Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004502.1 Hibiscus syriacus cultivar Beakdansim tig00009930_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: 55373
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:7933 original size:16 final size:16
Alignment explanation
Indices: 7895--7956 Score: 65
Period size: 16 Copynumber: 4.0 Consensus size: 16
7885 TTTATAACTG
7895 TAAAAAAA-TAAA-AA
1 TAAAAAAATTAAATAA
** *
7909 TAATTAAATAAAATAA
1 TAAAAAAATTAAATAA
7925 TAAAAAAATTAAATAA
1 TAAAAAAATTAAATAA
* *
7941 TACAATAATTAAATAA
1 TAAAAAAATTAAATAA
7957 AATACTAACA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
14 6 0.16
15 3 0.08
16 29 0.76
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.26
Consensus pattern (16 bp):
TAAAAAAATTAAATAA
Found at i:7947 original size:21 final size:22
Alignment explanation
Indices: 7895--7948 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
7885 TTTATAACTG
*
7895 TAAAAAAATAAAAATAATTAAA
1 TAAAACAATAAAAATAATTAAA
*
7917 TAAAATAATAAAAA-AATTAAA
1 TAAAACAATAAAAATAATTAAA
*
7938 TAATACAATAA
1 TAAAACAATAA
7949 TTAAATAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 16 0.55
22 13 0.45
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (22 bp):
TAAAACAATAAAAATAATTAAA
Found at i:7949 original size:37 final size:35
Alignment explanation
Indices: 7900--7970 Score: 106
Period size: 37 Copynumber: 2.0 Consensus size: 35
7890 AACTGTAAAA
7900 AAATAAAAATAATTAAATAAAATAATAAAAAAATT
1 AAATAAAAATAATTAAATAAAATAATAAAAAAATT
* *
7935 AAATAATACAATAATTAAATAAAATACTAACAAAAT
1 AAATAA-A-AATAATTAAATAAAATAATAAAAAAAT
7971 ATGATTAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 6 0.19
36 1 0.03
37 25 0.78
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.25
Consensus pattern (35 bp):
AAATAAAAATAATTAAATAAAATAATAAAAAAATT
Found at i:8753 original size:25 final size:23
Alignment explanation
Indices: 8726--8807 Score: 71
Period size: 25 Copynumber: 3.5 Consensus size: 23
8716 TTTTTTAAAA
8726 TTTATTTTTTTTACTTTTTATTTT
1 TTTATTTTTTTTACTTTTT-TTTT
* **
8750 ATTTCATGTTTTTT-C--TTCGTTT
1 -TTT-ATTTTTTTTACTTTTTTTTT
8772 TTTATTTTTTTTACATTTTTTTATT
1 TTTATTTTTTTTAC-TTTTTTT-TT
8797 TTTATTTTTTT
1 TTTATTTTTTT
8808 CCTTTTGATT
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
20 8 0.18
21 4 0.09
22 3 0.07
23 2 0.04
24 3 0.07
25 17 0.38
26 8 0.18
ACGTcount: A:0.12, C:0.06, G:0.02, T:0.79
Consensus pattern (23 bp):
TTTATTTTTTTTACTTTTTTTTT
Found at i:10924 original size:95 final size:95
Alignment explanation
Indices: 10754--11111 Score: 547
Period size: 95 Copynumber: 3.7 Consensus size: 95
10744 AGATTATAAT
10754 ATTATATATATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGGCTTTA
1 ATTATA-ATATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGGCTTTA
10819 TGGATAAGATTCAGCTAGCCTGATAAAGGTG
65 TGGATAAGATTCAGCTAGCCTGATAAAGGTG
* *
10850 ATTATAATATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCTCGGTTTTAT
1 ATTATAATATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGGCTTTAT
10915 GGATAAGATTCAGCTAGCCTGATAAAGGTG
66 GGATAAGATTCAGCTAGCCTGATAAAGGTG
* * ** * * *
10945 ATTATAATATACAATAAAGTTTGAGTTGTCCCTCTAGAGCAATTAATTAAACACCTCGACTTTAT
1 ATTATAATATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGGCTTTAT
* *
11010 TGATAATATTCAGCTAGCCTGATAAAGGTG
66 GGATAAGATTCAGCTAGCCTGATAAAGGTG
