Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002001.1 Hibiscus syriacus cultivar Beakdansim tig00004093_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: 75626
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:6333 original size:17 final size:18
Alignment explanation
Indices: 6311--6357 Score: 87
Period size: 17 Copynumber: 2.7 Consensus size: 18
6301 TGGCTTTTTG
6311 TTCTTTAATAATTGAA-T
1 TTCTTTAATAATTGAATT
6328 TTCTTTAATAATTGAATT
1 TTCTTTAATAATTGAATT
6346 TTCTTTAATAAT
1 TTCTTTAATAAT
6358 AAAAAATAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 16 0.55
18 13 0.45
ACGTcount: A:0.34, C:0.06, G:0.04, T:0.55
Consensus pattern (18 bp):
TTCTTTAATAATTGAATT
Found at i:11666 original size:19 final size:19
Alignment explanation
Indices: 11642--11680 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
11632 AAGTATAATT
11642 ATATCATTTTTAAAATTTA
1 ATATCATTTTTAAAATTTA
11661 ATATCATTTTTAAAATTTA
1 ATATCATTTTTAAAATTTA
11680 A
1 A
11681 GACTGATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (19 bp):
ATATCATTTTTAAAATTTA
Found at i:11690 original size:19 final size:19
Alignment explanation
Indices: 11644--11692 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
11634 GTATAATTAT
*
11644 ATCATTTTTAAAATTTAAT
1 ATCATTTTTAAAATTTAAG
11663 ATCATTTTTAAAATTTAAG
1 ATCATTTTTAAAATTTAAG
*
11682 ACTGATTTTTA
1 A-TCATTTTTA
11693 GGTATTATGG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 19 0.70
20 8 0.30
ACGTcount: A:0.39, C:0.06, G:0.04, T:0.51
Consensus pattern (19 bp):
ATCATTTTTAAAATTTAAG
Found at i:15919 original size:28 final size:26
Alignment explanation
Indices: 15861--15937 Score: 75
Period size: 26 Copynumber: 2.8 Consensus size: 26
15851 TTTTATATGT
*
15861 TTTCATTAT-AAATTTTATTGATAATTTA
1 TTTCATTTTAAAATTTTA-T-A-AATTTA
*
15889 TTTACTTTTTTAAAATTTTATAAATTTA
1 TTT-C-ATTTTAAAATTTTATAAATTTA
*
15917 TTTCATTTTAAATTTTTATAA
1 TTTCATTTTAAAATTTTATAA
15938 GTTCAATATT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
26 15 0.36
27 1 0.02
28 12 0.29
29 2 0.05
30 4 0.10
31 8 0.19
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.60
Consensus pattern (26 bp):
TTTCATTTTAAAATTTTATAAATTTA
Found at i:19325 original size:20 final size:21
Alignment explanation
Indices: 19300--19341 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
19290 TTTGTTTATT
19300 GCTGAATG-GAACCATTCAGC
1 GCTGAATGTGAACCATTCAGC
*
19320 GCTGAATGTTGAACCGTTCAGC
1 GCTGAATG-TGAACCATTCAGC
19342 ATTCAGCGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
22 11 0.58
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (21 bp):
GCTGAATGTGAACCATTCAGC
Found at i:31721 original size:21 final size:23
Alignment explanation
Indices: 31695--31742 Score: 73
Period size: 21 Copynumber: 2.2 Consensus size: 23
31685 TGCCTGCAAT
31695 ATTAGGTGCAACAATG-TT-AAA
1 ATTAGGTGCAACAATGTTTGAAA
*
31716 ATTAGGTGCAATAATGTTTGAAA
1 ATTAGGTGCAACAATGTTTGAAA
31739 ATTA
1 ATTA
31743 AATGGGTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 15 0.62
22 2 0.08
23 7 0.29
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.33
Consensus pattern (23 bp):
ATTAGGTGCAACAATGTTTGAAA
