Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003486.1 Hibiscus syriacus cultivar Beakdansim tig00007370_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: 87425
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:4981 original size:2 final size:2
Alignment explanation
Indices: 4974--5029 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
4964 ATATGAGTCA
4974 AT AT AT 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 AT AT AT
5016 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
5030 TATGAATGCT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7595 original size:2 final size:2
Alignment explanation
Indices: 7588--7614 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
7578 CCCTAACCAC
7588 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 T
7615 TTATTTATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:8185 original size:23 final size:22
Alignment explanation
Indices: 8144--8186 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
8134 ACCTCAGATT
*
8144 AATAAAAAAATATATATTTTTA
1 AATAAAAAAATATAAATTTTTA
*
8166 AATAAAAATAATTTAAATTTT
1 AATAAAAA-AATATAAATTTT
8187 AACATTATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
AATAAAAAAATATAAATTTTTA
Found at i:8186 original size:22 final size:22
Alignment explanation
Indices: 8144--8188 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
8134 ACCTCAGATT
*
8144 AATAAAAAAATATATATTTTTA
1 AATAAAAAAATATATAATTTTA
*
8166 AATAAAAATAATTTA-AATTTTA
1 AATAAAAA-AATATATAATTTTA
8188 A
1 A
8189 CATTATTAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
AATAAAAAAATATATAATTTTA
Found at i:9087 original size:15 final size:16
Alignment explanation
Indices: 9067--9099 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
9057 ATATGATCTG
9067 AATGAAA-ATATAATT
1 AATGAAATATATAATT
9082 AATGAAATTATATAATT
1 AATGAAA-TATATAATT
9099 A
1 A
9100 TAATCAATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
17 9 0.56
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (16 bp):
AATGAAATATATAATT
Found at i:21458 original size:19 final size:19
Alignment explanation
Indices: 21427--21473 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
21417 CAAAACCCCT
21427 AAAAGATACA-TTTAAAATTA
1 AAAAGATA-ATTTTAAAA-TA
21447 AAAAGATAATTTTAAAATA
1 AAAAGATAATTTTAAAATA
21466 AAAA-ATAA
1 AAAAGATAA
21474 AAAATAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.15
19 7 0.27
20 15 0.58
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.28
Consensus pattern (19 bp):
AAAAGATAATTTTAAAATA
Found at i:25721 original size:2 final size:2
Alignment explanation
Indices: 25714--25821 Score: 216
Period size: 2 Copynumber: 54.0 Consensus size: 2
25704 GAATCAGAAT
25714 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
25756 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
25798 AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG
25822 GGGGGGGTTA
Statistics
Matches: 106, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 106 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:27336 original size:24 final size:24
Alignment explanation
Indices: 27309--27370 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
27299 CGTTCGTGAA
*
27309 CGTTCGGTTATGTTCGTTTATATG
1 CGTTCAGTTATGTTCGTTTATATG
