Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019588.1 Corchorus olitorius cultivar O-4 contig19621, 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: 49780
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:129 original size:14 final size:13
Alignment explanation
Indices: 105--168 Score: 85
Period size: 13 Copynumber: 4.8 Consensus size: 13
95 TAAAGGACGT
105 TTTTCAAAAATGA
1 TTTTCAAAAATGA
118 TTTTCAAGAAATTG-
1 TTTTCAA-AAA-TGA
*
132 TTTTCAAGAATGA
1 TTTTCAAAAATGA
145 TTTTCAAAAATGA
1 TTTTCAAAAATGA
158 GTTTTCAAAAA
1 -TTTTCAAAAA
169 GGTTTTGAGT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
12 2 0.04
13 21 0.47
14 20 0.44
15 2 0.04
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39
Consensus pattern (13 bp):
TTTTCAAAAATGA
Found at i:138 original size:27 final size:27
Alignment explanation
Indices: 105--168 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
95 TAAAGGACGT
*
105 TTTTCAAAAATGATTTTCAAGAAAT-TG
1 TTTTCAAAAATGATTTTCAA-AAATGAG
*
132 TTTTCAAGAATGATTTTCAAAAATGAG
1 TTTTCAAAAATGATTTTCAAAAATGAG
159 TTTTCAAAAA
1 TTTTCAAAAA
169 GGTTTTGAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 4 0.12
27 29 0.88
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39
Consensus pattern (27 bp):
TTTTCAAAAATGATTTTCAAAAATGAG
Found at i:431 original size:6 final size:6
Alignment explanation
Indices: 420--452 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
410 AAAAAAAAGG
420 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAA
453 GATTGTTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:1900 original size:37 final size:36
Alignment explanation
Indices: 1859--2135 Score: 234
Period size: 37 Copynumber: 7.4 Consensus size: 36
1849 AGATTCTTGA
*
1859 TTAGGTTACTTATCAAATCCTTATTTAAGGTCCCTGT
1 TTAGGTT-CTCATCAAATCCTTATTTAAGGTCCCTGT
* * * * *
1896 TTAGGTGTCTCATCAAAACCTTGTTCAAGATTCCTGT
1 TTAGGT-TCTCATCAAATCCTTATTTAAGGTCCCTGT
* * * *
1933 TTAGATTTTTTATCAAATCCTTATTTAAGGTCCCTAT
1 TTAG-GTTCTCATCAAATCCTTATTTAAGGTCCCTGT
* * *
1970 TTAGGTGTCTCATCAAAACCTT-TTTCAAGATTCCTGT
1 TTAGGT-TCTCATCAAATCCTTATTT-AAGGTCCCTGT
*
2007 TTAGGTTTCTTATCAAAATCCTTATTTAAGGTCCCTGT
1 TTAGG-TTCTCATC-AAATCCTTATTTAAGGTCCCTGT
* * * *
2045 TTAGGTGTCTCATCAAAAT-CTTGTTCAAGATTCCTGT
1 TTAGGT-TCTCATC-AAATCCTTATTTAAGGTCCCTGT
* * * *
2082 TTAGGTTTCCCATTAAATCCTTATTTAAGGTACCTGA
1 TTAGG-TTCTCATCAAATCCTTATTTAAGGTCCCTGT
*
2119 TTAGGTGTCTCTTCAAA
1 TTAGGT-TCTCATCAAA
2136 ATCCCAGTTT
Statistics
Matches: 188, Mismatches: 41, Indels: 22
0.75 0.16 0.09
Matches are distributed among these distances:
