Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012017.1 Corchorus capsularis cultivar CVL-1 contig12038, 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: 15996
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Found at i:2110 original size:32 final size:32
Alignment explanation
Indices: 2060--2127 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
2050 GCAGGATAAT
* * *
2060 GGCGTCTAATGAATCAAACGCCACCATTTAGC
1 GGCGCCTAATGAAGCAAACGCCACCATATAGC
* *
2092 GGCGCCTAATGAAGCAAACGCCGCTATATAGC
1 GGCGCCTAATGAAGCAAACGCCACCATATAGC
2124 GGCG
1 GGCG
2128 TCTATAAAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.29, C:0.28, G:0.25, T:0.18
Consensus pattern (32 bp):
GGCGCCTAATGAAGCAAACGCCACCATATAGC
Found at i:2816 original size:11 final size:11
Alignment explanation
Indices: 2800--2824 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2790 AATTTTAGGG
2800 TTCTCCTTTCC
1 TTCTCCTTTCC
2811 TTCTCCTTTCC
1 TTCTCCTTTCC
2822 TTC
1 TTC
2825 CGTTCGATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (11 bp):
TTCTCCTTTCC
Found at i:3271 original size:23 final size:23
Alignment explanation
Indices: 3241--3285 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
3231 AGCTGAGTTC
3241 TGTTTTTATTCTTGCTGTTTTAT
1 TGTTTTTATTCTTGCTGTTTTAT
3264 TGTTTTTATTCTTGCTGTTTTA
1 TGTTTTTATTCTTGCTGTTTTA
3286 CTGATAGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.09, C:0.09, G:0.13, T:0.69
Consensus pattern (23 bp):
TGTTTTTATTCTTGCTGTTTTAT
Found at i:4265 original size:24 final size:24
Alignment explanation
Indices: 4233--4287 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
4223 GGATTTAGCA
4233 GCAAATGACGAACCAATTGAGGCT
1 GCAAATGACGAACCAATTGAGGCT
* *
4257 GCAAATGACGACCCCATTGAGGCT
1 GCAAATGACGAACCAATTGAGGCT
4281 GCAAATG
1 GCAAATG
4288 GAGAGAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.35, C:0.24, G:0.25, T:0.16
Consensus pattern (24 bp):
GCAAATGACGAACCAATTGAGGCT
Found at i:4351 original size:27 final size:27
Alignment explanation
Indices: 4314--4400 Score: 131
Period size: 27 Copynumber: 3.3 Consensus size: 27
4304 TCCGGCCCTC
4314 CCCACTTCGACCCCAGAAGTGGATCCT
1 CCCACTTCGACCCCAGAAGTGGATCCT
* * *
4341 CCCACTGCGACCCAAGCAGTGGATCCT
1 CCCACTTCGACCCCAGAAGTGGATCCT
*
4368 CCCACTTCGACCCCAGTAGTGGA-CCT
1 CCCACTTCGACCCCAGAAGTGGATCCT
4394 CCCACTT
1 CCCACTT
4401 TGCCTCGGGT
Statistics
Matches: 54, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
26 10 0.19
27 44 0.81
ACGTcount: A:0.21, C:0.43, G:0.18, T:0.18
Consensus pattern (27 bp):
CCCACTTCGACCCCAGAAGTGGATCCT
Found at i:6886 original size:32 final size:31
Alignment explanation
Indices: 6782--6879 Score: 133
Period size: 32 Copynumber: 3.1 Consensus size: 31
6772 TTGGGGTATA
*
6782 CCCTTATATAGCGGCGTCTAAATAACAAAACG
1 CCCTTATATAGCGGCGTCTAAAAAAC-AAACG
*
6814 CCCTTATATAGCGGCGTCTGAAAAACAAAGCG