Found at i:41669 original size:19 final size:17
Alignment explanation
Indices: 41647--41687 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 17
41637 ATTATGAATA
41647 AAAAAATATAAAATTATTT
1 AAAAAATATAAAA--ATTT
*
41666 AAAATATATAAAAATTT
1 AAAAAATATAAAAATTT
41683 AAAAA
1 AAAAA
41688 TTTTGACAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 8 0.40
19 12 0.60
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AAAAAATATAAAAATTT
Found at i:47784 original size:14 final size:12
Alignment explanation
Indices: 47759--47800 Score: 57
Period size: 12 Copynumber: 3.3 Consensus size: 12
47749 ATTAGGTTGA
47759 AAATTAATTTTT
1 AAATTAATTTTT
*
47771 AAATCATGATTTTT
1 AAAT--TAATTTTT
47785 AAATTAATTTTT
1 AAATTAATTTTT
47797 AAAT
1 AAAT
47801 GCTTGATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 15 0.58
14 11 0.42
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (12 bp):
AAATTAATTTTT
Found at i:49970 original size:21 final size:21
Alignment explanation
Indices: 49932--49979 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
49922 ATCGCTACGG
*
49932 TGCTGATATGATAATTCACGAA
1 TGCTGATATGACAATTCAC-AA
*
49954 -GCTGATATGACAGTTCACAA
1 TGCTGATATGACAATTCACAA
49974 TGCTGA
1 TGCTGA
49980 CGTGACAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (21 bp):
TGCTGATATGACAATTCACAA
Found at i:50867 original size:21 final size:20
Alignment explanation
Indices: 50817--50856 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
50807 ACTATGGACA
*
50817 ATCACATTAGCATCGTGAAT
1 ATCACATCAGCATCGTGAAT
50837 ATCACATCAGCATCGTGAAT
1 ATCACATCAGCATCGTGAAT
50857 TGTCACTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.28
Consensus pattern (20 bp):
ATCACATCAGCATCGTGAAT
Found at i:51738 original size:60 final size:60
Alignment explanation
Indices: 51594--51742 Score: 147
Period size: 60 Copynumber: 2.5 Consensus size: 60
51584 ACATCATATG
* ** * ** * *
51594 TCCCCAAACTATTACCCTCATTTTAAATTGGTCCTTAAACTATTGAATATTCCAATTTCA
1 TCCCCAAACTATGAATCTCATTCTAAATTAATCCTTAAACTATTGAACATTACAATTTCA
* * *
51654 TCCCCATACTATGAATCTCATTCTAAATTAATCCTTAAACTTTTGAACATTATAATTTCA
1 TCCCCAAACTATGAATCTCATTCTAAATTAATCCTTAAACTATTGAACATTACAATTTCA
* * * *
51714 -CGCCTAAACTGTGACTCTCTTTCTAAATT
1 TC-CCCAAACTATGAATCTCATTCTAAATT
51743 GGTCTCCAAA
Statistics
Matches: 72, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
59 1 0.01
60 71 0.99
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (60 bp):
TCCCCAAACTATGAATCTCATTCTAAATTAATCCTTAAACTATTGAACATTACAATTTCA
Found at i:55447 original size:3 final size:3
Alignment explanation
Indices: 55439--55468 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
55429 CAAGTCCAAG
55439 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
55469 TATTATTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:55473 original size:3 final size:3
Alignment explanation
Indices: 55467--55528 Score: 110
Period size: 3 Copynumber: 21.3 Consensus size: 3
55457 CATCATCATC
55467 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT ATT ATT A-T ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
55513 ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT A