36 9 0.05
37 140 0.74
38 36 0.19
39 3 0.02
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.42
Consensus pattern (36 bp):
TTAGGTTCTCATCAAATCCTTATTTAAGGTCCCTGT
Found at i:1918 original size:74 final size:74
Alignment explanation
Indices: 1828--2136 Score: 483
Period size: 74 Copynumber: 4.2 Consensus size: 74
1818 ACAAAATTCA
* * *
1828 GTCTCATCAAAACCTTGTTCAAGATTCTTGATTAGGTTACTTATCAAATCCTTATTTAAGGTCCC
1 GTCTCATCAAAACCTTGTTCAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTCCC
1893 TGTTTAGGT
66 TGTTTAGGT
* *
1902 GTCTCATCAAAACCTTGTTCAAGATTCCTGTTTAGATTTTTTATCAAATCCTTATTTAAGGTCCC
1 GTCTCATCAAAACCTTGTTCAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTCCC
*
1967 TATTTAGGT
66 TGTTTAGGT
*
1976 GTCTCATCAAAACCTTTTTCAAGATTCCTGTTTAGGTTTCTTATCAAAATCCTTATTTAAGGTCC
1 GTCTCATCAAAACCTTGTTCAAGATTCCTGTTTAGGTTTCTTATC-AAATCCTTATTTAAGGTCC
2041 CTGTTTAGGT
65 CTGTTTAGGT
* ** * *
2051 GTCTCATCAAAATCTTGTTCAAGATTCCTGTTTAGGTTTCCCATTAAATCCTTATTTAAGGTACC
1 GTCTCATCAAAACCTTGTTCAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTCCC
*
2116 TGATTAGGT
66 TGTTTAGGT
*
2125 GTCTCTTCAAAA
1 GTCTCATCAAAA
2137 TCCCAGTTTA
Statistics
Matches: 216, Mismatches: 18, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
74 148 0.69
75 68 0.31
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (74 bp):
GTCTCATCAAAACCTTGTTCAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTCCC
TGTTTAGGT
Found at i:2100 original size:149 final size:148
Alignment explanation
Indices: 1828--2136 Score: 485
Period size: 149 Copynumber: 2.1 Consensus size: 148
1818 ACAAAATTCA
*
1828 GTCTCATCAAAACCTTGTTCAAGATTCTTGATTAGGTTACTTATCAAATCCTTATTTAAGGTCCC
1 GTCTCATCAAAACCTTGTTCAAGATTCCTGATTAGGTTACTTATCAAATCCTTATTTAAGGTCCC
***
1893 TGTTTAGGTGTCTCATCAAAACCTTGTTCAAGATTCCTGTTTAGATTTTTTATCAAATCCTTATT
66 TGTTTAGGTGTCTCATCAAAACCTTGTTCAAGATTCCTGTTTAGATTTCCCATCAAATCCTTATT
*
1958 TAAGGTCCCT-ATTTAGGT
131 TAAGGTACCTGA-TTAGGT
* * *
1976 GTCTCATCAAAACCTTTTTCAAGATTCCTGTTTAGGTTTCTTATCAAAATCCTTATTTAAGGTCC
1 GTCTCATCAAAACCTTGTTCAAGATTCCTGATTAGGTTACTTATC-AAATCCTTATTTAAGGTCC
* * *
2041 CTGTTTAGGTGTCTCATCAAAATCTTGTTCAAGATTCCTGTTTAGGTTTCCCATTAAATCCTTAT
65 CTGTTTAGGTGTCTCATCAAAACCTTGTTCAAGATTCCTGTTTAGATTTCCCATCAAATCCTTAT
2106 TTAAGGTACCTGATTAGGT
130 TTAAGGTACCTGATTAGGT
*
2125 GTCTCTTCAAAA
1 GTCTCATCAAAA
2137 TCCCAGTTTA
Statistics
Matches: 147, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
148 41 0.28
149 105 0.71
150 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (148 bp):
GTCTCATCAAAACCTTGTTCAAGATTCCTGATTAGGTTACTTATCAAATCCTTATTTAAGGTCCC