* *
11040 ATTATAATAT-CTATACAATGATGTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGGCT
1 ATTATAATATACAATA-AA-G--CTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGGCT
11104 TTATGGAT
62 TTATGGAT
11112 CTAGCTATGC
Statistics
Matches: 238, Mismatches: 20, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
94 4 0.02
95 185 0.78
96 7 0.03
98 42 0.18
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (95 bp):
ATTATAATATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGGCTTTAT
GGATAAGATTCAGCTAGCCTGATAAAGGTG
Found at i:13556 original size:12 final size:12
Alignment explanation
Indices: 13541--13617 Score: 57
Period size: 12 Copynumber: 6.0 Consensus size: 12
13531 TTTTATTCTT
13541 TTTTTTAATTTA
1 TTTTTTAATTTA
13553 TTTTTTAATTT-
1 TTTTTTAATTTA
*
13564 TTTATTTTATTTCA
1 TTT-TTTAATTT-A
**
13578 CGTTTTTTTTCTTTGA
1 ---TTTTTTAATTT-A
13594 TTTTTTAATTTA
1 TTTTTTAATTTA
*
13606 TTTTTTATTTTA
1 TTTTTTAATTTA
13618 CCTTTTTTTC
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
11 3 0.06
12 30 0.57
13 9 0.17
16 8 0.15
17 3 0.06
ACGTcount: A:0.18, C:0.04, G:0.03, T:0.75
Consensus pattern (12 bp):
TTTTTTAATTTA
Found at i:13586 original size:40 final size:40
Alignment explanation
Indices: 13540--13626 Score: 113
Period size: 40 Copynumber: 2.2 Consensus size: 40
13530 CTTTTATTCT
* *
13540 TTTTTTTAATTT-ATTTTTTAATTTTTTATTTTATTTCACG
1 TTTTTTTAATTTGATTTTTTAATTTATT-TTTTATTTCACC
** *
13580 TTTTTTTTCTTTGATTTTTTAATTTATTTTTTATTTTACC
1 TTTTTTTAATTTGATTTTTTAATTTATTTTTTATTTCACC
13620 TTTTTTT
1 TTTTTTT
13627 CCTTTTGATT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
40 27 0.66
41 14 0.34
ACGTcount: A:0.16, C:0.06, G:0.02, T:0.76
Consensus pattern (40 bp):
TTTTTTTAATTTGATTTTTTAATTTATTTTTTATTTCACC
Found at i:13586 original size:41 final size:40
Alignment explanation
Indices: 13538--13626 Score: 117
Period size: 41 Copynumber: 2.2 Consensus size: 40
13528 AGCTTTTATT
*
13538 CTTTTTTTTAATTT-ATTTTTTAATTTTTTATTTTATTTCAC
1 CTTTTTTTT-ATTTGATTTTTTAATTTATT-TTTTATTTCAC
* * *
13579 GTTTTTTTTCTTTGATTTTTTAATTTATTTTTTATTTTAC
1 CTTTTTTTTATTTGATTTTTTAATTTATTTTTTATTTCAC
13619 CTTTTTTT
1 CTTTTTTT
13627 CCTTTTGATT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
40 20 0.48
41 22 0.52
ACGTcount: A:0.16, C:0.07, G:0.02, T:0.75
Consensus pattern (40 bp):
CTTTTTTTTATTTGATTTTTTAATTTATTTTTTATTTCAC
Found at i:13634 original size:41 final size:41
Alignment explanation
Indices: 13552--13649 Score: 121
Period size: 41 Copynumber: 2.4 Consensus size: 41
13542 TTTTTAATTT
* * *
13552 ATTTTTTAATTTTTTATTTTATTTCACGTTTTTTTTCTTTG
1 ATTTTTTAATTTATTATTTTATTTCACCTTTTTTTCCTTTG
*
13593 ATTTTTTAATTTATT-TTTTATTTTACCTTTTTTTCCTTTTG
1 ATTTTTTAATTTATTATTTTATTTCACCTTTTTTTCC-TTTG
*
13634 ATTTATT-A-TTATTATT
1 ATTTTTTAATTTATTATT
13650 ACTATTTTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
39 5 0.10
40 21 0.42
41 24 0.48
ACGTcount: A:0.17, C:0.07, G:0.03, T:0.72
Consensus pattern (41 bp):
ATTTTTTAATTTATTATTTTATTTCACCTTTTTTTCCTTTG
Found at i:13658 original size:33 final size:33
Alignment explanation
Indices: 13596--13659 Score: 78
Period size: 33 Copynumber: 1.9 Consensus size: 33
13586 TTCTTTGATT
*
13596 TTTTAATTTATTTTTTATTTTACCTTTTTTTCC
1 TTTTAATTTATTTATTATTTTACCTTTTTTTCC
*
13629 TTTTGATTTA-TTATTATTATTA-CTATTTTTT
1 TTTTAATTTATTTATTATT-TTACCT-TTTTTT