55529 CTACATTGTT
Statistics
Matches: 57, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 4 0.07
3 53 0.93
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:61703 original size:20 final size:18
Alignment explanation
Indices: 61680--61716 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
61670 TTTTAAAATA
61680 ATTAAAATAATTTATTTATT
1 ATTAAAAT-ATTT-TTTATT
61700 ATTAAAATATTTTTTAT
1 ATTAAAATATTTTTTAT
61717 AATTTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 4 0.24
20 8 0.47
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTAAAATATTTTTTATT
Found at i:61747 original size:26 final size:26
Alignment explanation
Indices: 61694--61749 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
61684 AAATAATTTA
* **
61694 TTTATTATTAAAATATTTTTTATAAT
1 TTTATTAATAAAATATTTGGTATAAT
61720 TTTATTAATAAATATATTTGGTAT-AT
1 TTTATTAATAAA-ATATTTGGTATAAT
61746 TTTA
1 TTTA
61750 CTGAAATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 17 0.65
27 9 0.35
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.59
Consensus pattern (26 bp):
TTTATTAATAAAATATTTGGTATAAT
Found at i:61893 original size:24 final size:26
Alignment explanation
Indices: 61866--61922 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 26
61856 TTAGATTATT
61866 ATATTAAT-ATTA-AAT-ATTTAAATA
1 ATATTAATCATTATAATAATTT-AATA
*
61890 ATATTATTCATTATTAATAATTTAATA
1 ATATTAATCATTA-TAATAATTTAATA
61917 ATATTA
1 ATATTA
61923 TTTCAGTGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 7 0.25
25 4 0.14
27 13 0.46
28 4 0.14
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (26 bp):
ATATTAATCATTATAATAATTTAATA
Found at i:61962 original size:24 final size:24
Alignment explanation
Indices: 61884--61962 Score: 68
Period size: 27 Copynumber: 3.0 Consensus size: 24
61874 ATTAAATATT
61884 TAAATAATATTATTCATTATTAATAA
1 TAAATAATATTATT--TTATTAATAA
* * *
61910 TTTAATAATATTATTTCAGTGAAATTAA
1 -TAAATAATATTATTTTA-T-TAA-TAA
*
61938 TAAATAATATAATTTTATTAATAA
1 TAAATAATATTATTTTATTAATAA
61962 T
1 T
61963 TTATTATATA
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
24 4 0.10
25 4 0.10
26 2 0.05
27 29 0.69
28 3 0.07
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.47
Consensus pattern (24 bp):
TAAATAATATTATTTTATTAATAA
Found at i:62008 original size:52 final size:52
Alignment explanation
Indices: 61884--62076 Score: 126
Period size: 53 Copynumber: 3.6 Consensus size: 52
61874 ATTAAATATT
* ** * *
61884 TAAATAATATTATTCATTATTAATAATTTAATAATATTATTTCAGTGAAATTAA
1 TAAATAATA-TAAT-ATTATTAATAATTTAATAATATTATTAAAATAAAATTAA
* *
61938 TAAATAATATAATTTTATTAATAATTTATTATATATTATTAAAATAAAATATAA
1 TAAATAATATAATATTATTAATAATTTAATA-ATATTATTAAAATAAAAT-TAA
* * * * ** *
61992 T-AAT-ATCTTATATTATT-ATAATATAATTGATTATT-TTATTATAATATTAA
1 TAAATAATATAATATTATTAATAATTTAA-T-AATATTATTAAAATAAAATTAA
* *
62042 AAATATAATATTATATTATT-ATAAATATTAATAAT
1 TAA-ATAATATAATATTATTAAT-AAT-TTAATAAT
62077 CTATTTTAAG
Statistics
Matches: 110, Mismatches: 20, Indels: 19
0.74 0.13 0.13
Matches are distributed among these distances:
50 3 0.03
51 17 0.15
52 33 0.30
53 37 0.34
54 17 0.15
55 3 0.03