TGTTTAGGTGTCTCATCAAAACCTTGTTCAAGATTCCTGTTTAGATTTCCCATCAAATCCTTATT
TAAGGTACCTGATTAGGT
Found at i:2172 original size:149 final size:149
Alignment explanation
Indices: 1867--2176 Score: 387
Period size: 149 Copynumber: 2.1 Consensus size: 149
1857 GATTAGGTTA
1867 CTTATC-AAATCCTTATTTAAGGTCCCTGTTTAGGTGTCTCATCAAAACCTTGTTCAAGATTCCT
1 CTTATCAAAATCCTTATTTAAGGTCCCTGTTTAGGTGTCTCATCAAAACCTTGTTCAAGATTCCT
*** * **
1931 GTTTAGATTTTTTATCAAATCCTTATTTAAGGTCCCTATTTAGGTGTCTCATCAAAACCTTTTTC
66 GTTTAGATTTCCCATCAAATCCTTATTTAAGGTACCTATTTAGGTGTCTCATCAAAACCAGTTTC
* ** **
1996 AAGATTCCTGTTTAGGTTT
131 AAGATTCCTATCAAAATTT
*
2015 CTTATCAAAATCCTTATTTAAGGTCCCTGTTTAGGTGTCTCATCAAAATCTTGTTCAAGATTCCT
1 CTTATCAAAATCCTTATTTAAGGTCCCTGTTTAGGTGTCTCATCAAAACCTTGTTCAAGATTCCT
* * *
2080 GTTTAGGTTTCCCATTAAATCCTTATTTAAGGTACCTGA-TTAGGTGTCTCTTCAAAATCCCAGT
66 GTTTAGATTTCCCATCAAATCCTTATTTAAGGTACCT-ATTTAGGTGTCTCATCAAAA--CCAGT
* * *
2144 TT-AGGTTTCTTATCAAAATTT
128 TTCAAGATTCCTATCAAAATTT
2165 -TGT-TCAAAATCC
1 CT-TATCAAAATCC
2177 ATTTCTTGTT
Statistics
Matches: 139, Mismatches: 18, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
148 6 0.04
149 115 0.83
150 13 0.09
151 5 0.04
ACGTcount: A:0.25, C:0.20, G:0.13, T:0.42
Consensus pattern (149 bp):
CTTATCAAAATCCTTATTTAAGGTCCCTGTTTAGGTGTCTCATCAAAACCTTGTTCAAGATTCCT
GTTTAGATTTCCCATCAAATCCTTATTTAAGGTACCTATTTAGGTGTCTCATCAAAACCAGTTTC
AAGATTCCTATCAAAATTT
Found at i:2367 original size:54 final size:54
Alignment explanation
Indices: 2233--2384 Score: 200
Period size: 54 Copynumber: 2.8 Consensus size: 54
2223 TCTCTCTAGA
* * *
2233 AAGTTGATCTTAAGTTGATCCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCT
1 AAGTTGATCTTAAGTTGATCCAGTGTGGTCTTCCATAGAAGTTTTCAAAAATCT
* ** * *
2287 AAGTTGATCTTCAGACGACCCTGTGTGGTCTTCCATAGGAA-TTTTCAAAAATCT
1 AAGTTGATCTTAAGTTGATCCAGTGTGGTCTTCCATA-GAAGTTTTCAAAAATCT
2341 AAGTTGATCTTAAGTTGATCCAGTGTGGTCATTCCA-AGAAGTTT
1 AAGTTGATCTTAAGTTGATCCAGTGTGGTC-TTCCATAGAAGTTT
2385 ACGATGATCA
Statistics
Matches: 82, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
53 3 0.04
54 71 0.87
55 8 0.10
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.36
Consensus pattern (54 bp):
AAGTTGATCTTAAGTTGATCCAGTGTGGTCTTCCATAGAAGTTTTCAAAAATCT
Found at i:2404 original size:54 final size:53
Alignment explanation
Indices: 2233--2420 Score: 175
Period size: 54 Copynumber: 3.5 Consensus size: 53
2223 TCTCTCTAGA
* *
2233 AAGTTGATCTTAAGTTGATCCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCT
1 AAGTTGATCTTAAGTTGACCCAGTGTGGTCTTCCATAGAAGTTTTC-GAGATCT