1 CCCTTATATAGCGGCGTCTAAAAAACAAA-CG
* *
6846 CCCTTATATAACAGCGTCTAAAGAAACAAACG
1 CCCTTATATAGCGGCGTCTAAA-AAACAAACG
6878 CC
1 CC
6880 GCTATATTTA
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
31 3 0.05
32 49 0.83
33 7 0.12
ACGTcount: A:0.38, C:0.27, G:0.16, T:0.19
Consensus pattern (31 bp):
CCCTTATATAGCGGCGTCTAAAAAACAAACG
Found at i:7016 original size:24 final size:24
Alignment explanation
Indices: 6931--7017 Score: 93
Period size: 24 Copynumber: 3.6 Consensus size: 24
6921 TGCAGGTAGC
** * *
6931 GGCGTCTGGATTCCCCCAAATAGT
1 GGCGTCTGGACGCCGCCAAATAGG
* *
6955 GGCGTCTGGGCGCCGCGAAATAGG
1 GGCGTCTGGACGCCGCCAAATAGG
*
6979 GGCGTCTGGTCGCCGCCAAATAGG
1 GGCGTCTGGACGCCGCCAAATAGG
* *
7003 GGCATCCGGACGCCG
1 GGCGTCTGGACGCCG
7018 TAATATGCTT
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 52 1.00
ACGTcount: A:0.17, C:0.30, G:0.37, T:0.16
Consensus pattern (24 bp):
GGCGTCTGGACGCCGCCAAATAGG
Found at i:10301 original size:30 final size:30
Alignment explanation
Indices: 10265--10321 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
10255 TGTTTAAATC
** *
10265 AGCTTGCATTAGTGTTTAGCATTTCATTTT
1 AGCTTGCATTAGCATTTAGCATATCATTTT
10295 AGCTTGCATTAGCATTTAGCATATCAT
1 AGCTTGCATTAGCATTTAGCATATCAT
10322 ATTTGCACTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.44
Consensus pattern (30 bp):
AGCTTGCATTAGCATTTAGCATATCATTTT
Found at i:13385 original size:36 final size:36
Alignment explanation
Indices: 13328--13778 Score: 436
Period size: 36 Copynumber: 12.5 Consensus size: 36
13318 CATATGCATC
* *
13328 AGTAAACA-CAGTAAAAGACTTAATTCTA-GGCAATTA
1 AGTAAA-AGCAGTCAAAGACTTAATTC-AGGGAAATTA
* * **
13364 AGTAAACA-TAGTCAAATACTTAATTCAACGAAATTA
1 AGTAAA-AGCAGTCAAAGACTTAATTCAGGGAAATTA
13400 AGTAAAAGCAGTC-AAGAACTTAATTCAGGGAAATTA
1 AGTAAAAGCAGTCAAAG-ACTTAATTCAGGGAAATTA
* *
13436 AGTAAAAGCAGT-TAAGAACTTAATTCAGGGTAATTA
1 AGTAAAAGCAGTCAAAG-ACTTAATTCAGGGAAATTA
* *
13472 AGTAAGAA-TAGTCAAAGACTTAATTCAGGGTAATTA
1 AGTAA-AAGCAGTCAAAGACTTAATTCAGGGAAATTA
* ** *
13508 AGTAAAAGCAGTCAAAGGCTTAATTCAGGCTAATAA
1 AGTAAAAGCAGTCAAAGACTTAATTCAGGGAAATTA
* * **
13544 AGTAAAAGCAGTTAAGGACTTAATTCAACGAAATTA
1 AGTAAAAGCAGTCAAAGACTTAATTCAGGGAAATTA
* * *
13580 AGTAACAGTCAG-CAAAGTCTTAATTCA-GGACAGTTA
1 AGTAAAAG-CAGTCAAAGACTTAATTCAGGGA-AATTA
* * *
13616 AGTAAAAGCAGTCACAGACTTAATTTAGGGTAATTA
1 AGTAAAAGCAGTCAAAGACTTAATTCAGGGAAATTA
* *
13652 AGTAAAAACAGTTAAAGGACTTAATTCAGGGAAATTA
1 AGTAAAAGCAGTCAAA-GACTTAATTCAGGGAAATTA
* *
13689 AGTAAAAGCAGTCAAGGACTTAATTCA-GAATAATTA
1 AGTAAAAGCAGTCAAAGACTTAATTCAGGGA-AATTA
* * *
13725 AGTTAAAA-CAGTTAAAGGATTTAATTCAGGGTAATTA
1 AG-TAAAAGCAGTCAAA-GACTTAATTCAGGGAAATTA
*
13762 AGTAAAAGCAGTTAAAG
1 AGTAAAAGCAGTCAAAG
13779 GATTTAGACA
Statistics
Matches: 348, Mismatches: 50, Indels: 34
0.81 0.12 0.08
Matches are distributed among these distances:
35 13 0.04
36 263 0.76
37 71 0.20
38 1 0.00