13660 ATGTTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 9 0.33
33 18 0.67
ACGTcount: A:0.19, C:0.08, G:0.02, T:0.72
Consensus pattern (33 bp):
TTTTAATTTATTTATTATTTTACCTTTTTTTCC
Found at i:13782 original size:13 final size:13
Alignment explanation
Indices: 13764--13788 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13754 TCGAGTTTTT
13764 AAATTTTAATTTA
1 AAATTTTAATTTA
13777 AAATTTTAATTT
1 AAATTTTAATTT
13789 TTCGCAATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
AAATTTTAATTTA
Found at i:16485 original size:2 final size:2
Alignment explanation
Indices: 16478--16506 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
16468 CTGTTCATCT
16478 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
16507 TTTAATTTAA
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:20389 original size:2 final size:2
Alignment explanation
Indices: 20384--20408 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20374 CCCCCCCCCT
20384 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
20409 TAAGAACAAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:34166 original size:19 final size:19
Alignment explanation
Indices: 34142--34181 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
34132 TATTGGAATA
34142 TGCATTCTAGAATATGCAG
1 TGCATTCTAGAATATGCAG
34161 TGCATTCTAGAATATGCAG
1 TGCATTCTAGAATATGCAG
34180 TG
1 TG
34182 TTAACATGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.33
Consensus pattern (19 bp):
TGCATTCTAGAATATGCAG
Found at i:36455 original size:81 final size:81
Alignment explanation
Indices: 36283--37233 Score: 1404
Period size: 81 Copynumber: 11.7 Consensus size: 81
36273 TTATAATTCC
* * * * *
36283 TTTATTCTTTTACCCAAAGGTATTTAAACC-TTCATCTAACTTGCATGATTGACAC-TTGTCTG-
1 TTTA-TCTTTTACTCAACGGTCTTT-AACCGTTCATCTAACTGGCATAATTGACACATT-TCTGC
36345 CAAATGCACAGCTAGGCCA
63 CAAATGCACAGCTAGGCCA
* * *
36364 TTTATCTTTTACTCAATGGTTTTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTACCAA
1 TTTATCTTTTACTCAACGGTCTTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTGCCAA
*
36429 ATGTACAGCTAGGCCA
66 ATGCACAGCTAGGCCA
* * * * *
36445 TTTATCTTTTACTCAACGGTCTTTAATCATTCATCTAACTGGCACAATTGACACCTTTCTACCAA
1 TTTATCTTTTACTCAACGGTCTTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTGCCAA
*
36510 ATGCATAGCTAGGCCA
66 ATGCACAGCTAGGCCA
* * * *
36526 TTTATCTTTTACTCAACGGTCTTTAACCATTCATCTAACTAGCATAATTGTCACCTTTCTGCCAA
1 TTTATCTTTTACTCAACGGTCTTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTGCCAA
* * *
36591 ATACATAGCTAAGCCA
66 ATGCACAGCTAGGCCA
* * * *
36607 TTTATGTTTTACTCAACGGTCTTTAACCGTTCATCTAGCTAGTATAATTGACACATTTCTGCCAA
1 TTTATCTTTTACTCAACGGTCTTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTGCCAA
36672 ATGCACAGCTAGGCCA
66 ATGCACAGCTAGGCCA
* * * * *
36688 TTTATCTTTTATTCAACGGTCTTTAACCGTTCATATAACTGCCATAGTTGACACATTTCTTCCAA
1 TTTATCTTTTACTCAACGGTCTTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTGCCAA
36753 ATGCACAGCTAGGCCA
66 ATGCACAGCTAGGCCA
* * * * *
36769 TTTATCTTTTATTCAACGATCTTTAATCGTTCATCTAACTGGCATAATTGACACCTTTCTACCAA
1 TTTATCTTTTACTCAACGGTCTTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTGCCAA
*
36834 ATGCACAACTAGGCCA
66 ATGCACAGCTAGGCCA
* *
36850 TTTATCTTTTACTCAACGGTCTTTAACCGTTCATCTAACTGGCATAATTAACACCTTTCTGCCAA