* *
27333 CGTTTAGTTATGTTCGTTTATGTG
1 CGTTCAGTTATGTTCGTTTATATG
*
27357 CGTTCATTTATGTT
1 CGTTCAGTTATGTT
27371 TAACCTAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.13, C:0.11, G:0.23, T:0.53
Consensus pattern (24 bp):
CGTTCAGTTATGTTCGTTTATATG
Found at i:28897 original size:10 final size:10
Alignment explanation
Indices: 28882--28956 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
28872 GGGTCTCCAA
28882 CGTTTATGTT
1 CGTTTATGTT
28892 CGTTTATGTT
1 CGTTTATGTT
28902 CG----TGTT
1 CGTTTATGTT
*
28908 CATTTATGTT
1 CGTTTATGTT
*
28918 CGTGTT-CGTTT
1 CGT-TTATG-TT
* *
28929 ATGTTTGTGTT
1 -CGTTTATGTT
28940 CGTTTATGTT
1 CGTTTATGTT
28950 CGTTTAT
1 CGTTTAT
28957 TTATTAAATG
Statistics
Matches: 50, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
6 5 0.10
10 34 0.68
11 8 0.16
12 3 0.06
ACGTcount: A:0.09, C:0.11, G:0.21, T:0.59
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:28913 original size:16 final size:16
Alignment explanation
Indices: 28888--28952 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
28878 CCAACGTTTA
28888 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
28904 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
*
28920 TGTTCGTTTATGTTTG
1 TGTTCGTTTATGTTCG
28936 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
28952 T
1 T
28953 TTATTTATTA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.08, C:0.11, G:0.23, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:30901 original size:2 final size:2
Alignment explanation
Indices: 30856--30882 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
30846 TATTTTTCTT
30856 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 T
30883 CAGGTCAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39585 original size:2 final size:2
Alignment explanation
Indices: 39580--39607 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
39570 AAAATAAGAA
39580 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
39608 GATTATAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40841 original size:15 final size:15
Alignment explanation
Indices: 40815--40881 Score: 75
Period size: 15 Copynumber: 4.5 Consensus size: 15
40805 CAGTCGATAT
40815 TTTTTTAG--TTAAA
1 TTTTTTAGTTTTAAA
40828 TTTTTTAGTTTTAAA
1 TTTTTTAGTTTTAAA
*
40843 TTTTTCAGTTTTAAA
1 TTTTTTAGTTTTAAA
*
40858 TATTTTAGATATTTAAA
1 TTTTTTAG-T-TTTAAA
*
40875 TTATTTA
1 TTTTTTA
40882 ATTAATGTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
13 8 0.18
15 25 0.56
16 1 0.02
17 11 0.24
ACGTcount: A:0.31, C:0.01, G:0.06, T:0.61
Consensus pattern (15 bp):
TTTTTTAGTTTTAAA
Found at i:42940 original size:20 final size:20
Alignment explanation
Indices: 42896--43021 Score: 105
Period size: 20 Copynumber: 6.2 Consensus size: 20
42886 AATGACCAAC
* *
42896 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
42915 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
**
42935 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
**
42955 AAAATCGCAACGCGATATTCC
1 AAAATCGCAACGCGAT-TTAG
* *
42976 AAGAATCGCAATGCGATTAAG
1 AA-AATCGCAACGCGATTTAG
* *
42997 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTTAG
43017 AAAAT
1 AAAAT
43022 GAGTAAATTC
Statistics
Matches: 85, Mismatches: 16, Indels: 11
0.76 0.14 0.10
