Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020340.1 Corchorus olitorius cultivar O-4 contig20373, 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: 20869
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Found at i:21 original size:5 final size:5
Alignment explanation
Indices: 11--50 Score: 62
Period size: 5 Copynumber: 8.0 Consensus size: 5
1 AGAGAGAGAG
* *
11 AGAAA AGAAA AGAAA AGAAA AGAAA AGGAA ATAAA AGAAA
1 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA
51 TTGGATTGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.03
Consensus pattern (5 bp):
AGAAA
Found at i:156 original size:15 final size:15
Alignment explanation
Indices: 114--160 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
104 GACGTTTTTC
*
114 AAAAATGATTTTCAA
1 AAAAATGACTTTCAA
* *
129 GAAACTG-CTTTCAA
1 AAAAATGACTTTCAA
143 AAAAATGACTTTCAA
1 AAAAATGACTTTCAA
158 AAA
1 AAA
161 TGAGTTTTCC
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 11 0.42
15 15 0.58
ACGTcount: A:0.51, C:0.13, G:0.09, T:0.28
Consensus pattern (15 bp):
AAAAATGACTTTCAA
Found at i:169 original size:14 final size:13
Alignment explanation
Indices: 109--174 Score: 53
Period size: 13 Copynumber: 4.7 Consensus size: 13
99 TAAAGGACGT
109 TTTTCAAAAATGA
1 TTTTCAAAAATGA
122 TTTTCAAGAAACTG-
1 TTTTCAA-AAA-TGA
*
136 CTTTCAAAAAAATGA
1 TTTTC--AAAAATGA
*
151 CTTTCAAAAATGA
1 TTTTCAAAAATGA
164 GTTTTCCAAAA
1 -TTTT-CAAAA
175 GGTTTTGAGT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
13 15 0.34
14 12 0.27
15 15 0.34
16 2 0.05
ACGTcount: A:0.44, C:0.14, G:0.09, T:0.33
Consensus pattern (13 bp):
TTTTCAAAAATGA
Found at i:866 original size:8 final size:8
Alignment explanation
Indices: 822--883 Score: 54
Period size: 8 Copynumber: 7.4 Consensus size: 8
812 TCTAAAGAAG
822 AAAGAAAA
1 AAAGAAAA
*
830 AAAAAAAA
1 AAAGAAAA
838 AGCAGAGAAAA
1 A--A-AGAAAA
**
849 AAAGTGAA
1 AAAGAAAA
857 AAAGAAAA
1 AAAGAAAA
865 AAAG-AAA
1 AAAGAAAA
872 AAAGAAAGA
1 AAAGAAA-A
881 AAA
1 AAA
884 ATCAAAAGGT
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
7 7 0.16
8 24 0.56
9 5 0.12
10 1 0.02
11 6 0.14
ACGTcount: A:0.81, C:0.02, G:0.16, T:0.02
Consensus pattern (8 bp):
AAAGAAAA
Found at i:1858 original size:37 final size:37
Alignment explanation
Indices: 1806--2008 Score: 155
Period size: 37 Copynumber: 5.4 Consensus size: 37
1796 TGTTCAAAAT
* *
1806 TCAAAATCTTGTTCAAGGTCTCTGTTTAGATTTCTTG
1 TCAAAATCTTATTCAAGGTCTCTGTTTAGATTTCTTA
* *
1843 TCAAAATCTTATTCAAGAT-TCCTGTTTAGGTTTCTTA
1 TCAAAATCTTATTCAAGGTCT-CTGTTTAGATTTCTTA
* * * * * *
1880 T-TAAATCCTTATTTAAGGTCCCTGTTTAGGTGTCTCA
1 TCAAAAT-CTTATTCAAGGTCTCTGTTTAGATTTCTTA
* * *
1917 TCAAAATCTTGTTCAAGAAT-TCTGTTTCGATTTCTTA