* ** * * *
2287 AAGTTGATCTTCAGACGACCCTGTGTGGTCTTCCATAGGAA-TTTTCAAAAATCT
1 AAGTTGATCTTAAGTTGACCCAGTGTGGTCTTCCATA-GAAGTTTTC-GAGATCT
* *
2341 AAGTTGATCTTAAGTTGATCCAGTGTGGTCATTCCA-AGAAGTTTACGATGATC-
1 AAGTTGATCTTAAGTTGACCCAGTGTGGTC-TTCCATAGAAGTTTTCGA-GATCT
* **
2394 AGAGTCGATCTCTAAACTGACCCAGTG
1 A-AGTTGATCT-TAAGTTGACCCAGTG
2421 CAGTCATTCC
Statistics
Matches: 108, Mismatches: 20, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
53 5 0.05
54 83 0.77
55 20 0.19
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.34
Consensus pattern (53 bp):
AAGTTGATCTTAAGTTGACCCAGTGTGGTCTTCCATAGAAGTTTTCGAGATCT
Found at i:2530 original size:33 final size:33
Alignment explanation
Indices: 2488--2565 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
2478 ATTAATTAAG
* * * *
2488 AAGTTCAAAATTTGCATTTCATTTCAAAATTCA
1 AAGTTCAAAATCTGCATATCATATCAAAACTCA
2521 AAGTTCAAAATCTGCATATCATATCAAAACTCA
1 AAGTTCAAAATCTGCATATCATATCAAAACTCA
2554 AAGTTCAAAATC
1 AAGTTCAAAATC
2566 CACATTTTCT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.44, C:0.18, G:0.06, T:0.32
Consensus pattern (33 bp):
AAGTTCAAAATCTGCATATCATATCAAAACTCA
Found at i:2806 original size:7 final size:7
Alignment explanation
Indices: 2704--2787 Score: 159
Period size: 7 Copynumber: 12.0 Consensus size: 7
2694 CATTTCATTG
2704 CTCAAAA
1 CTCAAAA
*
2711 TTCAAAA
1 CTCAAAA
2718 CTCAAAA
1 CTCAAAA
2725 CTCAAAA
1 CTCAAAA
2732 CTCAAAA
1 CTCAAAA
2739 CTCAAAA
1 CTCAAAA
2746 CTCAAAA
1 CTCAAAA
2753 CTCAAAA
1 CTCAAAA
2760 CTCAAAA
1 CTCAAAA
2767 CTCAAAA
1 CTCAAAA
2774 CTCAAAA
1 CTCAAAA
2781 CTCAAAA
1 CTCAAAA
2788 TTCATGGCTC
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 75 1.00
ACGTcount: A:0.57, C:0.27, G:0.00, T:0.15
Consensus pattern (7 bp):
CTCAAAA
Found at i:2882 original size:26 final size:27
Alignment explanation
Indices: 2846--2912 Score: 100
Period size: 26 Copynumber: 2.5 Consensus size: 27
2836 TCCTCAAAAG
* *
2846 TCAAAATTCAAAATTTGCATTTCAT-T
1 TCAAAACTCAAAATTTGCATGTCATGT
2872 TCAAAACTCAAAATTTGCATGTCATGT
1 TCAAAACTCAAAATTTGCATGTCATGT
*
2899 TCGAAACTCAAAAT
1 TCAAAACTCAAAAT
2913 CCAGAGTCTG
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
26 23 0.62
27 14 0.38
ACGTcount: A:0.40, C:0.18, G:0.07, T:0.34
Consensus pattern (27 bp):
TCAAAACTCAAAATTTGCATGTCATGT
Found at i:4263 original size:10 final size:10
Alignment explanation
Indices: 4242--4270 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
4232 TTAAAAAAGG
4242 AAATAAAA-T
1 AAATAAAATT
4251 AAATAAAATT
1 AAATAAAATT
4261 AAATAAAATT
1 AAATAAAATT