1 TTTATCTTTTACTCAACGGTCTTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTGCCAA
36915 ATGCACAGCTAGGCCA
66 ATGCACAGCTAGGCCA
*
36931 TTTATCTTTTACTCAACGGTCTTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTTCCAA
1 TTTATCTTTTACTCAACGGTCTTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTGCCAA
36996 ATGCACAGCTAGGCCA
66 ATGCACAGCTAGGCCA
* * * *
37012 TTTATCTTTTACTCAATGGTCTTTAACCATTTATCTAACTGGCATAATTGACACCTTTCTGCCAA
1 TTTATCTTTTACTCAACGGTCTTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTGCCAA
*
37077 ATGCACAACTAGGCCA
66 ATGCACAGCTAGGCCA
* *
37093 TTTATCTTTTACTCAACTGTCTTTAACCGTTCATCTAACTGGCATAATTGAAACATTTCTGCCAA
1 TTTATCTTTTACTCAACGGTCTTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTGCCAA
37158 ATGCACAGCTAGGCCA
66 ATGCACAGCTAGGCCA
* **
37174 GTTATCTTTTACTCAACAATCTTTAACCGTTCATCTAACTGGCATAATTGACACATTTCT
1 TTTATCTTTTACTCAACGGTCTTTAACCGTTCATCTAACTGGCATAATTGACACATTTCT
37234 AGTAAATGCA
Statistics
Matches: 793, Mismatches: 74, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
79 4 0.01
80 43 0.05
81 746 0.94
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.35
Consensus pattern (81 bp):
TTTATCTTTTACTCAACGGTCTTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTGCCAA
ATGCACAGCTAGGCCA
Found at i:37585 original size:55 final size:54
Alignment explanation
Indices: 37464--37629 Score: 217
Period size: 55 Copynumber: 3.0 Consensus size: 54
37454 GCATATATTT
* * * * *
37464 CCCATACGAAATTAATACACTTCGTATGGATTTCTTAG-TTTACACACATAGTT
1 CCCATACGAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACATAGTG
*
37517 CCCATACGAAAATTCATACACTTAGTATGAATTTATTAGTTTTGCACACATAGTG
1 CCCATACG-AAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACATAGTG
* * *
37572 CCCATACAGAAATTCATACACTTAATATGAATTTCTTAGTTTTTGCACGCTTAGTG
1 CCCATAC-GAAATTCATACACTTAGTATGAATTTCTTAG-TTTTGCACACATAGTG
37628 CC
1 CC
37630 ATTTGGTAAT
Statistics
Matches: 99, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
53 8 0.08
54 26 0.26
55 48 0.48
56 17 0.17
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (54 bp):
CCCATACGAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACATAGTG
Found at i:40869 original size:3 final size:3
Alignment explanation
Indices: 40863--40938 Score: 129
Period size: 3 Copynumber: 25.7 Consensus size: 3
40853 TAATTTTTTT
40863 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
40911 TAA TAA TAA TAA TAA -AA T-A TAAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TA
40939 TTCAAATGAA
Statistics
Matches: 70, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
2 4 0.06
3 64 0.91
4 2 0.03
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:41610 original size:65 final size:65
Alignment explanation
Indices: 41540--41696 Score: 228
Period size: 65 Copynumber: 2.4 Consensus size: 65
41530 CACACCCATT
*
41540 TCGAATGCATTTTGTGTACCGATGCACA-AGCCATGCATCGATGCACTCTTGAATAT-TTTGAAA
1 TCGAATGCATTTTGTGTACCGATGCACATA-CCATGCATCGATGCACTCCTGAAT-TGTTTGAAA
41603 CA
64 CA
**
41605 TCGAATGCATTTTGTGTACCGATGCACATACCATGCATCGATGCACTCCTGGCTTGTTTGAAACA
1 TCGAATGCATTTTGTGTACCGATGCACATACCATGCATCGATGCACTCCTGAATTGTTTGAAACA
* * *
41670 TCGAATGTAATTAGTGTACCGATGCAC
1 TCGAATGCATTTTGTGTACCGATGCAC
41697 CCCTAGTGTA
Statistics
Matches: 84, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
64 1 0.01
65 82 0.98
66 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (65 bp):