ACGTcount: A:0.46, C:0.11, G:0.18, T:0.26
Consensus pattern (36 bp):
AGTAAAAGCAGTCAAAGACTTAATTCAGGGAAATTA
Found at i:13517 original size:108 final size:107
Alignment explanation
Indices: 13344--13776 Score: 500
Period size: 108 Copynumber: 4.0 Consensus size: 107
13334 CACAGTAAAA
* * *
13344 GACTTAATTCTA-GGCAATTAAGTAAACATAGTCAAATACTTAATTCAACGA-AATTAAGTAAAA
1 GACTTAATTC-AGGGAAATTAAGTAAA-ATAGTCAAAGACTTAATTC-AGGATAATTAAGTAAAA
*
13407 GCAGTCAAGAACTTAATTCAGGGAAATTAAGTAAAAGCAGTTAAG
63 GCAGTCAAGAACTTAATTCAGGGTAATTAAGTAAAAGCAGTTAAG
* * *
13452 AACTTAATTCAGGGTAATTAAGTAAGAATAGTCAAAGACTTAATTCAGGGTAATTAAGTAAAAGC
1 GACTTAATTCAGGGAAATTAAGTAA-AATAGTCAAAGACTTAATTCAGGATAATTAAGTAAAAGC
* * *
13517 AGTCAA-AGGCTTAATTCAGGCTAATAAAGTAAAAGCAGTTAAG
65 AGTCAAGA-ACTTAATTCAGGGTAATTAAGTAAAAGCAGTTAAG
** * * * *
13560 GACTTAATTCAACGAAATTAAGTAACAGTCAG-CAAAGTCTTAATTCAGGACAGTTAAGTAAAAG
1 GACTTAATTCAGGGAAATTAAGTAA-AAT-AGTCAAAGACTTAATTCAGGATAATTAAGTAAAAG
* *
13624 CAGTCACAG-ACTTAATTTAGGGTAATTAAGTAAAAACAGTTAAAG
64 CAGTCA-AGAACTTAATTCAGGGTAATTAAGTAAAAGCAGTT-AAG
* * *
13669 GACTTAATTCAGGGAAATTAAGTAAAAGCAGTCAAGGACTTAATTCAGAATAATTAAGTTAAAA-
1 GACTTAATTCAGGGAAATTAAGTAAAA-TAGTCAAAGACTTAATTCAGGATAATTAAG-TAAAAG
* * *
13733 CAGTTAAAGGATTTAATTCAGGGTAATTAAGTAAAAGCAGTTAA
64 CAG-TCAAGAACTTAATTCAGGGTAATTAAGTAAAAGCAGTTAA
13777 AGGATTTAGA
Statistics
Matches: 275, Mismatches: 37, Indels: 25
0.82 0.11 0.07
Matches are distributed among these distances:
107 4 0.01
108 177 0.64
109 58 0.21
110 36 0.13
ACGTcount: A:0.45, C:0.11, G:0.18, T:0.26
Consensus pattern (107 bp):
GACTTAATTCAGGGAAATTAAGTAAAATAGTCAAAGACTTAATTCAGGATAATTAAGTAAAAGCA
GTCAAGAACTTAATTCAGGGTAATTAAGTAAAAGCAGTTAAG
Found at i:13831 original size:41 final size:41
Alignment explanation
Indices: 13784--14439 Score: 915
Period size: 41 Copynumber: 16.5 Consensus size: 41
13774 TAAAGGATTT
* * * *
13784 AGACAAGCACATACATAATTGCAAGGAAGGGAATTAGGTAA
1 AGACAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAA
* * *
13825 ACACAAGCACAGGCTTAATTTCAAGGAATGAAATTAGGTAA
1 AGACAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAA
*
13866 AGAAAAGCACA-ACCTTAATTTCAAGGAAGGAAATTAGGTAA
1 AGACAAGCACAGA-CTTAATTTCAAGGAAGGAAATTAGGTAA
*
13907 AGAAAAGCACAGACTTAATTTC----AAGGAAATTAGGTAA
1 AGACAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAA
*
13944 AGACAAGCACAAACTTAATTTCAAGGAAGGAAATTAGGTAA
1 AGACAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAA
13985 AGACAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAA
1 AGACAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAA
* *
14026 AGAAAAGCACA-AGCTTAACTTCAAGGAAGGAAATTAGGTAA
1 AGACAAGCACAGA-CTTAATTTCAAGGAAGGAAATTAGGTAA
*
14067 AGACAAACACAGACTTAATTTCAAGGAAGGAAATTAGGTAA
1 AGACAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAA
*
14108 AGAAAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAA
1 AGACAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAA
*
14149 AGAAAAGCACAGACTTAATTTCAA-G-A--AAATTAGGTAA
1 AGACAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAA
* * *
14186 AGAAAAACAAAGACTTAATTTCAAGGAAGGAAATTAGGTAA
1 AGACAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAA
* *
14227 AGAAAAGCACAAACTTAATTTC----AAGGAAATTAGGTAA
1 AGACAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAA
*
14264 AGATAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAA
1 AGACAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAA
14305 AGACAAGCACAGACTTAATTTC----AAGGAAATTAGGTAA
1 AGACAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAA
*
14342 AGACAAGCACATACTTAATTTCAAGGAAGGAAATTAGGTAA
1 AGACAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAA
* *
14383 TGACAAGCACAGACTTAATTTC----AAGGAAATTAAGTAA
1 AGACAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAA
*
14420 AGACAAGCCCAGACTTAATT
1 AGACAAGCACAGACTTAATT
14440 CAGGGTAATT
Statistics
Matches: 560, Mismatches: 35, Indels: 44
0.88 0.05 0.07
Matches are distributed among these distances:
37 171 0.31
38 1 0.00
39 2 0.00
40 2 0.00
41 382 0.68
42 2 0.00
ACGTcount: A:0.48, C:0.12, G:0.20, T:0.20
Consensus pattern (41 bp):
AGACAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAA
Found at i:13977 original size:78 final size:78
Alignment explanation
Indices: 13788--14439 Score: 921
Period size: 78 Copynumber: 8.2 Consensus size: 78
13778 GGATTTAGAC
* * * * * * *
13788 AAGCACATACATAATTGCAAGGAAGGGAATTAGGTAAACACAAGCACAGGCTTAATTTCAAGGAA
1 AAGCACAAACTTAATTTCAAGGAAGGAAATTAGGTAAAGAAAAGCACAGACTTAATTTCAA-G--
13853 TGAAATTAGGTAAAGAA
63 -GAAATTAGGTAAAGAA
*
13870 AAGCACAACCTTAATTTCAAGGAAGGAAATTAGGTAAAGAAAAGCACAGACTTAATTTCAAGGAA
1 AAGCACAAACTTAATTTCAAGGAAGGAAATTAGGTAAAGAAAAGCACAGACTTAATTTCAAGGAA
*
13935 ATTAGGTAAAGAC
66 ATTAGGTAAAGAA
*
13948 AAGCACAAACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGGAA
1 AAGCACAAACTTAATTTCAAGGAAGGAAATTAGGTAAAGAAAAGCACAGACTTAATTTC----AA
14013 GGAAATTAGGTAAAGAA
62 GGAAATTAGGTAAAGAA
* *
14030 AAGCACAAGCTTAACTTCAAGGAAGGAAATTAGGTAAAGACAAA-CACAGACTTAATTTCAAGGA
1 AAGCACAAACTTAATTTCAAGGAAGGAAATTAGGTAAAGA-AAAGCACAGACTTAATTTC----A
14094 AGGAAATTAGGTAAAGAA
61 AGGAAATTAGGTAAAGAA
* *
14112 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAAAAGCACAGACTTAATTTCAAGAAA
1 AAGCACAAACTTAATTTCAAGGAAGGAAATTAGGTAAAGAAAAGCACAGACTTAATTTCAAGGAA
14177 ATTAGGTAAAGAA
66 ATTAGGTAAAGAA
* *
14190 AAACA-AAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAAAAGCACAAACTTAATTTCAAGGA
1 AAGCACAA-ACTTAATTTCAAGGAAGGAAATTAGGTAAAGAAAAGCACAGACTTAATTTCAAGGA
*
14254 AATTAGGTAAAGAT
65 AATTAGGTAAAGAA
* *
14268 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGGAA
1 AAGCACAAACTTAATTTCAAGGAAGGAAATTAGGTAAAGAAAAGCACAGACTTAATTTCAAGGAA
*
14333 ATTAGGTAAAGAC
66 ATTAGGTAAAGAA
* * *