4271 GTTAATATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 8 0.42
10 11 0.58
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
AAATAAAATT
Found at i:5244 original size:220 final size:221
Alignment explanation
Indices: 4861--5309 Score: 855
Period size: 220 Copynumber: 2.0 Consensus size: 221
4851 ATGGTTAATC
*
4861 AAAATTAGGTGACCAATCACACCTAGATAAAAAAAGATTGGTGGCGACTCCTTTTCAAATGCGTC
1 AAAATTAGGTGACCAATCACACCTAGATAAAAAAAGATTGGTGGCGACTCATTTTCAAATGCGTC
4926 TAGCGCTCAAGTCTCACGATTTGCACGTTATGACATGATAGAAAAATAAGAGAGAGTGAGAGCTG
66 TAGCGCTCAAGTCTCACGATTTGCACGTTATGACATGATAGAAAAATAAGAGAGAGTGAGAGCTG
4991 GAAATCGTCAAAGAATTGAAAAATAATCTTAATAATTTGCATTAAAAGAATGGTATTACAATAAT
131 GAAATCGTCAAAGAATTGAAAAATAATCTTAATAATTTGCATTAAAAGAATGGTATTACAATAAT
5056 AAAATTGATCCGATATGTGAACAACA
196 AAAATTGATCCGATATGTGAACAACA
*
5082 AAAATTAGGTGGCCAATCACACCTAGAT-AAAAAAGATTGGTGGCGACTCATTTTCAAATGCGTC
1 AAAATTAGGTGACCAATCACACCTAGATAAAAAAAGATTGGTGGCGACTCATTTTCAAATGCGTC
*
5146 TAGCGTTCAAGTCTCACGATTTGCACGTTATGACATGATAGAAAAATAAGAGAGAGTGAGAGCTG
66 TAGCGCTCAAGTCTCACGATTTGCACGTTATGACATGATAGAAAAATAAGAGAGAGTGAGAGCTG
5211 GAAATCGTCAAAGAATTGAAAAATAATCTTAATAATTTGCATTAAAAGAATGGTATTACAATAAT
131 GAAATCGTCAAAGAATTGAAAAATAATCTTAATAATTTGCATTAAAAGAATGGTATTACAATAAT
5276 AAAATTGATCCGATATGTGAACAACA
196 AAAATTGATCCGATATGTGAACAACA
5302 AAAGATTA
1 AAA-ATTA
5310 ATTTTTTTGC
Statistics
Matches: 224, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
220 193 0.86
221 31 0.14
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (221 bp):
AAAATTAGGTGACCAATCACACCTAGATAAAAAAAGATTGGTGGCGACTCATTTTCAAATGCGTC
TAGCGCTCAAGTCTCACGATTTGCACGTTATGACATGATAGAAAAATAAGAGAGAGTGAGAGCTG
GAAATCGTCAAAGAATTGAAAAATAATCTTAATAATTTGCATTAAAAGAATGGTATTACAATAAT
AAAATTGATCCGATATGTGAACAACA
Found at i:7552 original size:30 final size:28
Alignment explanation
Indices: 7480--7553 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 28
7470 TTTGTAGCGT
7480 TTGGACGTTTTGTCCCATGAACTTCAATA
1 TTGGACGTTTTG-CCCATGAACTTCAATA
* * *
7509 TTGGACATTTTGCCACTTGAACTTCAATT
1 TTGGACGTTTTGCC-CATGAACTTCAATA
7538 TTGGGACGTTTTGCCC
1 TT-GGACGTTTTGCCC
7554 CCTCAAGCTA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
28 2 0.05
29 26 0.67
30 11 0.28
ACGTcount: A:0.20, C:0.22, G:0.19, T:0.39
Consensus pattern (28 bp):
TTGGACGTTTTGCCCATGAACTTCAATA
Found at i:7925 original size:43 final size:43
Alignment explanation
Indices: 7786--8116 Score: 372
Period size: 43 Copynumber: 7.8 Consensus size: 43
7776 CCAATAACCA
*
7786 AAAGTCCCCAAACACAATTATAACACAGGGGCAATACTCTATTCC
