Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007340.1 Hibiscus syriacus cultivar Beakdansim tig00019666_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: 137242
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:2852 original size:20 final size:20
Alignment explanation
Indices: 2785--2852 Score: 50
Period size: 20 Copynumber: 3.4 Consensus size: 20
2775 TAATAATAGT
*
2785 AATAATAATTAAAAGTA-AACA
1 AATAA-AATTAAAA-TATAATA
* * *
2806 TATAAAATTAACATATAATG
1 AATAAAATTAAAATATAATA
*
2826 AACAAAATTAAAACTAT-ATA
1 AATAAAATTAAAA-TATAATA
2846 AATAAAA
1 AATAAAA
2853 ATTGAAATTA
Statistics
Matches: 36, Mismatches: 9, Indels: 5
0.72 0.18 0.10
Matches are distributed among these distances:
19 2 0.06
20 27 0.75
21 7 0.19
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (20 bp):
AATAAAATTAAAATATAATA
Found at i:4092 original size:3 final size:3
Alignment explanation
Indices: 4084--4121 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
4074 GGCCTGTTTG
4084 TAA TAA TAA TAA TAA TATA TAA -AA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TA
4122 GAAAATGGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:4711 original size:6 final size:6
Alignment explanation
Indices: 4669--4709 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
4659 CATGTAAAAT
* * *
4669 TATTAA TATTAA TATTAA TATTAA AATTAA AATTAT TATTA
1 TATTAA TATTAA TATTAA TATTAA TATTAA TATTAA TATTA
4710 TTTAGCTTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (6 bp):
TATTAA
Found at i:10197 original size:17 final size:18
Alignment explanation
Indices: 10175--10208 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
10165 TTATAAAAAC
10175 TTTAAAT-TTTCATATAA
1 TTTAAATATTTCATATAA
*
10192 TTTAAATATTTTATATA
1 TTTAAATATTTCATATA
10209 TGTTATAGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTAAATATTTCATATAA
Found at i:11668 original size:19 final size:19
Alignment explanation
Indices: 11652--11688 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
11642 ATAATGATCG
11652 AATTATATAAAAATGATAA
1 AATTATATAAAAATGATAA
* *
11671 AATTATGTTAAAATGATA
1 AATTATATAAAAATGATA
11689 TTTTAATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (19 bp):
AATTATATAAAAATGATAA
Found at i:13665 original size:31 final size:29
Alignment explanation
Indices: 13623--13708 Score: 113
Period size: 30 Copynumber: 2.9 Consensus size: 29
13613 ACAACCTCGC
13623 TATT-CTAAGCTTTGCTAAGCTTCACTCA
1 TATTCCTAAGCTTTGCTAAGCTTCACTCA
*
13651 -ATTCTCTCATAGCTTTGCTAAGCTTTCAATCA
1 TATTC-CT-A-AGCTTTGCTAAGC-TTCACTCA
13683 TATTCCTAAGCTTTGCTAAGCTTCAC
1 TATTCCTAAGCTTTGCTAAGCTTCAC
13709 CCTCTCTCTT
Statistics
Matches: 50, Mismatches: 2, Indels: 11
0.79 0.03 0.17
Matches are distributed among these distances:
27 3 0.06
29 6 0.12
30 14 0.28
31 14 0.28
32 9 0.18
33 4 0.08
ACGTcount: A:0.24, C:0.26, G:0.10, T:0.40
Consensus pattern (29 bp):
TATTCCTAAGCTTTGCTAAGCTTCACTCA
Found at i:16076 original size:39 final size:39
Alignment explanation
Indices: 16002--16077 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
15992 AAGGACATGC
* * *
16002 GTAAGGACTTATCCTGTGCACAAAGCTGAGAAGCCTGCG
1 GTAAGGACTTACCCTGAGCAAAAAGCTGAGAAGCCTGCG
* *
16041 GTAAGGACTTACCCTGAGCAAAAAGTTGAGGAGCCTG