1 TCAAAATCTTATTCAAG-GTCTCTGTTTAGATTTCTTA
* *
1954 TC-AAATCCTTATTTAAGGGGTGC-CTGTTTAGATTTCTTG
1 TCAAAAT-CTTATTCAA--GGT-CTCTGTTTAGATTTCTTA
* *
1993 TCAAATTCTTGTTCAA
1 TCAAAATCTTATTCAA
2009 AAATTCCTAT
Statistics
Matches: 128, Mismatches: 27, Indels: 20
0.73 0.15 0.11
Matches are distributed among these distances:
36 9 0.07
37 86 0.67
38 6 0.05
39 24 0.19
40 3 0.02
ACGTcount: A:0.24, C:0.17, G:0.14, T:0.45
Consensus pattern (37 bp):
TCAAAATCTTATTCAAGGTCTCTGTTTAGATTTCTTA
Found at i:1942 original size:74 final size:75
Alignment explanation
Indices: 1820--2024 Score: 261
Period size: 74 Copynumber: 2.7 Consensus size: 75
1810 AATCTTGTTC
* * *
1820 AAGGTCTCTGTTTAGATTTCTTGTCAAAATCTTATTCAAG-ATTCCTGTTTAGGTTTCTTATTAA
1 AAGGTCCCTGTTTAGATTTCTTGTCAAAATCTTGTTCAAGAATTCCTGTTTAGGTTTCTTATCAA
1884 ATCCTTATTT
66 ATCCTTATTT
* * ** * *
1894 AAGGTCCCTGTTTAGGTGTCTCATCAAAATCTTGTTCAAGAATT-CTGTTTCGATTTCTTATCAA
1 AAGGTCCCTGTTTAGATTTCTTGTCAAAATCTTGTTCAAGAATTCCTGTTTAGGTTTCTTATCAA
1958 ATCCTTATTT
66 ATCCTTATTT
* * * *
1968 AAGGGGTGCCTGTTTAGATTTCTTGTCAAATTCTTGTTCAAAAATTCCTATTTAGGT
1 AA--GGTCCCTGTTTAGATTTCTTGTCAAAATCTTGTTCAAGAATTCCTGTTTAGGT
2025 GTTTAAGATG
Statistics
Matches: 108, Mismatches: 19, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
74 63 0.58
75 3 0.03
76 35 0.32
77 7 0.06
ACGTcount: A:0.24, C:0.16, G:0.15, T:0.45
Consensus pattern (75 bp):
AAGGTCCCTGTTTAGATTTCTTGTCAAAATCTTGTTCAAGAATTCCTGTTTAGGTTTCTTATCAA
ATCCTTATTT
Found at i:2109 original size:54 final size:54
Alignment explanation
Indices: 2027--2546 Score: 585
Period size: 54 Copynumber: 9.7 Consensus size: 54
2017 ATTTAGGTGT
*
2027 TTAAGATG-ACCTAGTGCGGTCTTCCATAGAAGTTTTCAGATATCTAAGTTGATC
1 TTAAGATGAACC-AGTGCGGTCTTCCATAGAAGTTTTCAGAGATCTAAGTTGATC
2081 TTAAGATGAACCAGTGCGGTCTTCCATAGAAGTTTTCAGAGATCTAAGTTGATC
1 TTAAGATGAACCAGTGCGGTCTTCCATAGAAGTTTTCAGAGATCTAAGTTGATC
* * *
2135 TTAAAATGACCCAGTGCGGTCTTCCATAGAAGTTTTCAGAGTTCTAAGTTGATC
1 TTAAGATGAACCAGTGCGGTCTTCCATAGAAGTTTTCAGAGATCTAAGTTGATC
* *
2189 CTAAGATGACCCAGTGCGGTCTTCCATAGAAGTTTTCAGAGATCTAAGTTGATC
1 TTAAGATGAACCAGTGCGGTCTTCCATAGAAGTTTTCAGAGATCTAAGTTGATC
* **
2243 TTAAGATGACCCAGTGCGAACTTCCATAGAAGTTTTCAGAGATCTAAGTTGATC
1 TTAAGATGAACCAGTGCGGTCTTCCATAGAAGTTTTCAGAGATCTAAGTTGATC
* * * * *
2297 TTAAAATG-ACCAAGTGTGGTCTTTCATGGAAGTTTTTAGAGATCTAAGTTGATC
1 TTAAGATGAACC-AGTGCGGTCTTCCATAGAAGTTTTCAGAGATCTAAGTTGATC
* * *
2351 TTCAGATG-ACCTAGTGCGGTCTTCCATAGAAGCTTTCTA-AGATCTATGTTGATC
1 TTAAGATGAACC-AGTGCGGTCTTCCATAGAAGTTTTC-AGAGATCTAAGTTGATC
* * * *** *
2405 TTCAA-ATGACCCAGTGCGGTCTTCCATAGAGGGTTTCAGAGAT-TTTTTTTATC
1 TT-AAGATGAACCAGTGCGGTCTTCCATAGAAGTTTTCAGAGATCTAAGTTGATC
* * * * *