1 AAAGTCCCCAAACACATTTATAACACAGGGGC-AT-CTCTATTCC
* * * *
7831 AAAGTCCTCAAACACATTTATAACACAGAGACATCTATA-T-C
1 AAAGTCCCCAAACACATTTATAACACAGGGGCATCTCTATTCC
*
7872 AAAGTCCCCAAACACATTTATAACACAGGGGTATCTCTATTCC
1 AAAGTCCCCAAACACATTTATAACACAGGGGCATCTCTATTCC
* * *
7915 AAAGTCCCCAAACGCATTTATAACACAGAGGCATCTATA-T-C
1 AAAGTCCCCAAACACATTTATAACACAGGGGCATCTCTATTCC
* * * *
7956 AAAGTCCCCAAACACAATTATAACATAGGGGCAAT-TCT-CTCTA
1 AAAGTCCCCAAACACATTTATAACACAGGGGC-ATCTCTATTC-C
* * * *
7999 AAAGTCCTCAAACACATTTATAACACAGAGGCATC-C-ATACT
1 AAAGTCCCCAAACACATTTATAACACAGGGGCATCTCTATTCC
* * *
8040 GAAGTCCCCAAACACATTTATAACACAGGGGCACCTCTATTTC
1 AAAGTCCCCAAACACATTTATAACACAGGGGCATCTCTATTCC
* *
8083 AAAGTCCTCAAACACATTTATAACACAGAGGCAT
1 AAAGTCCCCAAACACATTTATAACACAGGGGCAT
8117 TTCTCCTTTT
Statistics
Matches: 238, Mismatches: 38, Indels: 22
0.80 0.13 0.07
Matches are distributed among these distances:
41 98 0.41
42 10 0.04
43 100 0.42
44 2 0.01
45 28 0.12
ACGTcount: A:0.39, C:0.27, G:0.11, T:0.23
Consensus pattern (43 bp):
AAAGTCCCCAAACACATTTATAACACAGGGGCATCTCTATTCC
Found at i:7937 original size:84 final size:85
Alignment explanation
Indices: 7786--8116 Score: 483
Period size: 84 Copynumber: 3.9 Consensus size: 85
7776 CCAATAACCA
7786 AAAGTCCCCAAACACAATTATAACACAGGGGCAATACTCTATTCCAAAGTCCTCAAACACATTTA
1 AAAGTCCCCAAACACAATTATAACACAGGGGCAAT-CTCTATTCCAAAGTCCTCAAACACATTTA
*
7851 TAACACAGAGACATCTATATC
65 TAACACAGAGGCATCTATATC
* * * *
7872 AAAGTCCCCAAACACATTTATAACACAGGGG-TATCTCTATTCCAAAGTCCCCAAACGCATTTAT
1 AAAGTCCCCAAACACAATTATAACACAGGGGCAATCTCTATTCCAAAGTCCTCAAACACATTTAT
7936 AACACAGAGGCATCTATATC
66 AACACAGAGGCATCTATATC
* * *
7956 AAAGTCCCCAAACACAATTATAACATAGGGGCAAT-TCT-CTCTAAAAGTCCTCAAACACATTTA
1 AAAGTCCCCAAACACAATTATAACACAGGGGCAATCTCTATTC-CAAAGTCCTCAAACACATTTA
*
8019 TAACACAGAGGCATCCATA-C
65 TAACACAGAGGCATCTATATC
* * * *
8039 TGAAGTCCCCAAACACATTTATAACACAGGGGC-ACCTCTATTTCAAAGTCCTCAAACACATTTA
1 -AAAGTCCCCAAACACAATTATAACACAGGGGCAATCTCTATTCCAAAGTCCTCAAACACATTTA
8103 TAACACAGAGGCAT
65 TAACACAGAGGCAT
8117 TTCTCCTTTT
Statistics
Matches: 220, Mismatches: 20, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
83 4 0.02
84 181 0.82
85 5 0.02
86 30 0.14
ACGTcount: A:0.39, C:0.27, G:0.11, T:0.23
Consensus pattern (85 bp):
AAAGTCCCCAAACACAATTATAACACAGGGGCAATCTCTATTCCAAAGTCCTCAAACACATTTAT
AACACAGAGGCATCTATATC
Found at i:8188 original size:2 final size:2
Alignment explanation
Indices: 8181--8208 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
8171 AATTCCTATC
8181 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