1 GTAAGGACTTACCCTGAGCAAAAAGCTGAGAAGCCTG
16078 GAGCTTGCGG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.30, C:0.21, G:0.29, T:0.20
Consensus pattern (39 bp):
GTAAGGACTTACCCTGAGCAAAAAGCTGAGAAGCCTGCG
Found at i:16157 original size:85 final size:85
Alignment explanation
Indices: 16002--16158 Score: 192
Period size: 85 Copynumber: 1.8 Consensus size: 85
15992 AAGGACATGC
** * * ** *
16002 GTAAGGACTTATCCTGTGCACAAAGCTGAGAAGCCTGCGGTAAGGACTTACCCTGAGCAAAAAGT
1 GTAAGGACTTATCCTAAGCACAAAACCGAGAAGCCCACGGTAAGGACTTACCCTGAGCAAAAAGC
*
16067 TGAGGAGCCTGGAGCTTGCG
66 CGAGGAGCCTGGAGCTTGCG
* *
16087 GTAAGGACTTATCCTAAGCACAAAACCGATG-AGCCCACGGTAAGGACTTACCTTGGGCACAAAA
1 GTAAGGACTTATCCTAAGCACAAAACCGA-GAAGCCCACGGTAAGGACTTACCCTGAGCA-AAAA
16151 -CCGAGGAG
64 GCCGAGGAG
16159 TCAGTAGTAA
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
85 55 0.92
86 5 0.08
ACGTcount: A:0.31, C:0.23, G:0.28, T:0.18
Consensus pattern (85 bp):
GTAAGGACTTATCCTAAGCACAAAACCGAGAAGCCCACGGTAAGGACTTACCCTGAGCAAAAAGC
CGAGGAGCCTGGAGCTTGCG
Found at i:37116 original size:6 final size:6
Alignment explanation
Indices: 37105--37135 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
37095 GCGCTTGTTG
37105 ACATAC ACATAC ACATAC ACATAC ACATAC A
1 ACATAC ACATAC ACATAC ACATAC ACATAC A
37136 AAGAGACATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.52, C:0.32, G:0.00, T:0.16
Consensus pattern (6 bp):
ACATAC
Found at i:37144 original size:18 final size:18
Alignment explanation
Indices: 37104--37144 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
37094 CGCGCTTGTT
* *
37104 GACATACACATACACATA
1 GACATACACATACAAAGA
*
37122 CACATACACATACAAAGA
1 GACATACACATACAAAGA
37140 GACAT
1 GACAT
37145 GTACATATAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.27, G:0.07, T:0.15
Consensus pattern (18 bp):
GACATACACATACAAAGA
Found at i:39660 original size:18 final size:17
Alignment explanation
Indices: 39618--39665 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
39608 GATTGTTAAT
*
39618 GGTGAGAAAGAAAAGGA
1 GGTGAGGAAGAAAAGGA
39635 GGTGGAGGAAGAAAAGGA
1 GGT-GAGGAAGAAAAGGA
39653 GGATGAGG-AGAAA
1 GG-TGAGGAAGAAA
39666 GTTGTGAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 8 0.29
18 19 0.68
19 1 0.04
ACGTcount: A:0.48, C:0.00, G:0.46, T:0.06
Consensus pattern (17 bp):
GGTGAGGAAGAAAAGGA
Found at i:41068 original size:25 final size:25
Alignment explanation
Indices: 41034--41091 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
41024 CTGGAATAAG
41034 ATAATTTAGGGTTTGTGTTCTGCTT
1 ATAATTTAGGGTTTGTGTTCTGCTT
*
41059 ATAATTTAGGGTTTGTGTTCTGTTT
1 ATAATTTAGGGTTTGTGTTCTGCTT
41084 ATATATTT
1 ATA-ATTT
41092 CTGGGAACTG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 27 0.87
26 4 0.13
ACGTcount: A:0.19, C:0.05, G:0.21, T:0.55
Consensus pattern (25 bp):
ATAATTTAGGGTTTGTGTTCTGCTT
Found at i:47082 original size:59 final size:59
Alignment explanation
Indices: 47009--47120 Score: 188
Period size: 59 Copynumber: 1.9 Consensus size: 59
46999 GCACTAACCA
* *
47009 TATTCTCTTCCATGCAAACTAATGAAGGTTATTATAAGTATAGACAATTGAATGAACTG
1 TATTCTCTCCCATGCAAACTAATGAAGGTAATTATAAGTATAGACAATTGAATGAACTG
* *
47068 TATTCTCTCCCATGCAAACTAATGAAGGTAATTGTTAGTATAGACAATTGAAT