2458 TTAAGATGATCCAGTGCAGTCATTTCA-AAAAGTTTT-TGAGGATC-AGAGTTGATC
1 TTAAGATGAACCAGTGCGGTC-TTCCATAGAAGTTTTCAGA-GATCTA-AGTTGATC
* * * *
2512 CT-CGATGATCCAGTGCGGTCATTGCA-AGAAGTTTT
1 TTAAGATGAACCAGTGCGGTC-TTCCATAGAAGTTTT
2547 TAATGATTTA
Statistics
Matches: 405, Mismatches: 50, Indels: 23
0.85 0.10 0.05
Matches are distributed among these distances:
52 4 0.01
53 64 0.16
54 330 0.81
55 7 0.02
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (54 bp):
TTAAGATGAACCAGTGCGGTCTTCCATAGAAGTTTTCAGAGATCTAAGTTGATC
Found at i:2295 original size:162 final size:162
Alignment explanation
Indices: 2028--2447 Score: 655
Period size: 162 Copynumber: 2.6 Consensus size: 162
2018 TTTAGGTGTT
* *
2028 TAAGATGACCTAGTGCGGTCTTCCATAGAAGTTTTCAGATATCTAAGTTGATCTTAAGATGAACC
1 TAAGATGACCTAGTGCGGTCTTCCATAGAAGTTTTCAGAGATCTAAGTTGATCTTAAGATGACCC
*
2093 AGTGCGGTCTTCCATAGAAGTTTTCAGAGATCTAAGTTGATCTTAAAATGACCCAGTGCGGTCTT
66 AGTGCGGTCTTCCATAGAAGTTTTCAGAGATCTAAGTTGATCTTAAAATGACCAAGTGCGGTCTT
*
2158 CCATAGAAGTTTTCAGAGTTCTAAGTTGATCC
131 CCATAGAAGTTTTCAGAGATCTAAGTTGATCC
*
2190 TAAGATGACCCAGTGCGGTCTTCCATAGAAGTTTTCAGAGATCTAAGTTGATCTTAAGATGACCC
1 TAAGATGACCTAGTGCGGTCTTCCATAGAAGTTTTCAGAGATCTAAGTTGATCTTAAGATGACCC
** *
2255 AGTGCGAACTTCCATAGAAGTTTTCAGAGATCTAAGTTGATCTTAAAATGACCAAGTGTGGTCTT
66 AGTGCGGTCTTCCATAGAAGTTTTCAGAGATCTAAGTTGATCTTAAAATGACCAAGTGCGGTCTT
* * * *
2320 TCATGGAAGTTTTTAGAGATCTAAGTTGATCT
131 CCATAGAAGTTTTCAGAGATCTAAGTTGATCC
* * *
2352 TCAGATGACCTAGTGCGGTCTTCCATAGAAGCTTTCTA-AGATCTATGTTGATCTTCAA-ATGAC
1 TAAGATGACCTAGTGCGGTCTTCCATAGAAGTTTTC-AGAGATCTAAGTTGATCTT-AAGATGAC
* *
2415 CCAGTGCGGTCTTCCATAGAGGGTTTCAGAGAT
64 CCAGTGCGGTCTTCCATAGAAGTTTTCAGAGAT
2448 TTTTTTTATC
Statistics
Matches: 236, Mismatches: 20, Indels: 4
0.91 0.08 0.02
Matches are distributed among these distances:
162 233 0.99
163 3 0.01
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (162 bp):
TAAGATGACCTAGTGCGGTCTTCCATAGAAGTTTTCAGAGATCTAAGTTGATCTTAAGATGACCC
AGTGCGGTCTTCCATAGAAGTTTTCAGAGATCTAAGTTGATCTTAAAATGACCAAGTGCGGTCTT
CCATAGAAGTTTTCAGAGATCTAAGTTGATCC
Found at i:2626 original size:47 final size:47
Alignment explanation
Indices: 2567--2715 Score: 163
Period size: 47 Copynumber: 3.0 Consensus size: 47
2557 GTATGGTCAT
* *
2567 TCCAAGAAGTTTTCGATGATTAGAGTTGATCTCAAATTGGTCTAGTG
1 TCCAAGAAGTTTTCGATGATCAGAGTTGATCTCAAATTGATCTAGTG
*
2614 TCCAAGAAGTTTTCGATGATCAGAGTTGATCTCCAATTGATCTAGTGTAG
1 TCCAAGAAGTTTTCGATGATCAGAGTTGATCTCAAATTGATCTA--GT-G
* * * *
2664 TCATTCCAAGAAATTTACGATGATCAGAGTTTATCTCTAAATTGATCCAGTG
1 ----TCCAAGAAGTTTTCGATGATCAGAGTTGATCTC-AAATTGATCTAGTG
2716 CGGTCGTTCC
Statistics
Matches: 86, Mismatches: 8, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