TCGAATGCATTTTGTGTACCGATGCACATACCATGCATCGATGCACTCCTGAATTGTTTGAAACA
Found at i:41705 original size:19 final size:19
Alignment explanation
Indices: 41681--41734 Score: 108
Period size: 19 Copynumber: 2.8 Consensus size: 19
41671 CGAATGTAAT
41681 TAGTGTACCGATGCACCCC
1 TAGTGTACCGATGCACCCC
41700 TAGTGTACCGATGCACCCC
1 TAGTGTACCGATGCACCCC
41719 TAGTGTACCGATGCAC
1 TAGTGTACCGATGCAC
41735 TAAGTCTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.22, C:0.33, G:0.22, T:0.22
Consensus pattern (19 bp):
TAGTGTACCGATGCACCCC
Found at i:43047 original size:32 final size:33
Alignment explanation
Indices: 42998--43070 Score: 80
Period size: 32 Copynumber: 2.3 Consensus size: 33
42988 GTTTGACATG
*
42998 ATATGAT-TAGATAATAAAAAATTAAT-AAATAT
1 ATATGATATAAATAATAAAAAATT-ATGAAATAT
* * *
43030 ATATGATATAAAT-ATAAAACATTTTGAAATTT
1 ATATGATATAAATAATAAAAAATTATGAAATAT
43062 ATATGATAT
1 ATATGATAT
43071 TATATGTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
31 1 0.03
32 30 0.86
33 4 0.11
ACGTcount: A:0.53, C:0.01, G:0.07, T:0.38
Consensus pattern (33 bp):
ATATGATATAAATAATAAAAAATTATGAAATAT
Found at i:44926 original size:21 final size:21
Alignment explanation
Indices: 44902--44943 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
44892 TATTTCAATC
*
44902 TAAACTATTCATTTTAAAATA
1 TAAAATATTCATTTTAAAATA
* *
44923 TAAAATCTTTATTTTAAAATA
1 TAAAATATTCATTTTAAAATA
44944 ATAATTCTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (21 bp):
TAAAATATTCATTTTAAAATA
Found at i:44952 original size:21 final size:21
Alignment explanation
Indices: 44912--44956 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
44902 TAAACTATTC
44912 ATTTTAAAATATAAAATCTTT
1 ATTTTAAAATATAAAATCTTT
*
44933 ATTTTAAAATA-ATAATTCTTT
1 ATTTTAAAATATA-AAATCTTT
44954 ATT
1 ATT
44957 GACTAACGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.51
Consensus pattern (21 bp):
ATTTTAAAATATAAAATCTTT
Found at i:47038 original size:23 final size:23
Alignment explanation
Indices: 46994--47038 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
46984 GTTGATATCT
**
46994 AAAATCTGAATAACATTTAATTG
1 AAAATCTGAATAACATAAAATTG
*
47017 AAAATTTGAATAACATAAAATT
1 AAAATCTGAATAACATAAAATT
47039 TATGACTGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (23 bp):
AAAATCTGAATAACATAAAATTG
Found at i:49268 original size:101 final size:95
Alignment explanation
Indices: 49037--49276 Score: 252
Period size: 96 Copynumber: 2.4 Consensus size: 95
49027 AAATTAGTTA
* * *
49037 AAAAAAAGAAGGAGAATAGTCTCAAATTTAGGGTTAGTGTTTGAGATGAATAATGTCTAAGATTT
1 AAAAAAAGAAGGGGAAGAGTCTCAAATTTAGGGTTAGGGTTTGAGATGAATAATGTCTAAGATTT
* * * *
49102 GGGGGAACAGAAGAAGAATCGATTAAAGAAG
66 CGGGGAACAGAAGAAGAACCAACT-AAGAAG
* *
49133 AATAATAAGAA-GGGAAGAGTCACAAATTTAGGGTTAGGGTTTGAGGATGAATAATGTCTAATAT
1 AA-AAAAAGAAGGGGAAGAGTCTCAAATTTAGGGTTAGGGTTTGA-GATGAATAATGTCT-A-A-
*
49197 TTGGGATTTCGGGGAATAGAAGAAGAACCAACT-AG-AG
61 ----GATTTCGGGGAACAGAAGAAGAACCAACTAAGAAG
* *
49234 AAAAGAAGAAGGGGAAGAGTCTTAAATTTAGGGTTAGAGGTTT
1 AAAAAAAGAAGGGGAAGAGTCTCAAATTTAGGGTTAG-GGTTT
49277 TGATATTAAA
Statistics
Matches: 120, Mismatches: 13, Indels: 16
0.81 0.09 0.11
Matches are distributed among these distances:
96 31 0.26
97 21 0.17
98 1 0.01
99 1 0.01
100 7 0.06
101 28 0.23
102 7 0.06
104 24 0.20
ACGTcount: A:0.41, C:0.05, G:0.29, T:0.25