1 TATTCTCTCCCATGCAAACTAATGAAGGTAATTATAAGTATAGACAATTGAAT
47121 TTGTTAAAGC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
59 49 1.00
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (59 bp):
TATTCTCTCCCATGCAAACTAATGAAGGTAATTATAAGTATAGACAATTGAATGAACTG
Found at i:48800 original size:103 final size:103
Alignment explanation
Indices: 48621--48848 Score: 438
Period size: 103 Copynumber: 2.2 Consensus size: 103
48611 CGTAACATAA
*
48621 AATTTTGTGTCTGTTTTTAATGTACTATGTATACTCTTTAAGATTTTCGATAGTTAGGGAAGAGA
1 AATTTTGTGTCCGTTTTTAATGTACTATGTATACTCTTTAAGATTTTCGATAGTTAGGGAAGAGA
48686 AAATTCAGACCAAAAGATAATGTTTATGTTGATATTCC
66 AAATTCAGACCAAAAGATAATGTTTATGTTGATATTCC
*
48724 AATTTTGTGTCCGTTTTTAATGTACTATGTATACTCTTTAAGATTTTCGATATTTAGGGAAGAGA
1 AATTTTGTGTCCGTTTTTAATGTACTATGTATACTCTTTAAGATTTTCGATAGTTAGGGAAGAGA
48789 AAATTCAGACCAAAAGATAATGTTTATGTTGATATTCC
66 AAATTCAGACCAAAAGATAATGTTTATGTTGATATTCC
48827 AATTTTGTGTCCGTTTTTAATG
1 AATTTTGTGTCCGTTTTTAATG
48849 GCTAACGACG
Statistics
Matches: 123, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 123 1.00
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.42
Consensus pattern (103 bp):
AATTTTGTGTCCGTTTTTAATGTACTATGTATACTCTTTAAGATTTTCGATAGTTAGGGAAGAGA
AAATTCAGACCAAAAGATAATGTTTATGTTGATATTCC
Found at i:54473 original size:21 final size:21
Alignment explanation
Indices: 54439--54478 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
54429 TAAAGCGCCC
*
54439 AATAATAACTTTTTCGGTAGA
1 AATAATAACTTTTTAGGTAGA
54460 AATAATAA-TGTTTTAGGTA
1 AATAATAACT-TTTTAGGTA
54479 ATTTTTTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.40, C:0.05, G:0.15, T:0.40
Consensus pattern (21 bp):
AATAATAACTTTTTAGGTAGA
Found at i:55664 original size:56 final size:60
Alignment explanation
Indices: 55542--55668 Score: 154
Period size: 59 Copynumber: 2.2 Consensus size: 60
55532 TATCAAATTT
* * * *
55542 AGGTACCAAATTGAATAAAAAAAATACAGGTACAGCATTATGAAAAAAGCTGTCAAATTC
1 AGGTACTAAATTGAATAAAAAAAACACAAGTACAGCATTATGAAAAAAGCTGTCAAAATC
* * * *
55602 ATGTACTAAATTGGA-AAGAAAAACACAAGTACCGCATTA-G-AAAAAG-TGTCAAAATC
1 AGGTACTAAATTGAATAAAAAAAACACAAGTACAGCATTATGAAAAAAGCTGTCAAAATC
55658 AGGTACTAAAT
1 AGGTACTAAAT
55669 GATGCATTAA
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
56 19 0.33
57 6 0.10
58 1 0.02
59 20 0.34
60 12 0.21
ACGTcount: A:0.50, C:0.13, G:0.16, T:0.21
Consensus pattern (60 bp):
AGGTACTAAATTGAATAAAAAAAACACAAGTACAGCATTATGAAAAAAGCTGTCAAAATC
Found at i:59970 original size:15 final size:17
Alignment explanation
Indices: 59950--59989 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
59940 TGAATTATAT
59950 ATTATTTTA-TGATTA-
1 ATTATTTTATTGATTAG
59965 ATTA-TTTATTGATTAG
1 ATTATTTTATTGATTAG
*
59981 ATAATTTTA
1 ATTATTTTA
59990 GTTGTTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 4 0.19
15 10 0.48
16 3 0.14
17 4 0.19
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.57
Consensus pattern (17 bp):
ATTATTTTATTGATTAG
Found at i:60289 original size:23 final size:22
Alignment explanation
Indices: 60236--60292 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
60226 AACGTGATGC
*
60236 CCAATCAACAGCTTCTAGAAGA
1 CCAATCAGCAGCTTCTAGAAGA
* *
60258 CTCAGTCAGCAGGTTCTAGAAGA