47 41 0.48
49 2 0.02
50 1 0.01
52 1 0.01
53 2 0.02
54 30 0.35
55 9 0.10
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (47 bp):
TCCAAGAAGTTTTCGATGATCAGAGTTGATCTCAAATTGATCTAGTG
Found at i:2685 original size:54 final size:55
Alignment explanation
Indices: 2614--2731 Score: 157
Period size: 54 Copynumber: 2.2 Consensus size: 55
2604 TGGTCTAGTG
* * * * *
2614 TCCAAGAAGTTTTCGATGATCAGAGTTGATCTC-CAATTGATCTAGTGTAGTCAT
1 TCCAAGAAATTTACGATGATCAGAGTTGATCTCTAAATTGATCCAGTGCAGTCAT
* * *
2668 TCCAAGAAATTTACGATGATCAGAGTTTATCTCTAAATTGATCCAGTGCGGTCGT
1 TCCAAGAAATTTACGATGATCAGAGTTGATCTCTAAATTGATCCAGTGCAGTCAT
2723 TCCAAGAAA
1 TCCAAGAAA
2732 GGTTTCCTGA
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
54 30 0.55
55 25 0.45
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (55 bp):
TCCAAGAAATTTACGATGATCAGAGTTGATCTCTAAATTGATCCAGTGCAGTCAT
Found at i:3075 original size:7 final size:7
Alignment explanation
Indices: 2974--3077 Score: 91
Period size: 7 Copynumber: 14.9 Consensus size: 7
2964 ATTTCATTGC
2974 TCAAAAT
1 TCAAAAT
*
2981 TCGAAAT
1 TCAAAAT
*
2988 TCGAAAT
1 TCAAAAT
**
2995 TTGAAAT
1 TCAAAAT
*
3002 TCGAAAT
1 TCAAAAT
*
3009 TCAAAAC
1 TCAAAAT
* *
3016 TGAAAAC
1 TCAAAAT
*
3023 TCAAAAC
1 TCAAAAT
*
3030 TCAAAAC
1 TCAAAAT
*
3037 TCAAAAC
1 TCAAAAT
3044 TCAAAAT
1 TCAAAAT
3051 TCAAAAT
1 TCAAAAT
*
3058 TCAAAAA
1 TCAAAAT
*
3065 TCAAATT
1 TCAAAAT
3072 TCAAAA
1 TCAAAA
3078 CCTACATTTC
Statistics
Matches: 85, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 85 1.00
ACGTcount: A:0.54, C:0.17, G:0.05, T:0.24
Consensus pattern (7 bp):
TCAAAAT
Found at i:3094 original size:23 final size:23
Alignment explanation
Indices: 3065--3110 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
3055 AATTCAAAAA
3065 TCAAATTTCAAAACCTACATTTC
1 TCAAATTTCAAAACCTACATTTC
*
3088 TCAAATTTCAAAACCTGCATTTC
1 TCAAATTTCAAAACCTACATTTC
3111 AGCATTTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.37, C:0.26, G:0.02, T:0.35
Consensus pattern (23 bp):
TCAAATTTCAAAACCTACATTTC
Found at i:3134 original size:7 final size:7
Alignment explanation
Indices: 3124--3157 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
3114 ATTTCATTCT
3124 TCAAAAG
1 TCAAAAG
3131 TCAAAAG
1 TCAAAAG
*
3138 TCAAAAA
1 TCAAAAG
*
3145 TCAAAAT
1 TCAAAAG
3152 TCAAAA
1 TCAAAA
3158 TTTGCATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.62, C:0.15, G:0.06, T:0.18
Consensus pattern (7 bp):
TCAAAAG
Found at i:3224 original size:34 final size:33
Alignment explanation
Indices: 3138--3225 Score: 97
Period size: 33 Copynumber: 2.6 Consensus size: 33
3128 AAGTCAAAAG
* * ** *
3138 TCAAAAATCAAAATTCAAAATTTGCATTTTTTT
1 TCAAAACTCAAAATCCAAAATTTGCATTCATGT