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (52 bp):
TAAATAATATAATATTATTAATAATTTAATAATATTATTAAAATAAAATTAA
Found at i:62056 original size:22 final size:23
Alignment explanation
Indices: 62028--62074 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
62018 TTGATTATTT
62028 TATTATAATATTAAAAATA-TAA
1 TATTATAATATTAAAAATATTAA
* *
62050 TATTATATTATTATAAATATTAA
1 TATTATAATATTAAAAATATTAA
62073 TA
1 TA
62075 ATCTATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TATTATAATATTAAAAATATTAA
Found at i:62081 original size:23 final size:22
Alignment explanation
Indices: 62031--62085 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
62021 ATTATTTTAT
* *
62031 TATAATATTAAAAATATAATAT
1 TATATTATTAAAAATATAATAA
*
62053 TATATTATTATAAATATTAATAA
1 TATATTATTAAAAATA-TAATAA
*
62076 TCTATT-TTAA
1 TATATTATTAA
62086 GTATTTTAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 17 0.63
23 10 0.37
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
TATATTATTAAAAATATAATAA
Found at i:64700 original size:23 final size:24
Alignment explanation
Indices: 64660--64713 Score: 92
Period size: 23 Copynumber: 2.3 Consensus size: 24
64650 CAATGATTAA
64660 ATGTAAATTAATATAGTTTAATTT
1 ATGTAAATTAATATAGTTTAATTT
64684 ATGTAAATT-ATATAGTTTAATTT
1 ATGTAAATTAATATAGTTTAATTT
*
64707 AGGTAAA
1 ATGTAAA
64714 GAAAAAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 20 0.69
24 9 0.31
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (24 bp):
ATGTAAATTAATATAGTTTAATTT
Found at i:64982 original size:23 final size:23
Alignment explanation
Indices: 64956--65019 Score: 110
Period size: 23 Copynumber: 2.8 Consensus size: 23
64946 TTTAATTGAT
*
64956 AATTTAAATAACATTTGATCTAA
1 AATTTGAATAACATTTGATCTAA
*
64979 AATTTGAATAACATTTTATCTAA
1 AATTTGAATAACATTTGATCTAA
65002 AATTTGAATAACATTTGA
1 AATTTGAATAACATTTGA
65020 GTTATTCAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.45, C:0.08, G:0.06, T:0.41
Consensus pattern (23 bp):
AATTTGAATAACATTTGATCTAA
Found at i:65019 original size:11 final size:11
Alignment explanation
Indices: 64957--65019 Score: 54
Period size: 11 Copynumber: 5.5 Consensus size: 11
64947 TTAATTGATA
*
64957 ATTTAAATAAC
1 ATTTGAATAAC
* *
64968 ATTTGATCTAAA
1 ATTTGA-ATAAC
64980 ATTTGAATAAC
1 ATTTGAATAAC
* * *
64991 ATTTTATCTAAA
1 ATTTGA-ATAAC
65003 ATTTGAATAAC
1 ATTTGAATAAC
65014 ATTTGA
1 ATTTGA
65020 GTTATTCAAG
Statistics
Matches: 39, Mismatches: 11, Indels: 4
0.72 0.20 0.07
Matches are distributed among these distances:
11 22 0.56
12 17 0.44
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.41
Consensus pattern (11 bp):
ATTTGAATAAC
Found at i:65791 original size:15 final size:15
Alignment explanation
Indices: 65773--65823 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
65763 AACTATATAC
65773 TATATTAATATAAAT
1 TATATTAATATAAAT
*
65788 TATAGTTAAGAT-AAT
1 TATA-TTAATATAAAT
* *
65803 TAACATTAATATAAAC
1 T-ATATTAATATAAAT
65819 TATAT
1 TATAT
65824 AGTATATTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
15 17 0.61
16 11 0.39
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (15 bp):
TATATTAATATAAAT
Found at i:65839 original size:53 final size:56