Matches are distributed among these distances:
18 1 0.01
19 18 0.21
20 46 0.54
21 6 0.07
22 14 0.16
ACGTcount: A:0.43, C:0.21, G:0.19, T:0.17
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:43021 original size:62 final size:57
Alignment explanation
Indices: 42896--43008 Score: 154
Period size: 62 Copynumber: 1.9 Consensus size: 57
42886 AATGACCAAC
*
42896 AAAATCGCAACGCGATATCAAAATCGCAACGCGATTTAGAAAATCGCAACGGTCAAAAG
1 AAAATCGCAACGCGATATCAAAATCGCAACGCGATTAAGAAAATCGCAACGGTC--AAG
* *
42955 AAAATCGCAACGCGATATTCCAAGAATCGCAATGCGATTAAGAGAATCGCAACG
1 AAAATCGCAACGCGATA-T-CAA-AATCGCAACGCGATTAAGAAAATCGCAACG
43009 CGATTCAGAA
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
59 17 0.35
60 1 0.02
61 3 0.06
62 27 0.56
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.16
Consensus pattern (57 bp):
AAAATCGCAACGCGATATCAAAATCGCAACGCGATTAAGAAAATCGCAACGGTCAAG
Found at i:45237 original size:27 final size:27
Alignment explanation
Indices: 45179--45237 Score: 109
Period size: 27 Copynumber: 2.2 Consensus size: 27
45169 GAAATCTACA
*
45179 ATCAAACAACAGTAATTGAACTCTGCC
1 ATCACACAACAGTAATTGAACTCTGCC
45206 ATCACACAACAGTAATTGAACTCTGCC
1 ATCACACAACAGTAATTGAACTCTGCC
45233 ATCAC
1 ATCAC
45238 TATTGCTTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.39, C:0.29, G:0.10, T:0.22
Consensus pattern (27 bp):
ATCACACAACAGTAATTGAACTCTGCC
Found at i:46732 original size:2 final size:2
Alignment explanation
Indices: 46725--46749 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
46715 AGTTGCTCCC
46725 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 T
46750 TGTGTAATAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:46982 original size:32 final size:32
Alignment explanation
Indices: 46946--47006 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
46936 AAGACTTCGC
46946 GTCTTTCTAGCGTTTTCTACCAAAGACGTTGT
1 GTCTTTCTAGCGTTTTCTACCAAAGACGTTGT
*
46978 GTCTTTCTAGCGTTTTCTACTAAAGACGT
1 GTCTTTCTAGCGTTTTCTACCAAAGACGT
47007 CGGGTTTTCC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.20, C:0.21, G:0.18, T:0.41
Consensus pattern (32 bp):
GTCTTTCTAGCGTTTTCTACCAAAGACGTTGT
Found at i:53518 original size:128 final size:128
Alignment explanation
Indices: 53290--53790 Score: 896
Period size: 128 Copynumber: 3.9 Consensus size: 128
53280 TAATCGGAGT
* *
53290 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCTATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCAGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
53355 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *
53418 ACTATTCACATGAAGGCGCGTTCCCGGGGGGGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCAGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
*
53483 TATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
53546 ACTATTCACATGAAGGCGCGTTCCCAGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCAGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
53611 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *** *
53674 TC-AGGGGACATGAAGGCGCGTTCCCAGGGGGGCGCCTTCCATTATTTCGTCAGAGAATATGTTA
1 ACTA-TTCACATGAAGGCGCGTTCCCAGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTA
53738 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
65 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