14346 AAGCACATACTTAATTTCAAGGAAGGAAATTAGGTAATGACAAGCACAGACTTAATTTCAAGGAA
1 AAGCACAAACTTAATTTCAAGGAAGGAAATTAGGTAAAGAAAAGCACAGACTTAATTTCAAGGAA
* *
14411 ATTAAGTAAAGAC
66 ATTAGGTAAAGAA
* *
14424 AAGCCCAGACTTAATT
1 AAGCACAAACTTAATT
14440 CAGGGTAATT
Statistics
Matches: 528, Mismatches: 34, Indels: 20
0.91 0.06 0.03
Matches are distributed among these distances:
77 1 0.00
78 321 0.61
79 1 0.00
81 4 0.01
82 199 0.38
83 2 0.00
ACGTcount: A:0.48, C:0.12, G:0.20, T:0.21
Consensus pattern (78 bp):
AAGCACAAACTTAATTTCAAGGAAGGAAATTAGGTAAAGAAAAGCACAGACTTAATTTCAAGGAA
ATTAGGTAAAGAA
Found at i:14003 original size:119 final size:119
Alignment explanation
Indices: 13810--14439 Score: 920
Period size: 119 Copynumber: 5.3 Consensus size: 119
13800 AATTGCAAGG
* * * *
13810 AAGGGAATTAGGTAAACACAAGCACAGGCTTAATTTCAAGGAATGAAATTAGGTAAAGAAAAGCA
1 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAAAAGCA
13875 CA-ACCTTAATTTCAAGGAAGGAAATTAGGTAAAGAAAAGCACAGACTTAATTTC
66 CAGA-CTTAATTTCAAGGAAGGAAATTAGGTAAAGAAAAGCACAGACTTAATTTC
* *
13929 AAGGAAATTAGGTAAAGACAAGCACAAACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCA
1 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAAAAGCA
*
13994 CAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAAAAGCACA-AGCTTAACTTC
66 CAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAAAAGCACAGA-CTTAATTTC
*
14048 AAGGAAGGAAATTAGGTAAAGACAAACACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAAA
1 ----AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAAA
14113 AGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAAAAGCACAGACTTAATTTC
62 AGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAAAAGCACAGACTTAATTTC
* * * *
14171 AAGAAAATTAGGTAAAGAAAAACAAAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAAAAGCA
1 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAAAAGCA
* *
14236 CAAACTTAATTTC----AAGGAAATTAGGTAAAGATAAGCACAGACTTAATTTC
66 CAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAAAAGCACAGACTTAATTTC
*
14286 AAGGAAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTC----AAGGAAATTAGGTAAAGACA
1 ----AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAAA
* * *
14347 AGCACATACTTAATTTCAAGGAAGGAAATTAGGTAATGACAAGCACAGACTTAATTTC
62 AGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAAAAGCACAGACTTAATTTC
* *
14405 AAGGAAATTAAGTAAAGACAAGCCCAGACTTAATT
1 AAGGAAATTAGGTAAAGACAAGCACAGACTTAATT
14440 CAGGGTAATT
Statistics
Matches: 470, Mismatches: 26, Indels: 34
0.89 0.05 0.06
Matches are distributed among these distances:
115 104 0.22
118 1 0.00
119 250 0.53
120 1 0.00
123 113 0.24
124 1 0.00
ACGTcount: A:0.48, C:0.12, G:0.20, T:0.21
Consensus pattern (119 bp):
AAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAAAAGCA
CAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAAAAGCACAGACTTAATTTC
Found at i:14174 original size:23 final size:23