8209 CATGTGCACC
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:9603 original size:29 final size:29
Alignment explanation
Indices: 9556--9657 Score: 107
Period size: 29 Copynumber: 3.4 Consensus size: 29
9546 CATTAGCTTG
9556 AAGGGGCAAAACGTCCCAAAATTTAAA-TTC
1 AAGGGGCAAAACGT-CCAAAA-TTAAAGTTC
* * *
9586 AGGGGGTAAAATGTCCAAAATTAAAGTTC
1 AAGGGGCAAAACGTCCAAAATTAAAGTTC
*
9615 AAGGGGCAAAACGTCCAAACGTTAAAAGTTC
1 AAGGGGCAAAACGTCCAAA-ATT-AAAGTTC
*
9646 AACGGGGAAAAA
1 AA-GGGGCAAAA
9658 GAATATTAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
28 5 0.08
29 25 0.42
30 13 0.22
31 9 0.15
32 8 0.13
ACGTcount: A:0.44, C:0.16, G:0.23, T:0.18
Consensus pattern (29 bp):
AAGGGGCAAAACGTCCAAAATTAAAGTTC
Found at i:12176 original size:7 final size:7
Alignment explanation
Indices: 12164--12190 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
12154 GGAGAGTCTT
12164 GATTTTA
1 GATTTTA
12171 GATTTTA
1 GATTTTA
12178 GATTTTA
1 GATTTTA
12185 GATTTT
1 GATTTT
12191 TTTTTAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.15, T:0.59
Consensus pattern (7 bp):
GATTTTA
Found at i:13216 original size:9 final size:9
Alignment explanation
Indices: 13182--13210 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
13172 TTTGGACCTG
13182 GAAGATGAA
1 GAAGATGAA
13191 GAAGATGAA
1 GAAGATGAA
13200 GAAGATGAA
1 GAAGATGAA
13209 GA
1 GA
13211 GCATGACGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.34, T:0.10
Consensus pattern (9 bp):
GAAGATGAA
Found at i:16404 original size:23 final size:26
Alignment explanation
Indices: 16345--16404 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 26
16335 ATTTTACTAT
16345 TTTAATTAAAATACTTCTATAGTTTTA
1 TTTAATTAAAATACTTCTATA-TTTTA
* * *
16372 CTCAACTAAAA-AC-TCTAT-TTTTA
1 TTTAATTAAAATACTTCTATATTTTA
16395 TTTAATTAAA
1 TTTAATTAAA
16405 TCTAATATCC
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
23 12 0.44
25 5 0.19
26 2 0.07
27 8 0.30
ACGTcount: A:0.40, C:0.12, G:0.02, T:0.47
Consensus pattern (26 bp):
TTTAATTAAAATACTTCTATATTTTA
Found at i:17477 original size:102 final size:103
Alignment explanation
Indices: 17357--17661 Score: 560
Period size: 103 Copynumber: 3.0 Consensus size: 103
17347 ACCTATTTTA
17357 TTTTTATCAATTTACTAATTTAATTAAAAAACTTAGATATATTAGAATTTTTAAAACATATTTCT
1 TTTTTATCAATTTACTAATTTAATTAAAAAACTTAGATATATTAGAATTTTTAAAACATATTTCT
17422 TAAATGACATTGTTTAAATTTTACAGTTTTTTTAA-TT
66 TAAATGACATTGTTTAAATTTTACAGTTTTTTTAATTT
*
17459 TTTTTATCAATTTACTAATTTAATTAAAAAACTTAGATATATTAAAATTTTTAAAACATATTTCT
1 TTTTTATCAATTTACTAATTTAATTAAAAAACTTAGATATATTAGAATTTTTAAAACATATTTCT