*
3171 TCAAAACTCGAAA-CTCAAAATTTGCATGTCATGT
1 TCAAAACTCAAAATC-CAAAATTTGCAT-TCATGT
3205 TCAAAACTCAAAATCCAAAAT
1 TCAAAACTCAAAATCCAAAAT
3226 CTGCTTTTCT
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
33 23 0.51
34 21 0.47
35 1 0.02
ACGTcount: A:0.44, C:0.18, G:0.06, T:0.32
Consensus pattern (33 bp):
TCAAAACTCAAAATCCAAAATTTGCATTCATGT
Found at i:8860 original size:27 final size:27
Alignment explanation
Indices: 8814--8865 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
8804 AATACAATGT
*
8814 AAACAAATTAGCAATATCTAGTTAGCA
1 AAACAAATTAGCAATATCTAATTAGCA
*
8841 AAACTAAATTAG-AATTTCTAATTAG
1 AAAC-AAATTAGCAATATCTAATTAG
8866 TTCACCCAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 15 0.68
28 7 0.32
ACGTcount: A:0.48, C:0.12, G:0.10, T:0.31
Consensus pattern (27 bp):
AAACAAATTAGCAATATCTAATTAGCA
Found at i:10240 original size:2 final size:2
Alignment explanation
Indices: 10235--10259 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10225 TATATAATCA
10235 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
10260 ATCTATGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10818 original size:21 final size:21
Alignment explanation
Indices: 10792--10838 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
10782 GTATGTGTAT
*
10792 TTTTGT-CCCACTTTATGTGGG
1 TTTTGTGCCC-CTTTATGTAGG
*
10813 TTTTGTGTCCCTTTATGTAGG
1 TTTTGTGCCCCTTTATGTAGG
10834 TTTTG
1 TTTTG
10839 GTTAGTTAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.09, C:0.15, G:0.23, T:0.53
Consensus pattern (21 bp):
TTTTGTGCCCCTTTATGTAGG
Found at i:15643 original size:92 final size:92
Alignment explanation
Indices: 15482--15663 Score: 319
Period size: 92 Copynumber: 2.0 Consensus size: 92
15472 TACTTAAAGA
* *
15482 TACCCTTATTAATGTGACTTTTGAATGTCATGAGGTTTTTAATCTGAGCCCTTGATTCAAGCATT
1 TACCCTCATTAATGTGACTTTTGAATGTCATGAGGTTTTTAATCTGAGCCCTTGATTCAAGCATA
*
15547 CATGGGCCGTTGGATTAGTTCTTTAAG
66 CATGGGCCATTGGATTAGTTCTTTAAG
*
15574 TACCCTCATTAATGTGACTTTTGAATGTCATGGGGTTTTTAATCTGAGCCCTTGATTCAAGCATA
1 TACCCTCATTAATGTGACTTTTGAATGTCATGAGGTTTTTAATCTGAGCCCTTGATTCAAGCATA
*
15639 CATGGGCCATTGGATTAGTTGTTTA
66 CATGGGCCATTGGATTAGTTCTTTA
15664 CCCTCCTATA
Statistics
Matches: 85, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
92 85 1.00
ACGTcount: A:0.23, C:0.16, G:0.21, T:0.40
Consensus pattern (92 bp):
TACCCTCATTAATGTGACTTTTGAATGTCATGAGGTTTTTAATCTGAGCCCTTGATTCAAGCATA
CATGGGCCATTGGATTAGTTCTTTAAG
Found at i:18224 original size:69 final size:69
Alignment explanation
Indices: 18136--18273 Score: 258
Period size: 69 Copynumber: 2.0 Consensus size: 69
18126 TGGCAGTGTT
*
18136 TTGGGTAGGCTATGACTTGTGTTTGTTTGCCCATTGTCGTCCTTTTTGAGTTTAAGTTGTCTTTG