1 C-CAATCAGCAGCTTCTAGAAGA
60281 TCCAATCAGCAG
1 -CCAATCAGCAG
60293 TGGTATGGAG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 1 0.03
23 27 0.93
24 1 0.03
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (22 bp):
CCAATCAGCAGCTTCTAGAAGA
Found at i:71510 original size:18 final size:17
Alignment explanation
Indices: 71456--71504 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
71446 TTGGACCCTT
* *
71456 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
71474 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
71492 AGTGCATTCGATG
1 AGTGCA-TCGATG
71505 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:71604 original size:58 final size:56
Alignment explanation
Indices: 71485--71594 Score: 141
Period size: 58 Copynumber: 1.9 Consensus size: 56
71475 AGTGCATCGA
* *
71485 TGCATCAAGTGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGCTGG
1 TGCATCAAATGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGCATGGCTGG
* * *
71541 TGCATCAAATGCATTCGATGTTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGG
1 TGCATCAAATGCATTCGATG--TTTCA-AAATAGCCACAGTGCATCGATGCATGG
71595 TATGTGCATC
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
56 19 0.41
58 24 0.52
59 3 0.07
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (56 bp):
TGCATCAAATGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGCATGGCTGG
Found at i:72742 original size:21 final size:21
Alignment explanation
Indices: 72718--72761 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
72708 GAGCTGGAGG
* *
72718 AGGAGGAGCACGAGAGGAGCT
1 AGGAGCAGCACGAGAGGAACT
* *
72739 AGGAGCAGCTCGTGAGGAACT
1 AGGAGCAGCACGAGAGGAACT
72760 AG
1 AG
72762 CTCCCGGAGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.43, T:0.09
Consensus pattern (21 bp):
AGGAGCAGCACGAGAGGAACT
Found at i:80444 original size:18 final size:18
Alignment explanation
Indices: 80413--80447 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
80403 TGATGGTTTG
**
80413 TAATTTTGGGTTTAGATA
1 TAATTTTGAATTTAGATA
80431 TAATTTTGAATTTAGAT
1 TAATTTTGAATTTAGAT
80448 TTTTTAATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.51
Consensus pattern (18 bp):
TAATTTTGAATTTAGATA
Found at i:85953 original size:18 final size:18
Alignment explanation
Indices: 85930--85970 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
85920 GGGTAATCTT
85930 TTTGCTGATCTTGAACTA
1 TTTGCTGATCTTGAACTA
85948 TTTGCTGATCTTGAACTA
1 TTTGCTGATCTTGAACTA
85966 TTTGC
1 TTTGC
85971 AACTCCATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.20, C:0.17, G:0.17, T:0.46
Consensus pattern (18 bp):
TTTGCTGATCTTGAACTA
Found at i:87220 original size:39 final size:39
Alignment explanation
Indices: 87177--87260 Score: 91
Period size: 39 Copynumber: 2.2 Consensus size: 39
87167 AACGGTGAAG
*
87177 TAGGGAGTG-AGATGCGA-AGGAGAAATGAAAAAGGGGAAT
1 TAGGGAGTGAAG-GGCGAGAGGA-AAATGAAAAAGGGGAAT
* * **
87216 TAGGGATTGAAGGGCGAGAGGAAAATGAGATTGGGGAAT
1 TAGGGAGTGAAGGGCGAGAGGAAAATGAAAAAGGGGAAT
87255 TAGGGA
1 TAGGGA
87261 TTATGGCAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
39 32 0.84
40 6 0.16
ACGTcount: A:0.39, C:0.02, G:0.43, T:0.15
Consensus pattern (39 bp):
TAGGGAGTGAAGGGCGAGAGGAAAATGAAAAAGGGGAAT