Consensus pattern (95 bp):
AAAAAAAGAAGGGGAAGAGTCTCAAATTTAGGGTTAGGGTTTGAGATGAATAATGTCTAAGATTT
CGGGGAACAGAAGAAGAACCAACTAAGAAG
Found at i:49488 original size:102 final size:102
Alignment explanation
Indices: 49283--49504 Score: 279
Period size: 103 Copynumber: 2.2 Consensus size: 102
49273 GTTTTGATAT
** * *
49283 TAAAAAATAGGTTAGGTT-AAGGTTTTTGGTGTTTGTAAGGATCAAACGATGGTTTTACGGATAA
1 TAAAAAATAGGTT-GGTTCAAAATTTTTGGTGTTTGTAAGGATCAAAAGATGATTTTACGGATAA
* *
49347 AAAGATGATGAACAAGCTCAAAGTTTTGGGTTTTGATC
65 AAAGATGATGAACAAGCACAAAGTTTTGGGTTTTAATC
* * ** *
49385 TAAAAAAATTGGTTGGTTCAAAATTTTTGGTGTTTGTAAGGATTAAAAGATGATTTTGGGGATGA
1 T-AAAAAATAGGTTGGTTCAAAATTTTTGGTGTTTGTAAGGATCAAAAGATGATTTTACGGATAA
* *
49450 ACA-ATGATGAACATGCA-ACAAGTTTTGGGTTTTAATC
65 AAAGATGATGAACAAGCACA-AAGTTTTGGGTTTTAATC
49487 TAAAAAATAGGTTGGTTC
1 TAAAAAATAGGTTGGTTC
49505 TAGGTTTTGG
Statistics
Matches: 103, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
101 17 0.17
102 35 0.34
103 51 0.50
ACGTcount: A:0.34, C:0.06, G:0.24, T:0.35
Consensus pattern (102 bp):
TAAAAAATAGGTTGGTTCAAAATTTTTGGTGTTTGTAAGGATCAAAAGATGATTTTACGGATAAA
AAGATGATGAACAAGCACAAAGTTTTGGGTTTTAATC
Found at i:49915 original size:19 final size:17
Alignment explanation
Indices: 49884--49918 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 17
49874 TGATCCCTAT
49884 ATATTTTATAATTTATC
1 ATATTTTATAATTTATC
49901 ATATTTTGATAAATTTAT
1 ATATTTT-AT-AATTTAT
49919 TTTTAATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 2 0.12
19 7 0.44
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.57
Consensus pattern (17 bp):
ATATTTTATAATTTATC
Found at i:50021 original size:14 final size:14
Alignment explanation
Indices: 50004--50040 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
49994 TTTTAAATTA
50004 TTAATTTTTTATAT
1 TTAATTTTTTATAT
50018 TTAATTTTTTATAT
1 TTAATTTTTTATAT
50032 TTAATTTTT
1 TTAATTTTT
50041 AATTTATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
TTAATTTTTTATAT
Found at i:50102 original size:31 final size:30
Alignment explanation
Indices: 50059--50185 Score: 123
Period size: 31 Copynumber: 4.0 Consensus size: 30
50049 ATAAAATAAA
50059 ATATGACATATATATGCATGCATCATACATAC
1 ATAT-ACATATATAT-CATGCATCATACATAC
50091 ATATACATATATATC-TGCATCATACTCATAC
1 ATATACATATATATCATGCATCATA--CATAC
*
50122 ATGTACATATATA-CATGCATCATACTCATAC
1 ATATACATATATATCATGCATCATA--CATAC
* *
50153 ATACATCATACATATATACATGCATTATACATA
1 ATATA-CAT--ATATAT-CATGCATCATACATA
50186 TATTCACTAT
Statistics
Matches: 83, Mismatches: 4, Indels: 14
0.82 0.04 0.14
Matches are distributed among these distances:
29 9 0.11
30 2 0.02
31 46 0.55
32 7 0.08
34 9 0.11
36 10 0.12
ACGTcount: A:0.41, C:0.20, G:0.06, T:0.33
Consensus pattern (30 bp):
ATATACATATATATCATGCATCATACATAC
Found at i:50173 original size:19 final size:19
Alignment explanation
Indices: 50125--50188 Score: 87
Period size: 19 Copynumber: 3.5 Consensus size: 19
50115 CTCATACATG
50125 TACATATATACATGCATCA
1 TACATATATACATGCATCA
* *
50144 TAC-T-CATACATACATCA
1 TACATATATACATGCATCA
*
50161 TACATATATACATGCATTA
1 TACATATATACATGCATCA
50180 TACATATAT
1 TACATATAT
50189 TCACTATCTG
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
17 14 0.37
18 2 0.05
19 22 0.58
ACGTcount: A:0.42, C:0.20, G:0.03, T:0.34
Consensus pattern (19 bp):
TACATATATACATGCATCA