1 TTGGGTAGACTATGACTTGTGTTTGTTTGCCCATTGTCGTCCTTTTTGAGTTTAAGTTGTCTTTG
18201 TCTA
66 TCTA
*
18205 TTGGGTAGACTATGACTTGTGTTTGTTTGCCCATTGTCGTCCTTTTTTAGTTTAAGTTGTCTTTG
1 TTGGGTAGACTATGACTTGTGTTTGTTTGCCCATTGTCGTCCTTTTTGAGTTTAAGTTGTCTTTG
18270 TCTA
66 TCTA
18274 CATGGATGCT
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 67 1.00
ACGTcount: A:0.12, C:0.14, G:0.23, T:0.50
Consensus pattern (69 bp):
TTGGGTAGACTATGACTTGTGTTTGTTTGCCCATTGTCGTCCTTTTTGAGTTTAAGTTGTCTTTG
TCTA
Found at i:18686 original size:76 final size:76
Alignment explanation
Indices: 18560--19037 Score: 659
Period size: 76 Copynumber: 6.1 Consensus size: 76
18550 GGCAATTTAC
* * * *
18560 TTCTTTTACTTCCTCCCTATGTGTCTCTTTCGCACATAGGGTGGCAATTTACACTTGGAAGTTTT
1 TTCTTTTACTTCCTCCCTATGTGTCTCATCCGCACATAGGGTGACAAGTTACACTTGGAAGTTTT
*
18625 TACTTCCGAGT
66 TACTTCCAAGT
* *
18636 TTCTTTTACTTCCTCCCTATGTGTCTCATCCGCACATAGGGTGGCAATTTACACTTGGAAGTTTT
1 TTCTTTTACTTCCTCCCTATGTGTCTCATCCGCACATAGGGTGACAAGTTACACTTGGAAGTTTT
18701 TACTTCCAAGT
66 TACTTCCAAGT
* *
18712 TTCTTTTACTTCCTCCCTATGTGTCACATCCGCACATAGGGTGACAAGTTACACTTGAAAGTTTT
1 TTCTTTTACTTCCTCCCTATGTGTCTCATCCGCACATAGGGTGACAAGTTACACTTGGAAGTTTT
18777 TACTTCCAAGT
66 TACTTCCAAGT
* *
18788 TTCTTTTACTTCCTCCCTATGTTTCTCATCCGCACATCCGCACATAGGGTGACCAGTTACACTTG
1 TTCTTTTACTTCCTCCCTATG--TGTC-T-----CATCCGCACATAGGGTGACAAGTTACACTTG
18853 GAAGTTTTTACTTCCAAGT
58 GAAGTTTTTACTTCCAAGT
*
18872 TTCTTTTACTTCCTCCCTATGTGTCTCATCCGCACATCCGCACATAGGGTGACCAGTTACACTTG
1 TTCTTTTACTTCCTCCCTATGTG--TC-T-----CATCCGCACATAGGGTGACAAGTTACACTTG
18937 GAAGTTTTTACTTCCAAGT
58 GAAGTTTTTACTTCCAAGT
* * * *
18956 TTCTTTTACTTCCTCCCTACGTGTCTCATCCGCACATAGGGTGGCAATTTACACTTGGAAGTTTC
1 TTCTTTTACTTCCTCCCTATGTGTCTCATCCGCACATAGGGTGACAAGTTACACTTGGAAGTTTT
*
19021 TACTTCCAAAT
66 TACTTCCAAGT
19032 TTCTTT
1 TTCTTT
19038 GAGTTCTTAT
Statistics
Matches: 374, Mismatches: 18, Indels: 20
0.91 0.04 0.05
Matches are distributed among these distances:
76 217 0.58
78 3 0.01
81 1 0.00
82 3 0.01
84 150 0.40
ACGTcount: A:0.20, C:0.26, G:0.15, T:0.38
Consensus pattern (76 bp):
TTCTTTTACTTCCTCCCTATGTGTCTCATCCGCACATAGGGTGACAAGTTACACTTGGAAGTTTT
TACTTCCAAGT
Found at i:18877 original size:84 final size:84
Alignment explanation
Indices: 18736--18992 Score: 478
Period size: 84 Copynumber: 3.1 Consensus size: 84
18726 CCCTATGTGT
* *
18736 CACATCCGCACATAGGGTGACAAGTTACACTTGAAAGTTTTTACTTCCAAGTTTCTTTTACTTCC
1 CACATCCGCACATAGGGTGACCAGTTACACTTGGAAGTTTTTACTTCCAAGTTTCTTTTACTTCC
*
18801 TCCCTATGTTTCTCATCCG
66 TCCCTATGTGTCTCATCCG
18820 CACATCCGCACATAGGGTGACCAGTTACACTTGGAAGTTTTTACTTCCAAGTTTCTTTTACTTCC
1 CACATCCGCACATAGGGTGACCAGTTACACTTGGAAGTTTTTACTTCCAAGTTTCTTTTACTTCC