Found at i:99117 original size:24 final size:25
Alignment explanation
Indices: 99087--99135 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
99077 ATTGTTAATG
99087 AATAAGGTAA-GTTTTTCATTCTAT
1 AATAAGGTAAGGTTTTTCATTCTAT
*
99111 AATAAGGTAATGGTTTTTTATTCTA
1 AATAAGGTAA-GGTTTTTCATTCTA
99136 AACTAAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 10 0.45
26 12 0.55
ACGTcount: A:0.33, C:0.06, G:0.14, T:0.47
Consensus pattern (25 bp):
AATAAGGTAAGGTTTTTCATTCTAT
Found at i:104206 original size:17 final size:18
Alignment explanation
Indices: 104179--104219 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
104169 TTATAATAAA
104179 AATATAAAATATA-TTTAT
1 AATA-AAAATATATTTTAT
104197 AATAAAAATATATTTTAT
1 AATAAAAATATATTTTAT
104215 AATAA
1 AATAA
104220 CTCACTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AATAAAAATATATTTTAT
Found at i:104722 original size:25 final size:23
Alignment explanation
Indices: 104694--104744 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
104684 ATTATGAGAA
*
104694 AAAAGATGAGTAAATATATATATGT
1 AAAAGATGAAT-AATAT-TATATGT
* *
104719 AAAAGTTGAATAATATTATGTGT
1 AAAAGATGAATAATATTATATGT
104742 AAA
1 AAA
104745 TTACACCACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 9 0.39
24 5 0.22
25 9 0.39
ACGTcount: A:0.51, C:0.00, G:0.16, T:0.33
Consensus pattern (23 bp):
AAAAGATGAATAATATTATATGT
Found at i:107010 original size:17 final size:17
Alignment explanation
Indices: 106966--107010 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
106956 TCAAATTATC
* * *
106966 ATATAATTTAATTTTTT
1 ATATAATTTTATTGTTG
106983 ATATAATTTTTATTGTTG
1 ATATAA-TTTTATTGTTG
107001 ATATAATTTT
1 ATATAATTTT
107011 GTATCTTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (17 bp):
ATATAATTTTATTGTTG
Found at i:107669 original size:59 final size:60
Alignment explanation
Indices: 107573--107704 Score: 164
Period size: 59 Copynumber: 2.2 Consensus size: 60
107563 AATTTAGGGT
107573 AAAGTATAC-AAATGGTCCCTCGACTATAGGATATTGCTTTATTGAGTCACC-CAACTAATA
1 AAAGT-TACAAAATGGTCCCTCGACTATAGGATATTGCTTTATTGAGTC-CCTCAACTAATA
* * ** *
107633 AAAGTTACAAAATGGT-TCTCGACTATAGGA-AGTTGCTTTGTTGAGTCCCTTGACTATTA
1 AAAGTTACAAAATGGTCCCTCGACTATAGGATA-TTGCTTTATTGAGTCCCTCAACTAATA
107692 AAAGTTACAAAAT
1 AAAGTTACAAAAT
107705 AGTCACTCTA
Statistics
Matches: 64, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
58 3 0.05
59 49 0.77
60 12 0.19
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Consensus pattern (60 bp):
AAAGTTACAAAATGGTCCCTCGACTATAGGATATTGCTTTATTGAGTCCCTCAACTAATA
Found at i:111903 original size:31 final size:31
Alignment explanation
Indices: 111863--111921 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
111853 GAACGGTCCT
* *
111863 TAATGTTATCGATTAGTTCGATTTTAGTATA
1 TAATATTATCGATCAGTTCGATTTTAGTATA
* *
111894 TAATATTATCGATCCGTTTGATTTTAGT
1 TAATATTATCGATCAGTTCGATTTTAGT
111922 CTCTCACTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.27, C:0.08, G:0.15, T:0.49
Consensus pattern (31 bp):
TAATATTATCGATCAGTTCGATTTTAGTATA
Found at i:115103 original size:37 final size:38
Alignment explanation
Indices: 115047--115120 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 38
115037 CGGTAATCCG
* *
115047 TTCGTTTATGTTCGTTCATTTATGTCAGTATATGTTCA