Found at i:50292 original size:28 final size:28
Alignment explanation
Indices: 50253--50327 Score: 90
Period size: 22 Copynumber: 2.9 Consensus size: 28
50243 AGACATGATT
50253 CATACATATCTAAGTATAACATATAT--
1 CATACATATCTAAGTATAACATATATAA
*
50279 -A-ACATA-C-AAGTCTAACATATATAA
1 CATACATATCTAAGTATAACATATATAA
*
50303 CACACATATCTAAGTATAACATATA
1 CATACATATCTAAGTATAACATATA
50328 CCTACCATGT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
22 14 0.34
23 1 0.02
24 5 0.12
25 2 0.05
26 5 0.12
27 1 0.02
28 13 0.32
ACGTcount: A:0.49, C:0.17, G:0.04, T:0.29
Consensus pattern (28 bp):
CATACATATCTAAGTATAACATATATAA
Found at i:50353 original size:7 final size:7
Alignment explanation
Indices: 50341--50681 Score: 62
Period size: 7 Copynumber: 49.0 Consensus size: 7
50331 ACCATGTAGT
50341 TATTATA
1 TATTATA
50348 TATTATA
1 TATTATA
*
50355 TAGTATA
1 TATTATA
50362 TA-TATA
1 TATTATA
50368 TTATTATA
1 -TATTATA
50376 GTA-TATA
1 -TATTATA
*
50383 -GTTATA
1 TATTATA
*
50389 AATTATA
1 TATTATA
*
50396 TAGTATA
1 TATTATA
50403 TA-TATA
1 TATTATA
50409 TAGTT-TA
1 TA-TTATA
50416 TA-TATA
1 TATTATA
* *
50422 AACTATA
1 TATTATA
50429 TAATT-TA
1 T-ATTATA
50436 TATTAATA
1 TATT-ATA
* *
50444 AATTATC
1 TATTATA
50451 TAGTTTATCA
1 TA--TTAT-A
*
50461 TAGTATA
1 TATTATA
*
50468 TA-TAGTT
1 TATTA-TA
50475 TA-TATA
1 TATTATA
*
50481 TAATATA
1 TATTATA
*
50488 TAAATATA
1 T-ATTATA
* * *
50496 AACTACA
1 TATTATA
*
50503 TAGTATA
1 TATTATA
50510 TA-TATA
1 TATTATA
50516 GT-TTATA
1 -TATTATA
*
50523 TACTATA
1 TATTATA
50530 T-TGTAT-
1 TAT-TATA
*
50536 TAATA-A
1 TATTATA
50542 TA-TATA
1 TATTATA
50548 TAGTTTATA
1 TA--TTATA
*
50557 TAGTATA
1 TATTATA
*
50564 TAAATATA
1 T-ATTATA
* *
50572 AACTATA
1 TATTATA
50579 TATTATA
1 TATTATA
*
50586 TGGTT-TA
1 T-ATTATA
50593 TA-TATA
1 TATTATA
50599 -ATT-TA
1 TATTATA
*
50604 TGTTAT-
1 TATTATA
50610 TATT-TA
1 TATTATA
*
50616 TATTTTA
1 TATTATA
*
50623 TAATATA
1 TATTATA
50630 TAGTTTATACA
1 TA--TTAT--A
50641 TATTATA
1 TATTATA
50648 TTATTATA
1 -TATTATA
**
50656 CGTT-TA
1 TATTATA
*
50662 CA-TATA
1 TATTATA
*
50668 TATTAAA
1 TATTATA
50675 TATTATA
1 TATTATA
50682 ATTGTTTCAA
Statistics
Matches: 248, Mismatches: 44, Indels: 84
0.66 0.12 0.22
Matches are distributed among these distances:
5 9 0.04
6 56 0.23
7 124 0.50
8 37 0.15
9 17 0.07
10 2 0.01
11 3 0.01
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (7 bp):
TATTATA
Found at i:50363 original size:9 final size:9
Alignment explanation
Indices: 50351--50565 Score: 67
Period size: 9 Copynumber: 25.4 Consensus size: 9
50341 TATTATATAT
50351 TATATAGTA
1 TATATAGTA
50360 TATATA-TA
1 TATATAGTA
50368 T-TATTA-TA
1 TATA-TAGTA
50376 GTATATAGT-
1 -TATATAGTA
*
50385 TATA-AAT-
1 TATATAGTA
50392 TATATAGTA
1 TATATAGTA
50401 TATATA-TA
1 TATATAGTA
*
50409 TAGTTTA-TA
1 TA-TATAGTA
* *
50418 TATAAACTA
1 TATATAGTA
50427 TATA-A-T-
1 TATATAGTA
*
50433 T-TATATTA
1 TATATAGTA
*
50441 -ATA-AAT-
1 TATATAGTA
* *
50447 TATCTAGTT
1 TATATAGTA
50456 TATCATAGTA
1 TAT-ATAGTA
*
50466 TATATAGTT
1 TATATAGTA
50475 TATATA-TAA
1 TATATAGT-A
*
50484 TATATA-AA
1 TATATAGTA
* *
50492 TATAAACTA
1 TATATAGTA
*
50501 CATAGTA-TA
1 TATA-TAGTA
*
50510 TATATAGTT
1 TATATAGTA
*
50519 TATATACTA
1 TATATAGTA
50528 TAT-T-GTA
1 TATATAGTA
*
50535 T-TAATAATA
1 TAT-ATAGTA
*
50544 TATATAGTT
1 TATATAGTA
50553 TATATAGTA
1 TATATAGTA
50562 TATA