53791 AATAAGGTAA
Statistics
Matches: 361, Mismatches: 11, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
127 1 0.00
128 360 1.00
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.32
Consensus pattern (128 bp):
ACTATTCACATGAAGGCGCGTTCCCAGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
Found at i:54286 original size:33 final size:32
Alignment explanation
Indices: 54183--54287 Score: 131
Period size: 33 Copynumber: 3.2 Consensus size: 32
54173 TAAGTTGAAA
*
54183 TTTAATGTTAAATTTCGAATACTATAATTTATAT
1 TTTAAT-TTAAATTTCGAATAATATAATTT-TAT
*
54217 TTTAAATTTAAATTT-GAATAATATTATTTTATT
1 TTT-AATTTAAATTTCGAATAATATAATTTTA-T
*
54250 TTTATTTTAAATTTCGAATAATATAATTTGTAT
1 TTTAATTTAAATTTCGAATAATATAATTT-TAT
54283 TTTAA
1 TTTAA
54288 AAACATTTAT
Statistics
Matches: 62, Mismatches: 5, Indels: 9
0.82 0.07 0.12
Matches are distributed among these distances:
32 12 0.19
33 34 0.55
34 13 0.21
35 3 0.05
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (32 bp):
TTTAATTTAAATTTCGAATAATATAATTTTAT
Found at i:54896 original size:21 final size:21
Alignment explanation
Indices: 54808--54901 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
54798 TATGGTATAA
*
54808 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
54829 AA-CCTGGCGGGCTAGGCATGT
1 AACCCT-GCGGGCTAGGAATGT
54850 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
54871 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
54892 AACCCTGCGG
1 AACCCTGCGG
54902 AGATGGCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 3 0.04
21 63 0.91
22 3 0.04
ACGTcount: A:0.20, C:0.27, G:0.35, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:54931 original size:21 final size:21
Alignment explanation
Indices: 54905--54952 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
54895 CCTGCGGAGA
*
54905 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
54926 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
54947 GGGCAT
1 TGGCAT
54953 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:56728 original size:34 final size:32
Alignment explanation
Indices: 56674--56778 Score: 99
Period size: 32 Copynumber: 3.2 Consensus size: 32
56664 TTAATAATTC
*
56674 TAAATAAATAATAATTATATAAATATTATTTTAATA
1 TAAAAAAATAAT-ATTATATAAATA-TA--TTAATA
56710 -AAAAAAATAATATTATATAAATATATTAATA
1 TAAAAAAATAATATTATATAAATATATTAATA
* * *
56741 TAAAAATAATAACTATT-TA-AAAAATACTAACA
1 TAAAAA-AATAA-TATTATATAAATATATTAATA
56773 TAAAAA
1 TAAAAA
56779 TAAATTTCTT
Statistics
Matches: 62, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
31 6 0.10
32 21 0.34
33 9 0.15
34 16 0.26
35 10 0.16
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (32 bp):
TAAAAAAATAATATTATATAAATATATTAATA
Found at i:57770 original size:30 final size:31
Alignment explanation
Indices: 57736--57793 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
57726 CGTTAAAAAC
57736 TAAGAAAACAAAAG-AAAAATAA-AAATAATA
1 TAAGAAAA-AAAAGAAAAAATAAGAAATAATA
* *
57766 TAAGAGAATAAAGAAAAAATAAGAAATA
1 TAAGAAAAAAAAGAAAAAATAAGAAATA
57794 TTGACGACGC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 4 0.17
30 15 0.62
31 5 0.21
ACGTcount: A:0.74, C:0.02, G:0.10, T:0.14
Consensus pattern (31 bp):
TAAGAAAAAAAAGAAAAAATAAGAAATAATA
Found at i:61189 original size:7 final size:7