Alignment explanation
Indices: 14107--14177 Score: 62
Period size: 23 Copynumber: 3.3 Consensus size: 23
14097 AAATTAGGTA
14107 AAGAAAAGCACAGACTTAATTTC
1 AAGAAAAGCACAGACTTAATTTC
* * ** *
14130 AAG-GAAGGA-A-A-TT-AGGTA
1 AAGAAAAGCACAGACTTAATTTC
14148 AAGAAAAGCACAGACTTAATTTC
1 AAGAAAAGCACAGACTTAATTTC
14171 AAGAAAA
1 AAGAAAA
14178 TTAGGTAAAG
Statistics
Matches: 33, Mismatches: 10, Indels: 10
0.62 0.19 0.19
Matches are distributed among these distances:
18 5 0.15
19 6 0.18
20 2 0.06
21 2 0.06
22 6 0.18
23 12 0.36
ACGTcount: A:0.52, C:0.11, G:0.18, T:0.18
Consensus pattern (23 bp):
AAGAAAAGCACAGACTTAATTTC
Found at i:14483 original size:35 final size:35
Alignment explanation
Indices: 14388--14579 Score: 199
Period size: 36 Copynumber: 5.4 Consensus size: 35
14378 GGTAATGACA
* * *
14388 AGCACAGACTTAATTTCAAGGAAATTAAGTAAAGA-C
1 AGCAAAGACTTAA-TTCAAAGTAATTAAGTAAA-ATC
** **
14424 AAGCCCAGACTTAATTCAGGGTAATTAAGTAAAATC
1 -AGCAAAGACTTAATTCAAAGTAATTAAGTAAAATC
*
14460 AGCAAAAACTTAATTCAAAGTAATTAAGT-AAATC
1 AGCAAAGACTTAATTCAAAGTAATTAAGTAAAATC
*
14494 AGCAAAGACTTAATTTCAAAGAAATTAAGTAAAATC
1 AGCAAAGACTTAA-TTCAAAGTAATTAAGTAAAATC
* * *
14530 AGCAAAGACTTAATCCAAAGATGATTAAGTAAGATC
1 AGCAAAGACTTAATTCAAAG-TAATTAAGTAAAATC
*
14566 AGATAAAGACTTAA
1 AG-CAAAGACTTAA
14580 CCCAAGGGGA
Statistics
Matches: 135, Mismatches: 15, Indels: 10
0.84 0.09 0.06
Matches are distributed among these distances:
34 17 0.13
35 46 0.34
36 50 0.37
37 22 0.16
ACGTcount: A:0.49, C:0.13, G:0.14, T:0.24
Consensus pattern (35 bp):
AGCAAAGACTTAATTCAAAGTAATTAAGTAAAATC
Found at i:14531 original size:70 final size:73
Alignment explanation
Indices: 14446--14579 Score: 211
Period size: 70 Copynumber: 1.9 Consensus size: 73
14436 AATTCAGGGT
*
14446 AATTAAGTAAAATCAGCAAAAACTTAATTCAAAG-TAATTAAGTAA-ATCAG-CAAAGACTTAAT
1 AATTAAGTAAAATCAGCAAAAACTTAATCCAAAGATAATTAAGTAAGATCAGACAAAGACTTAAT
14508 TTCAAAGA
66 TTCAAAGA
* * *
14516 AATTAAGTAAAATCAGCAAAGACTTAATCCAAAGATGATTAAGTAAGATCAGATAAAGACTTAA
1 AATTAAGTAAAATCAGCAAAAACTTAATCCAAAGATAATTAAGTAAGATCAGACAAAGACTTAA
14580 CCCAAGGGGA
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
70 32 0.56
71 10 0.18
72 5 0.09
73 10 0.18
ACGTcount: A:0.52, C:0.11, G:0.12, T:0.25
Consensus pattern (73 bp):
AATTAAGTAAAATCAGCAAAAACTTAATCCAAAGATAATTAAGTAAGATCAGACAAAGACTTAAT
TTCAAAGA
Found at i:14592 original size:36 final size:36
Alignment explanation
Indices: 14447--14598 Score: 161
Period size: 36 Copynumber: 4.3 Consensus size: 36
14437 ATTCAGGGTA
* *
14447 ATTAAGTAAAATCAGCAAAAACTTAATTCAAAGTA--
1 ATTAAGTAAAATCAGCAAAGACTTAATCCAAAG-AGG
* *
14482 ATTAAGT-AAATCAGCAAAGACTTAATTTCAAAGA-A
1 ATTAAGTAAAATCAGCAAAGACTTAA-TCCAAAGAGG
*
14517 ATTAAGTAAAATCAGCAAAGACTTAATCCAAAGATG
1 ATTAAGTAAAATCAGCAAAGACTTAATCCAAAGAGG
* * * *
14553 ATTAAGTAAGATCAGATAAAGACTTAA-CCCAAGGGG
