0.10
17 5 0.12
18 16 0.40
20 6 0.15
21 5 0.12
22 4 0.10
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.27
Consensus pattern (18 bp):
GTATCGATACTGAAGTGG
Done.