18885 TCCCTATGTGTCTCATCCG
66 TCCCTATGTGTCTCATCCG
18904 CACATCCGCACATAGGGTGACCAGTTACACTTGGAAGTTTTTACTTCCAAGTTTCTTTTACTTCC
1 CACATCCGCACATAGGGTGACCAGTTACACTTGGAAGTTTTTACTTCCAAGTTTCTTTTACTTCC
*
18969 TCCCTACGTGTCTCATCCG
66 TCCCTATGTGTCTCATCCG
18988 CACAT
1 CACAT
18993 AGGGTGGCAA
Statistics
Matches: 169, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 169 1.00
ACGTcount: A:0.21, C:0.29, G:0.14, T:0.35
Consensus pattern (84 bp):
CACATCCGCACATAGGGTGACCAGTTACACTTGGAAGTTTTTACTTCCAAGTTTCTTTTACTTCC
TCCCTATGTGTCTCATCCG
Found at i:18993 original size:160 final size:152
Alignment explanation
Indices: 18560--19037 Score: 677
Period size: 160 Copynumber: 3.0 Consensus size: 152
18550 GGCAATTTAC
* * * * *
18560 TTCTTTTACTTCCTCCCTATGTGTCTCTTTCGCACATAGGGTGGCAATTTACACTTGGAAGTTTT
1 TTCTTTTACTTCCTCCCTATGTGTCACATCCGCACATAGGGTGACAAGTTACACTTGGAAGTTTT
*
18625 TACTTCCGAGTTTCTTTTACTTCCTCCCTATGTGTCTCATCCGCACATAGGGTGGCAATTTACAC
66 TACTTCCAAGTTTCTTTTACTTCCTCCCTATGTGTCTCATCCGCACATAGGGTGGCAATTTACAC
18690 TTGGAAGTTTTTACTTCCAAGT
131 TTGGAAGTTTTTACTTCCAAGT
*
18712 TTCTTTTACTTCCTCCCTATGTGTCACATCCGCACATAGGGTGACAAGTTACACTTGAAAGTTTT
1 TTCTTTTACTTCCTCCCTATGTGTCACATCCGCACATAGGGTGACAAGTTACACTTGGAAGTTTT
* * *
18777 TACTTCCAAGTTTCTTTTACTTCCTCCCTATGTTTCTCATCCGCACATCCGCACATAGGGTGACC
66 TACTTCCAAGTTTCTTTTACTTCCTCCCTATG--TGTC-T-----CATCCGCACATAGGGTGGCA
*
18842 AGTTACACTTGGAAGTTTTTACTTCCAAGT
123 ATTTACACTTGGAAGTTTTTACTTCCAAGT
*
18872 TTCTTTTACTTCCTCCCTATGTGTCTCATCCGCACATCCGCACATAGGGTGACCAGTTACACTTG
1 TTCTTTTACTTCCTCCCTATGTG-----T---CACATCCGCACATAGGGTGACAAGTTACACTTG
*
18937 GAAGTTTTTACTTCCAAGTTTCTTTTACTTCCTCCCTACGTGTCTCATCCGCACATAGGGTGGCA
58 GAAGTTTTTACTTCCAAGTTTCTTTTACTTCCTCCCTATGTGTCTCATCCGCACATAGGGTGGCA
* *
19002 ATTTACACTTGGAAGTTTCTACTTCCAAAT
123 ATTTACACTTGGAAGTTTTTACTTCCAAGT
19032 TTCTTT
1 TTCTTT
19038 GAGTTCTTAT
Statistics
Matches: 290, Mismatches: 20, Indels: 24
0.87 0.06 0.07
Matches are distributed among these distances:
152 90 0.31
154 3 0.01
155 1 0.00
160 121 0.42
165 2 0.01
166 3 0.01
168 70 0.24
ACGTcount: A:0.20, C:0.26, G:0.15, T:0.38
Consensus pattern (152 bp):
TTCTTTTACTTCCTCCCTATGTGTCACATCCGCACATAGGGTGACAAGTTACACTTGGAAGTTTT
TACTTCCAAGTTTCTTTTACTTCCTCCCTATGTGTCTCATCCGCACATAGGGTGGCAATTTACAC
TTGGAAGTTTTTACTTCCAAGT
Found at i:19186 original size:40 final size:40
Alignment explanation
Indices: 19088--19298 Score: 190
Period size: 40 Copynumber: 5.0 Consensus size: 40
19078 TAGCGAGCGA
* * * *
19088 GAGTTTTTTCTTCCAAATTTTGTACTTGGAAATTTTTTTTTT
1 GAGTTTATACTTCCAAATTTTATACTTGGAAA--TTTCTTTT
*
19130 CGAGTTTATACTTCCAAATTTTATACCTGGAAATTTCTTTT
1 -GAGTTTATACTTCCAAATTTTATACTTGGAAATTTCTTTT
* *