*
17524 TATATGACATTGTTTAAATTTTACAG-TTTTTTAATTTT
66 TAAATGACATTGTTTAAATTTTACAGTTTTTTTAA-TTT
*
17562 TTTTTATCAATTTACTAATTTAATTAAAAAACTTAGATATATTAGAATTTTTAAAACATATTTTT
1 TTTTTATCAATTTACTAATTTAATTAAAAAACTTAGATATATTAGAATTTTTAAAACATATTTCT
17627 TAAATGACATTGTTTAAATTTTACAGTTTTTTTAA
66 TAAATGACATTGTTTAAATTTTACAGTTTTTTTAA
17662 GAAATAAACT
Statistics
Matches: 195, Mismatches: 5, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
101 8 0.04
102 89 0.46
103 90 0.46
104 8 0.04
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.50
Consensus pattern (103 bp):
TTTTTATCAATTTACTAATTTAATTAAAAAACTTAGATATATTAGAATTTTTAAAACATATTTCT
TAAATGACATTGTTTAAATTTTACAGTTTTTTTAATTT
Found at i:18441 original size:21 final size:22
Alignment explanation
Indices: 18417--18457 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
18407 GTTTATAATA
*
18417 TTCTTGGGTCA-TCGGGTTATC
1 TTCTCGGGTCATTCGGGTTATC
*
18438 TTCTCGGGTTATTCGGGTTA
1 TTCTCGGGTCATTCGGGTTA
18458 CGAGTTTGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.10, C:0.17, G:0.29, T:0.44
Consensus pattern (22 bp):
TTCTCGGGTCATTCGGGTTATC
Found at i:18879 original size:83 final size:85
Alignment explanation
Indices: 18789--18959 Score: 258
Period size: 84 Copynumber: 2.0 Consensus size: 85
18779 TCTATTTTTA
*
18789 TTTAATTAAATCTAAT-TCTTTATAACTATTTTATTTTTATCATTTTACTATTTTAATTACAAAA
1 TTTAATTAAATCTAATCTCTTTATAACTATTTTATTTTTACCATTTTACTATTTTAATTAC-AAA
*
18853 ACTTA-A-ATGTATTAGAATT
65 ACTTAGATATATATTAGAATT
* * *
18872 TTTAATTATATCTAATCTCTTTATAACTATTTTATTTTTACCATTTTTCTATTTTAATTACATAA
1 TTTAATTAAATCTAATCTCTTTATAACTATTTTATTTTTACCATTTTACTATTTTAATTACAAAA
*
18937 CTTAGATATATATTATAATT
66 CTTAGATATATATTAGAATT
18957 TTT
1 TTT
18960 TTTAAATATA
Statistics
Matches: 79, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
83 22 0.28
84 43 0.54
85 14 0.18
ACGTcount: A:0.35, C:0.09, G:0.02, T:0.54
Consensus pattern (85 bp):
TTTAATTAAATCTAATCTCTTTATAACTATTTTATTTTTACCATTTTACTATTTTAATTACAAAA
CTTAGATATATATTAGAATT
Found at i:48194 original size:22 final size:21
Alignment explanation
Indices: 48169--48222 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
48159 GAAGTTTGTG
48169 TTTGAAGACTTATTGAAGATAA
1 TTTGAAGA-TTATTGAAGATAA
*
48191 TTTGAAGA-T-TTGAAGATCA
1 TTTGAAGATTATTGAAGATAA
48210 -TTGAAGAATTATT
1 TTTGAAG-ATTATT
48223 TCCAAGAAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 6 0.21
19 10 0.36
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.04, G:0.19, T:0.39
Consensus pattern (21 bp):
TTTGAAGATTATTGAAGATAA
Done.