Alignment explanation
Indices: 61179--61207 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
61169 AAGAAGGAAA
61179 AGAGAGG
1 AGAGAGG
61186 AGAGAGG
1 AGAGAGG
61193 AGAGAGG
1 AGAGAGG
61200 AGAGAGG
1 AGAGAGG
61207 A
1 A
61208 CGATGAAGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (7 bp):
AGAGAGG
Found at i:62767 original size:391 final size:391
Alignment explanation
Indices: 62046--63223 Score: 1892
Period size: 391 Copynumber: 3.0 Consensus size: 391
62036 CTTTAACTAT
* ** *
62046 TAAAAGTTACATAATTATCCTCTAACTATATAATGTTGCCTTATTAAATCCCTTGACTATAAAAG
1 TAAAAGTTACATAATTATCCTCTAACTATAGAATGTTGTTTTATTAAATCCCTTGACTATAAAAA
* * * **
62111 GTTACAAAATGATCATCCAACTACTCATTATGTTTCAAACTCGTCATTTTTTGTTAAAAAATTGA
66 GTTACAAAATGATCATTCAACTATTCATTATGTTTCAAACTTGTCATTTTCCGTTAAAAAATTGA
* * * *
62176 AGGTTGTTTAAGCTGGATGTCAACAAGATGAATGAGATATGATAATCATTTGAGAATCTAGTATC
131 CGGTTGTTTAAGCTGGATGTCAACATGATGAATGAGATATGATAATCATTTGAGATTATAGTATC
* *
62241 AAATTTTATCATATCACAATCAACAAATTAATGTTCAGCTCAAAATATTGTCAATTTTTAATGAA
196 AAATTTTATCATATCACAATCAACAAATTAACGTTCAACTCAAAATATTGTCAATTTTTAATGAA
* ** *
62306 AAATGATGAGTTTGGAACATAATAAATAGTCGAATGACCATTTTGTAACTTTTAATAGTTGAATG
261 AAAGGATGAGTTTGGAACATAATAAATAGTCGGGTGACCATTTTGTAACTTTTAATAGTTGAGTG
*
62371 ACTCAACAAAACAACACTCTATAGTCGGATGAATGTTTTGTAACTTTTAATAGCCGAGTGACTTA
326 ACTCAACAAAACAACACTCTATAGTCGGATGACTGTTTTGTAACTTTTAATAGCCGAGTGACTTA
62436 A
391 A
*
62437 TAAAAGTTACATAATTATCCTCTAACTATAGAATGTTGTTTTATTAAATCCATTGACTATAAAAA
1 TAAAAGTTACATAATTATCCTCTAACTATAGAATGTTGTTTTATTAAATCCCTTGACTATAAAAA
62502 GTTACAAAATGATCATTCAACTATTCATTATGTTTCAAACTTGTCATTTTCCGTTAAAAAAATT-
66 GTTACAAAATGATCATTCAACTATTCATTATGTTTCAAACTTGTCATTTTCCGTT-AAAAAATTG
62566 ACGGTTGTTTAAGCTGGATGTCAACATGATGAATGAGATATGATAATCATTTGAGATTATAGTAT
130 ACGGTTGTTTAAGCTGGATGTCAACATGATGAATGAGATATGATAATCATTTGAGATTATAGTAT
* *
62631 CATATTTTATTATATCACAATCAACAAATTAACGTTCAACTCAAAATATTGTCAATTTTTAATGA
195 CAAATTTTATCATATCACAATCAACAAATTAACGTTCAACTCAAAATATTGTCAATTTTTAATGA
** * * * *
62696 AAAAGGATGAGTTTAAAACATAATGAATAGGCGGGTGACCATTTTGGAACTTTTAATAGTTGAGG
260 AAAAGGATGAGTTTGGAACATAATAAATAGTCGGGTGACCATTTTGTAACTTTTAATAGTTGAGT
* * * *
62761 GACTCAACAAAACAACACCCTATAGTCGGATGACTGTTTTGTAACATTTAATAGTCGAGTGATTT
325 GACTCAACAAAACAACACTCTATAGTCGGATGACTGTTTTGTAACTTTTAATAGCCGAGTGACTT
62826 AA
390 AA
62828 TAAAAGTTACATAATTATCCTCTAACTATAGAATGTTGTTTTATTAAATCCCTTGACTATAAAAA
1 TAAAAGTTACATAATTATCCTCTAACTATAGAATGTTGTTTTATTAAATCCCTTGACTATAAAAA
*
62893 GTTACAAAATGATCATTCAACTATTCATTATGTTTTAAACTTGTCATTTTCCGTTAAAAAATTGA
66 GTTACAAAATGATCATTCAACTATTCATTATGTTTCAAACTTGTCATTTTCCGTTAAAAAATTGA
* * * * *
62958 CGATTGTTTAAGTTGGATGTCAACATGATGAGTAAGATATGATAATCATTTGAGATTTTAGTATC
131 CGGTTGTTTAAGCTGGATGTCAACATGATGAATGAGATATGATAATCATTTGAGATTATAGTATC
* * * * *
63023 AAATTTTATCATATCGCAATCAACAGATTAACGTTCATCTTAAAATACTGT-ACATTTTTAATGA
196 AAATTTTATCATATCACAATCAACAAATTAACGTTCAACTCAAAATATTGTCA-ATTTTTAATGA
* *
63087 AAAAGGATGAGTTTGGAACATAATAAATAATTGGGTGACCATTTTGTAACTTTTAATAGTTGAGT
260 AAAAGGATGAGTTTGGAACATAATAAATAGTCGGGTGACCATTTTGTAACTTTTAATAGTTGAGT
* *
63152 GACTCAACAAAACAACACTCTATAGTCGGATGACTGTTTTGTAACTTTTAATAGCCGAATGACCT
325 GACTCAACAAAACAACACTCTATAGTCGGATGACTGTTTTGTAACTTTTAATAGCCGAGTGACTT
63217 AA
390 AA