1 TTCGTTTATATTCATTCATTTATGTCAGTATATGTTCA
* *
115085 TTCG-TTATATTCATTCATTTATGTCCGTGTATGTTC
1 TTCGTTTATATTCATTCATTTATGTCAGTATATGTTC
115121 GTTTATATTC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 28 0.88
38 4 0.12
ACGTcount: A:0.18, C:0.15, G:0.15, T:0.53
Consensus pattern (38 bp):
TTCGTTTATATTCATTCATTTATGTCAGTATATGTTCA
Found at i:115299 original size:23 final size:23
Alignment explanation
Indices: 115264--115325 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
115254 ACTTAAATAA
115264 TTTAT-TTTCATTTATTGTGTTCG
1 TTTATGTTT-ATTTATTGTGTTCG
*
115287 TTTATGTTTATTTATTGTGTTTG
1 TTTATGTTTATTTATTGTGTTCG
*
115310 TTTACGTTTATTTATT
1 TTTATGTTTATTTATT
115326 ATATTTGTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 33 0.92
24 3 0.08
ACGTcount: A:0.15, C:0.05, G:0.13, T:0.68
Consensus pattern (23 bp):
TTTATGTTTATTTATTGTGTTCG
Found at i:115332 original size:23 final size:23
Alignment explanation
Indices: 115286--115337 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
115276 TATTGTGTTC
* * *
115286 GTTTATGTTTATTTATTGTGTTT
1 GTTTACGTTTATTTATTATATTT
115309 GTTTACGTTTATTTATTATATTT
1 GTTTACGTTTATTTATTATATTT
115332 GTTTAC
1 GTTTAC
115338 ATACTCATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.17, C:0.04, G:0.13, T:0.65
Consensus pattern (23 bp):
GTTTACGTTTATTTATTATATTT
Found at i:116109 original size:38 final size:38
Alignment explanation
Indices: 116067--116139 Score: 101
Period size: 38 Copynumber: 1.9 Consensus size: 38
116057 CAGAAATTTC
* *
116067 TAGAATTAGGACTCAGGAAAGGATAGTCTAATTACTTA
1 TAGAATTAGAACTCAGGAAAGAATAGTCTAATTACTTA
* * *
116105 TAGAATTAGAACTCGGGAAATAATAGTCTACTTAC
1 TAGAATTAGAACTCAGGAAAGAATAGTCTAATTAC
116140 AAGGTAGTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 30 1.00
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (38 bp):
TAGAATTAGAACTCAGGAAAGAATAGTCTAATTACTTA
Found at i:118108 original size:22 final size:23
Alignment explanation
Indices: 118056--118108 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 23
118046 ATAATTTTAT
* * *
118056 ATAAAATTTTAAAAAATAAAATT
1 ATAAATTTTTAAAAAAGAAAATC
* *
118079 ATATATTTTTAAAAAAGAACA-C
1 ATAAATTTTTAAAAAAGAAAATC
118101 ATAAATTT
1 ATAAATTT
118109 CGAAATAACC
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
22 7 0.29
23 17 0.71
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (23 bp):
ATAAATTTTTAAAAAAGAAAATC
Found at i:130800 original size:18 final size:18
Alignment explanation
Indices: 130767--130801 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
130757 AAAATCGGTT
* *
130767 AATTAACCGAATTTATTG
1 AATTAACCAAAATTATTG
130785 AATTAACCAAAATTATT
1 AATTAACCAAAATTATT
130802 AAATATTATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.11, G:0.06, T:0.37
Consensus pattern (18 bp):
AATTAACCAAAATTATTG
Found at i:136294 original size:23 final size:23
Alignment explanation
Indices: 136266--136309 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
136256 TAAGGTAAAC
*
136266 AATTAAAT-AATAAATATAATTAT
1 AATTAAATCAAAAAATA-AATTAT
136289 AATTAAATCAAAAAATAAATT
1 AATTAAATCAAAAAATAAATT
136310 TGGGGTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (23 bp):
AATTAAATCAAAAAATAAATTAT
Done.