Alignment explanation
Indices: 65759--65900 Score: 175
Period size: 53 Copynumber: 2.6 Consensus size: 56
65749 TAGTATAGTT
* *
65759 TATAAACTATATACTATATTAATATAAATTATAGTTAAGATAATTA-ACA-T-TAA-
1 TATAAACTATATAGTATATTAATATAAACTATAGTTAAGA-AATTATACACTATAAG
* * *
65812 TATAAACTATATAGTATATTAATATAAACTATAGTTTATAAATTATATACTATAAG
1 TATAAACTATATAGTATATTAATATAAACTATAGTTAAGAAATTATACACTATAAG
* *
65868 TTATAAACTATATAGTACACTAATATAAACTAT
1 -TATAAACTATATAGTATATTAATATAAACTAT
65901 TGTTTATAAA
Statistics
Matches: 77, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
52 5 0.06
53 38 0.49
54 1 0.01
55 3 0.04
57 30 0.39
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.39
Consensus pattern (56 bp):
TATAAACTATATAGTATATTAATATAAACTATAGTTAAGAAATTATACACTATAAG
Found at i:65863 original size:21 final size:20
Alignment explanation
Indices: 65821--65881 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 20
65811 ATATAAACTA
* * *
65821 TATAGTATATTAATATAAAC
1 TATAGTTTATAAATATATAC
65841 TATAGTTTATAAATTATATAC
1 TATAGTTTATAAA-TATATAC
65862 TATAAG-TTATAAACTATATA
1 TAT-AGTTTATAAA-TATATA
65882 GTACACTAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 11 0.31
21 22 0.63
22 2 0.06
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.43
Consensus pattern (20 bp):
TATAGTTTATAAATATATAC
Found at i:65892 original size:57 final size:54
Alignment explanation
Indices: 65758--65916 Score: 187
Period size: 57 Copynumber: 2.9 Consensus size: 54
65748 ATAGTATAGT
* * * * *
65758 TTATAAACTATATACTATATTAATATAAATTATAGTTAAGATAATTA-ACATTAA
1 TTATAAACTATATAGTATATTAATATAAACTATAGTTTATA-AATTATATATTAA
65812 -TATAAACTATATAGTATATTAATATAAACTATAGTTTATAAATTATATACTATAA
1 TTATAAACTATATAGTATATTAATATAAACTATAGTTTATAAATTATATA-T-TAA
* * * *
65867 GTTATAAACTATATAGTACACTAATATAAACTATTGTTTATAAACTATAT
1 -TTATAAACTATATAGTATATTAATATAAACTATAGTTTATAAATTATAT
65917 GTTACATATA
Statistics
Matches: 91, Mismatches: 9, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
52 5 0.05
53 38 0.42
54 1 0.01
55 3 0.03
57 44 0.48
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (54 bp):
TTATAAACTATATAGTATATTAATATAAACTATAGTTTATAAATTATATATTAA
Found at i:65910 original size:14 final size:15
Alignment explanation
Indices: 65891--65919 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
65881 AGTACACTAA
65891 TATAAACTAT-TGTT
1 TATAAACTATATGTT
65905 TATAAACTATATGTT
1 TATAAACTATATGTT
65920 ACATATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.48
Consensus pattern (15 bp):
TATAAACTATATGTT
Found at i:65945 original size:22 final size:22
Alignment explanation
Indices: 65919--65987 Score: 79
Period size: 22 Copynumber: 3.1 Consensus size: 22
65909 AACTATATGT
65919 TACATATATATATAGTTTATATA
1 TACATATA-ATATAGTTTATATA
65942 -ACATATAA-ATAGATTGTATATA
1 TACATATAATATAG-TT-TATATA
* *
65964 TACATATACTATAGGTTATATA
1 TACATATAATATAGTTTATATA
65986 TA
1 TA
65988 TAGTTTATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
20 4 0.10
21 3 0.08
22 21 0.52
23 8 0.20
24 4 0.10
ACGTcount: A:0.45, C:0.06, G:0.07, T:0.42
Consensus pattern (22 bp):
TACATATAATATAGTTTATATA
Found at i:65963 original size:24 final size:25