19171 GAGTTTATACTTCCAAATTTCATACTTGGAAATTTCTTAACACCGAGTGA
1 GAGTTTATACTTCCAAATTTTATACTTGGAAATTTCTT---------T-T
* * *
19221 GAGTTTTTACTTCCAAATTTTGTACTTGGAAATTTCGTTT
1 GAGTTTATACTTCCAAATTTTATACTTGGAAATTTCTTTT
*
19261 GAGTTTATACTTCCAAATTTCT-TACTTGGGAATTTCTT
1 GAGTTTATACTTCCAAATTT-TATACTTGGAAATTTCTT
19299 AACACCGGAT
Statistics
Matches: 141, Mismatches: 16, Indels: 25
0.77 0.09 0.14
Matches are distributed among these distances:
40 69 0.49
41 9 0.06
43 28 0.20
49 1 0.01
50 34 0.24
ACGTcount: A:0.25, C:0.15, G:0.13, T:0.47
Consensus pattern (40 bp):
GAGTTTATACTTCCAAATTTTATACTTGGAAATTTCTTTT
Found at i:19199 original size:133 final size:130
Alignment explanation
Indices: 19028--19298 Score: 377
Period size: 133 Copynumber: 2.1 Consensus size: 130
19018 TTCTACTTCC
* * * * *
19028 AAATTTC-TTTGAGTTCTTATTTCCAAATTTCATGCTTGGAAGTTTCTTAATAGCGAGCGAGAGT
1 AAATTTCTTTTGAGTTCTTACTTCCAAATTTCATACTTGGAAATTTCTTAACACCGAGCGAGAGT
* **
19092 TTTTTCTTCCAAATTTTGTACTTGGAAATTTTTTTTTTCGAGTTTATACTTCCAAATTT-TATAC
66 TTTTACTTCCAAATTTTGTACTTGGAAA--TTTCGTTT-GAGTTTATACTTCCAAATTTCT-TAC
19156 CTGG
127 CTGG
*
19160 AAATTTCTTTTGAGTT-TATACTTCCAAATTTCATACTTGGAAATTTCTTAACACCGAGTGAGAG
1 AAATTTCTTTTGAGTTCT-TACTTCCAAATTTCATACTTGGAAATTTCTTAACACCGAGCGAGAG
*
19224 TTTTTACTTCCAAATTTTGTACTTGGAAATTTCGTTTGAGTTTATACTTCCAAATTTCTTACTTG
65 TTTTTACTTCCAAATTTTGTACTTGGAAATTTCGTTTGAGTTTATACTTCCAAATTTCTTACCTG
19289 G
130 G
*
19290 GAATTTCTT
1 AAATTTCTT
19299 AACACCGGAT
Statistics
Matches: 125, Mismatches: 11, Indels: 8
0.87 0.08 0.06
Matches are distributed among these distances:
130 34 0.27
131 7 0.06
132 8 0.06
133 76 0.61
ACGTcount: A:0.25, C:0.15, G:0.14, T:0.46
Consensus pattern (130 bp):
AAATTTCTTTTGAGTTCTTACTTCCAAATTTCATACTTGGAAATTTCTTAACACCGAGCGAGAGT
TTTTACTTCCAAATTTTGTACTTGGAAATTTCGTTTGAGTTTATACTTCCAAATTTCTTACCTGG
Found at i:19251 original size:90 final size:90
Alignment explanation
Indices: 19131--19305 Score: 296
Period size: 90 Copynumber: 1.9 Consensus size: 90
19121 TTTTTTTTTC
*
19131 GAGTTTATACTTCCAAATTTTATACCTGGAAATTTCTTTTGAGTTTATACTTCCAAATTTCATAC
1 GAGTTTATACTTCCAAATTTTATACCTGGAAATTTCGTTTGAGTTTATACTTCCAAATTTCATAC
19196 TTGGAAATTTCTTAACACCGAGTGA
66 TTGGAAATTTCTTAACACCGAGTGA
* * * *
19221 GAGTTTTTACTTCCAAATTTTGTACTTGGAAATTTCGTTTGAGTTTATACTTCCAAATTTCTTAC
1 GAGTTTATACTTCCAAATTTTATACCTGGAAATTTCGTTTGAGTTTATACTTCCAAATTTCATAC
*
19286 TTGGGAATTTCTTAACACCG
66 TTGGAAATTTCTTAACACCG
19306 GATGTCTGAT
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
90 79 1.00
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.43
Consensus pattern (90 bp):
GAGTTTATACTTCCAAATTTTATACCTGGAAATTTCGTTTGAGTTTATACTTCCAAATTTCATAC
TTGGAAATTTCTTAACACCGAGTGA
Done.