1 ATTAAGTAAAATCAG-CAAAGACTTAATCCAAAGAGG
14589 ATTAAGTAAA
1 ATTAAGTAAA
14599 GAAGAGGAGT
Statistics
Matches: 103, Mismatches: 9, Indels: 9
0.85 0.07 0.07
Matches are distributed among these distances:
34 18 0.17
35 28 0.27
36 47 0.46
37 10 0.10
ACGTcount: A:0.51, C:0.12, G:0.14, T:0.24
Consensus pattern (36 bp):
ATTAAGTAAAATCAGCAAAGACTTAATCCAAAGAGG
Found at i:14681 original size:36 final size:35
Alignment explanation
Indices: 14608--14839 Score: 272
Period size: 36 Copynumber: 6.6 Consensus size: 35
14598 AGAAGAGGAG
* *
14608 TTAATTCAGGGTAATTAAGTAGAGTC---AAAGAC
1 TTAATTCAGGGCAATTAAGTAGAGTCAATAAAGAA
* *
14640 TTAATTCAAGGCAATTAAGTGGAGTCAATAAAAGAA
1 TTAATTCAGGGCAATTAAGTAGAGTCAAT-AAAGAA
*
14676 TTAATTCAGGGCAATTAAGTGGAGTCAATAAAGAA
1 TTAATTCAGGGCAATTAAGTAGAGTCAATAAAGAA
* *
14711 CTTAATTCAGGGAAATTAAGTAGAGTCAATAAAGGAC
1 -TTAATTCAGGGCAATTAAGTAGAGTCAATAAA-GAA
* *
14748 TTAATTTAGGGCAATTAAGTAGAGTCAATAAAGAGC
1 TTAATTCAGGGCAATTAAGTAGAGTCAATAAAGA-A
* * * *
14784 TTAATTCAGGGTAATTATGTAAAGTTAATAAAGAA
1 TTAATTCAGGGCAATTAAGTAGAGTCAATAAAGAA
*
14819 TTTAATTCAGGGAAATTAAGT
1 -TTAATTCAGGGCAATTAAGT
14840 GGAACATTGA
Statistics
Matches: 174, Mismatches: 18, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
32 23 0.13
35 8 0.05
36 141 0.81
37 2 0.01
ACGTcount: A:0.43, C:0.08, G:0.21, T:0.28
Consensus pattern (35 bp):
TTAATTCAGGGCAATTAAGTAGAGTCAATAAAGAA
Found at i:14793 original size:108 final size:104
Alignment explanation
Indices: 14608--14839 Score: 313
Period size: 108 Copynumber: 2.2 Consensus size: 104
14598 AGAAGAGGAG
* *
14608 TTAATTCAGGGTAATTAAGTAGAGTCAAAGACTTAATTCAAGGCAATTAAGTGGAGTCAATAAAA
1 TTAATTCAGGGAAATTAAGTAGAGTCAAAGACTTAATTCAAGGCAATTAAGTAGAGTCAATAAAA
**
14673 GAATTAATTCAGGGCAATTAAGTGGAGTCAATAAAGAAC
66 GAATTAATTCAGGGCAATTAAGTAAAGTCAATAAAGAAC
* *
14712 TTAATTCAGGGAAATTAAGTAGAGTCAATAAAGGACTTAATTTAGGGCAATTAAGTAGAGTCAAT
1 TTAATTCAGGGAAATTAAGTAGAGTC---AAA-GACTTAATTCAAGGCAATTAAGTAGAGTCAAT
* * * * *
14777 -AAAGAGCTTAATTCAGGGTAATTATGTAAAGTTAATAAAGAAT
62 AAAAGA-ATTAATTCAGGGCAATTAAGTAAAGTCAATAAAGAAC
14820 TTAATTCAGGGAAATTAAGT
1 TTAATTCAGGGAAATTAAGT
14840 GGAACATTGA
Statistics
Matches: 112, Mismatches: 11, Indels: 6
0.87 0.09 0.05
Matches are distributed among these distances:
104 25 0.22
107 8 0.07
108 79 0.71
ACGTcount: A:0.43, C:0.08, G:0.21, T:0.28
Consensus pattern (104 bp):
TTAATTCAGGGAAATTAAGTAGAGTCAAAGACTTAATTCAAGGCAATTAAGTAGAGTCAATAAAA
GAATTAATTCAGGGCAATTAAGTAAAGTCAATAAAGAAC
Found at i:15478 original size:19 final size:18
Alignment explanation
Indices: 15454--15490 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
15444 TTGAAGATTT
15454 CTTGAAGATAATTTGAAGA
1 CTTGAAGATAA-TTGAAGA
*
15473 CTTGAAGATCATTGAAGA
1 CTTGAAGATAATTGAAGA
15491 ATTATTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.30
Consensus pattern (18 bp):
CTTGAAGATAATTGAAGA
Done.