Alignment explanation
Indices: 65936--65989 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
65926 ATATATAGTT
*
65936 TATATAACATATA-AATAGATTGTA
1 TATATAACATATACAATAGATTATA
* *
65960 TATAT-ACATATACTATAGGTTATA
1 TATATAACATATACAATAGATTATA
65984 TATATA
1 TATATA
65990 GTTTATATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.41
Consensus pattern (25 bp):
TATATAACATATACAATAGATTATA
Found at i:65989 original size:13 final size:13
Alignment explanation
Indices: 65967--66000 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
65957 GTATATATAC
65967 ATATACTATAGGTT
1 ATATA-TATAGGTT
*
65981 ATATATATAGTTT
1 ATATATATAGGTT
65994 ATATATA
1 ATATATA
66001 CTATATATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.47
Consensus pattern (13 bp):
ATATATATAGGTT
Found at i:65992 original size:57 final size:56
Alignment explanation
Indices: 65923--66063 Score: 196
Period size: 57 Copynumber: 2.5 Consensus size: 56
65913 ATATGTTACA
* *
65923 TATATATATAGTTTATATA-ACATATAAATAGATTGTATATATACATATACTATAGGT
1 TATATATATAGTTTATATATACATATAAATAG-TT-TATACATACATATACTATAAGT
*
65980 TATATATATAGTTTATATATAC-TATATATAGTTTATACATACATATACTATAAGT
1 TATATATATAGTTTATATATACATATAAATAGTTTATACATACATATACTATAAGT
*
66035 TACATATATAGTTTACATATATACATATA
1 TATATATATAGTTT--ATATATACATATA
66064 CTATAAGTTA
Statistics
Matches: 76, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
55 33 0.43
56 2 0.03
57 35 0.46
58 6 0.08
ACGTcount: A:0.43, C:0.07, G:0.06, T:0.43
Consensus pattern (56 bp):
TATATATATAGTTTATATATACATATAAATAGTTTATACATACATATACTATAAGT
Found at i:65996 original size:20 final size:20
Alignment explanation
Indices: 65925--66026 Score: 79
Period size: 20 Copynumber: 5.3 Consensus size: 20
65915 ATGTTACATA
65925 TATATATAGTTTATATA-AC
1 TATATATAGTTTATATATAC
* * *
65944 ATATAAATAGATTGTATATA-
1 -TATATATAGTTTATATATAC
* * * **
65964 TACATATACTATAGGT-TA-
1 TATATATAGTTTATATATAC
65982 TATATATAGTTTATATATAC
1 TATATATAGTTTATATATAC
*
66002 TATATATAGTTTATACATAC
1 TATATATAGTTTATATATAC
66022 -ATATA
1 TATATA
66027 CTATAAGTTA
Statistics
Matches: 62, Mismatches: 17, Indels: 7
0.72 0.20 0.08
Matches are distributed among these distances:
18 13 0.21
19 15 0.24
20 33 0.53
21 1 0.02
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.44
Consensus pattern (20 bp):
TATATATAGTTTATATATAC
Found at i:66048 original size:35 final size:36
Alignment explanation
Indices: 66003--66080 Score: 131
Period size: 37 Copynumber: 2.2 Consensus size: 36
65993 TATATATACT
66003 ATATATAGTTT-ATACATACATATACTATAAGTTAC
1 ATATATAGTTTAATACATACATATACTATAAGTTAC
*
66038 ATATATAGTTTACATATATACATATACTATAAGTTAC
1 ATATATAGTTTA-ATACATACATATACTATAAGTTAC
66075 ATATAT
1 ATATAT
66081 TAACTATTAT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
35 11 0.28
37 29 0.73
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (36 bp):
ATATATAGTTTAATACATACATATACTATAAGTTAC
Found at i:66234 original size:21 final size:20
Alignment explanation
Indices: 66194--66238 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
66184 AATTTATATA
66194 GTTTAGGTTTAGGATATAAG
1 GTTTAGGTTTAGGATATAAG
*