63219 TAAAA
1 TAAAA
63224 TATTATACTA
Statistics
Matches: 723, Mismatches: 61, Indels: 6
0.92 0.08 0.01
Matches are distributed among these distances:
390 9 0.01
391 706 0.98
392 8 0.01
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.36
Consensus pattern (391 bp):
TAAAAGTTACATAATTATCCTCTAACTATAGAATGTTGTTTTATTAAATCCCTTGACTATAAAAA
GTTACAAAATGATCATTCAACTATTCATTATGTTTCAAACTTGTCATTTTCCGTTAAAAAATTGA
CGGTTGTTTAAGCTGGATGTCAACATGATGAATGAGATATGATAATCATTTGAGATTATAGTATC
AAATTTTATCATATCACAATCAACAAATTAACGTTCAACTCAAAATATTGTCAATTTTTAATGAA
AAAGGATGAGTTTGGAACATAATAAATAGTCGGGTGACCATTTTGTAACTTTTAATAGTTGAGTG
ACTCAACAAAACAACACTCTATAGTCGGATGACTGTTTTGTAACTTTTAATAGCCGAGTGACTTA
A
Found at i:63831 original size:4 final size:4
Alignment explanation
Indices: 63822--63896 Score: 141
Period size: 4 Copynumber: 18.8 Consensus size: 4
63812 TGTTCATCCA
*
63822 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TGTG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
63870 TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TAT
63897 TTGTGTGTGT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
4 69 1.00
ACGTcount: A:0.24, C:0.00, G:0.25, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:72057 original size:6 final size:6
Alignment explanation
Indices: 72046--72084 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
72036 ATACCTTCTG
* * *
72046 TTTGCA TTTGCA TTTGCA TTTTCA TTTTCA TTTTCA TTT
1 TTTGCA TTTGCA TTTGCA TTTGCA TTTGCA TTTGCA TTT
72085 TTTTTTTGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.15, C:0.15, G:0.08, T:0.62
Consensus pattern (6 bp):
TTTGCA
Found at i:72063 original size:12 final size:12
Alignment explanation
Indices: 72046--72084 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
72036 ATACCTTCTG
*
72046 TTTGCATTTGCA
1 TTTGCATTTTCA
72058 TTTGCATTTTCA
1 TTTGCATTTTCA
*
72070 TTTTCATTTTCA
1 TTTGCATTTTCA
72082 TTT
1 TTT
72085 TTTTTTTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.15, C:0.15, G:0.08, T:0.62
Consensus pattern (12 bp):
TTTGCATTTTCA
Found at i:72085 original size:6 final size:6
Alignment explanation
Indices: 72050--72085 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
72040 CTTCTGTTTG
* *
72050 CATTTG CATTTG CATTTT CATTTT CATTTT CATTTT
1 CATTTT CATTTT CATTTT CATTTT CATTTT CATTTT
72086 TTTTTTGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.17, C:0.17, G:0.06, T:0.61
Consensus pattern (6 bp):
CATTTT
Found at i:80171 original size:36 final size:36
Alignment explanation
Indices: 80119--80197 Score: 117
Period size: 36 Copynumber: 2.2 Consensus size: 36
80109 TGGCAACCAA
80119 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* *
80154 CTTTGAAAAATGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
80190 -GTTGAAAA
1 CTTTGAAAA
80198 TAGGAATGGG
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 12 0.30
36 28 0.70
ACGTcount: A:0.30, C:0.05, G:0.20, T:0.44
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:82445 original size:2 final size:2
Alignment explanation
Indices: 82401--82428 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
82391 TTTCAAAACA
82401 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
82429 TTAACATTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.