1 TATA
50566 AATATAAACT
Statistics
Matches: 156, Mismatches: 26, Indels: 48
0.68 0.11 0.21
Matches are distributed among these distances:
5 2 0.01
6 3 0.02
7 17 0.11
8 35 0.22
9 87 0.56
10 12 0.08
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (9 bp):
TATATAGTA
Found at i:50380 original size:13 final size:12
Alignment explanation
Indices: 50344--50418 Score: 56
Period size: 13 Copynumber: 6.6 Consensus size: 12
50334 ATGTAGTTAT
50344 TATATATTATA-
1 TATATATTATAG
50355 TAGTATA-TATA-
1 TA-TATATTATAG
50366 TAT-TATTATAG
1 TATATATTATAG
50377 TATATAGTTATA-
1 TATATA-TTATAG
*
50389 AAT-TA-TATAG
1 TATATATTATAG
50399 TATATATATATAG
1 TATATAT-TATAG
*
50412 TTTATAT
1 TATATAT
50419 ATAAACTATA
Statistics
Matches: 52, Mismatches: 3, Indels: 16
0.73 0.04 0.23
Matches are distributed among these distances:
9 6 0.12
10 7 0.13
11 15 0.29
12 8 0.15
13 16 0.31
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.51
Consensus pattern (12 bp):
TATATATTATAG
Found at i:50421 original size:13 final size:14
Alignment explanation
Indices: 50346--50418 Score: 64
Period size: 15 Copynumber: 5.4 Consensus size: 14
50336 GTAGTTATTA
50346 TATATTATATAG--
1 TATATTATATAGTT
*
50358 TATA-TATATATTAT
1 TATATTATATAGT-T
*
50372 TATAGTATATAGTT
1 TATATTATATAGTT
* *
50386 ATAAATTATATAGTA
1 -TATATTATATAGTT
50401 TATA-TATATAGTT
1 TATATTATATAGTT
50414 TATAT
1 TATAT
50419 ATAAACTATA
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
11 6 0.12
12 4 0.08
13 12 0.25
14 8 0.17
15 18 0.38
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (14 bp):
TATATTATATAGTT
Found at i:50598 original size:2 final size:2
Alignment explanation
Indices: 50344--50586 Score: 84
Period size: 2 Copynumber: 120.5 Consensus size: 2
50334 ATGTAGTTAT
50344 TA TA TA T- TA TA TA GTA TA TA TA TA T- TA T- TA TA GTA TA TA GT-
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA
* * *
50385 TA TA AA T- TA TA TA GTA TA TA TA TA TA GTT TA TA TA TA AA CTA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA -TA
* * * *
50427 TA TA -A TT TA TA T- TA -A TA AA T- TA TC TA GTT TA TCA TA GTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA T-A TA -TA
* * * *
50466 TA TA TA GTT TA TA TA TA -A TA TA TA AA TA TA AA CTA CA TA GTA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA
* *
50508 TA TA TA TA GTT TA TA TA CTA TA T- TG TA T- TA -A TA -A TA TA TA
1 TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
50548 TA GTT TA TA TA GTA TA TA AA TA TA AA CTA TA TA T- TA TA T
1 TA -TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA T
50587 GGTTTATATA
Statistics
Matches: 178, Mismatches: 31, Indels: 64
0.65 0.11 0.23
Matches are distributed among these distances:
1 15 0.08
2 138 0.78
3 25 0.14
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (2 bp):
TA
Found at i:50668 original size:25 final size:25
Alignment explanation
Indices: 50614--50668 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
50604 TGTTATTATT
* *
50614 TATATTTTATAATATATAGTTTATA
1 TATATTATATAATATATAGTTTACA
* *
50639 CATATTATATTAT-TATACGTTTACA
1 TATATTATATAATATATA-GTTTACA
50664 TATAT
1 TATAT
50669 ATTAAATATT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
24 4 0.17
25 20 0.83
ACGTcount: A:0.38, C:0.05, G:0.04, T:0.53
Consensus pattern (25 bp):
TATATTATATAATATATAGTTTACA
Done.