66214 GTTTAGAGTTTAAGG-TTTAAG
1 GTTTAG-GTTT-AGGATATAAG
66235 GTTT
1 GTTT
66239 CTATAAACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 6 0.27
21 13 0.59
22 3 0.14
ACGTcount: A:0.27, C:0.00, G:0.29, T:0.44
Consensus pattern (20 bp):
GTTTAGGTTTAGGATATAAG
Found at i:66289 original size:19 final size:19
Alignment explanation
Indices: 66278--66339 Score: 79
Period size: 19 Copynumber: 3.2 Consensus size: 19
66268 ATAGTTTATC
*
66278 TATATATATATATATAGGT
1 TATATATATATATATAGTT
* *
66297 TATATATATGTATACAGTT
1 TATATATATATATATAGTT
*
66316 TATATATATTATACATAGTT
1 TATATATA-TATATATAGTT
66336 TATA
1 TATA
66340 CATAAATTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
19 24 0.67
20 12 0.33
ACGTcount: A:0.40, C:0.03, G:0.08, T:0.48
Consensus pattern (19 bp):
TATATATATATATATAGTT
Found at i:66293 original size:23 final size:23
Alignment explanation
Indices: 66265--66310 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
66255 TAATTTACTT
* *
66265 TATATAGTTTATCTATATATATA
1 TATATAGGTTATATATATATATA
*
66288 TATATAGGTTATATATATGTATA
1 TATATAGGTTATATATATATATA
66311 CAGTTTATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.39, C:0.02, G:0.09, T:0.50
Consensus pattern (23 bp):
TATATAGGTTATATATATATATA
Found at i:66581 original size:18 final size:18
Alignment explanation
Indices: 66549--66595 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
66539 TTATACATAA
*
66549 TATATATATATATATAGCT
1 TATA-ATATAAATATAGCT
*
66568 TATAATATAAATATAGTT
1 TATAATATAAATATAGCT
66586 TAT-ATATAAA
1 TATAATATAAA
66596 GTTATATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 7 0.27
18 15 0.58
19 4 0.15
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (18 bp):
TATAATATAAATATAGCT
Found at i:66621 original size:32 final size:31
Alignment explanation
Indices: 66546--66624 Score: 81
Period size: 32 Copynumber: 2.5 Consensus size: 31
66536 TAGTTATACA
* *
66546 TAATATATA-TATATATATAGCTTATAATAT
1 TAATATAAATTATATATAAAGCTTATAATAT
* **
66576 AAATATAGTTTATATATAAAG-TTATATTATAT
1 TAATATAAATTATATATAAAGCTTATA--ATAT
66608 TAATATAAATTATATAT
1 TAATATAAATTATATAT
66625 TTTAATGCTT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
30 11 0.28
31 10 0.26
32 18 0.46
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (31 bp):
TAATATAAATTATATATAAAGCTTATAATAT
Found at i:66768 original size:15 final size:15
Alignment explanation
Indices: 66750--66808 Score: 52
Period size: 15 Copynumber: 4.1 Consensus size: 15
66740 TACTTAATAT
66750 ACTATATATATATAA
1 ACTATATATATATAA
*
66765 ACTATATACATA-AA
1 ACTATATATATATAA
* *
66779 TCT-TATATATTATAT
1 ACTATATATA-TATAA
*
66794 A-TTTATATATATAA
1 ACTATATATATATAA
66808 A
1 A
66809 TTACATAGTT
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
13 5 0.14
14 12 0.34
15 18 0.51
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (15 bp):
ACTATATATATATAA
Found at i:66871 original size:2 final size:2
Alignment explanation
Indices: 66866--66902 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
66856 TTTGTCTTTT
66866 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
66903 AAAAATTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.