Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008373.1 Corchorus capsularis cultivar CVL-1 contig08394, 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: 11238
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Found at i:842 original size:33 final size:34
Alignment explanation
Indices: 805--878 Score: 116
Period size: 33 Copynumber: 2.2 Consensus size: 34
795 CCGAATCGTT
*
805 TGGCCGGTTG-TAGCCGGCCATGTCCATGTCGCG
1 TGGCCGGTTGATAGCCGGACATGTCCATGTCGCG
*
838 TGGCCGG-TGATGGCCGGACATGTCCATGTCGCG
1 TGGCCGGTTGATAGCCGGACATGTCCATGTCGCG
871 TGGCCGGT
1 TGGCCGGT
879 CTTGTGGCCG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
32 2 0.05
33 35 0.95
ACGTcount: A:0.09, C:0.28, G:0.39, T:0.23
Consensus pattern (34 bp):
TGGCCGGTTGATAGCCGGACATGTCCATGTCGCG
Found at i:3733 original size:75 final size:75
Alignment explanation
Indices: 3596--3742 Score: 186
Period size: 75 Copynumber: 2.0 Consensus size: 75
3586 TTTATCTAGA
* * * * *
3596 CTGTGAACAAAGGAATGATGAGTTTTAGTGAAAATAGGTTTCAAAATTAGTTTCAATAAAAGCAA
1 CTGTGAACAAAAGAATGATGAGTTTTAATCAAAAGAGGTTTCAAAATCAGTTTCAATAAAAGCAA
*
3661 TGGTTTCGAG
66 TGATTTCGAG
* * * * * *
3671 CTGTGAGCAAAAGAATGATGAGTTTTAATCAAAAGATGTTTCAAAATCGGTTTTAGTCAAAGCAA
1 CTGTGAACAAAAGAATGATGAGTTTTAATCAAAAGAGGTTTCAAAATCAGTTTCAATAAAAGCAA
3736 TGATTTC
66 TGATTTC
3743 AAGGTGATTG
Statistics
Matches: 60, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
75 60 1.00
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (75 bp):
CTGTGAACAAAAGAATGATGAGTTTTAATCAAAAGAGGTTTCAAAATCAGTTTCAATAAAAGCAA
TGATTTCGAG
Found at i:4104 original size:12 final size:11
Alignment explanation
Indices: 4087--4126 Score: 53
Period size: 12 Copynumber: 3.4 Consensus size: 11
4077 ACAGTTTCCC
4087 AGAAAAAATAGA
1 AGAAAAAA-AGA
4099 AGAAAAAAAGAA
1 AGAAAAAAAG-A
4111 AGAAAGAAAAGA
1 AGAAA-AAAAGA
4123 AGAA
1 AGAA
4127 GAATAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 2 0.08
12 19 0.73
13 5 0.19
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.03
Consensus pattern (11 bp):
AGAAAAAAAGA
Found at i:4225 original size:44 final size:44
Alignment explanation
Indices: 4171--4308 Score: 213
Period size: 44 Copynumber: 3.1 Consensus size: 44
4161 ACAACTATGA
* *
4171 TTTTCAAAAAGAGCCATTGTTTTCAAAAGGTTTTGATAAAATGG
1 TTTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAAATGG
* * * *
4215 TTTTAAAAAAGAGTCATGGTTTTCAAAAGGTTTTAATAAAACAGT
1 TTTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAAA-TGG
4260 TTTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAAATGG
1 TTTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAAATGG
4304 TTTTC
1 TTTTC
4309 CAAAGTTGTG
Statistics
Matches: 83, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
44 43 0.52
45 40 0.48
ACGTcount: A:0.37, C:0.08, G:0.17, T:0.38
Consensus pattern (44 bp):
TTTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAAATGG
Found at i:5880 original size:50 final size:50
Alignment explanation
Indices: 5783--5881 Score: 135
Period size: 50 Copynumber: 2.0 Consensus size: 50
5773 AAGTTTTATA
* *
5783 ATAAGATTGCATTCCATTTGTAAGACCAATATCAAAATTCGATTTTCAAG
1 ATAAGATTGCATTCCATTTGTAAGACCAAGATCAAAATTCGACTTTCAAG
* * * * *
5833 ATAATATTGCATTCCATTTGTGAGTCCAAGATCAAAATTTGCCTTTCAA
1 ATAAGATTGCATTCCATTTGTAAGACCAAGATCAAAATTCGACTTTCAA
5882 AGGGCATTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 42 1.00
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.35
Consensus pattern (50 bp):
ATAAGATTGCATTCCATTTGTAAGACCAAGATCAAAATTCGACTTTCAAG
Found at i:6419 original size:69 final size:69
Alignment explanation
Indices: 6343--7480 Score: 1536
Period size: 69 Copynumber: 16.6 Consensus size: 69
6333 AATGCTTTGA
* ** * **
6343 CTTTTCCATAAGCTTAACTCGTTTCCGTACGAGAGAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
6408 GGGG
66 GGGG
** * * * *
6412 CTTTTCCACAAGCCAAACTCGTTTCCGCACGAGTCAGTT-TAGCATTGGTTTCATCCAAGCAACA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
6476 GGGG
66 GGGG
*
6480 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGTCTTGGTTCCATCCAAGCAGCA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
*
6545 GCGG
66 GGGG
**
6549 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGAGAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
6614 GGGG
66 GGGG
** * * * *
6618 CTTTTCCACAAGCCAAACTCGTTTCCGCACGAGTCAATT-TAGCCTTGGTTTCATCCAAGCAACA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
6682 GGGG
66 GGGG
* * *
6686 CTTTTCCATAAGCCAAACTCGTTTCCATATGAGTTAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
6751 GGGG
66 GGGG
* * * * *
6755 CTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAATT-TAGCCTTGGTTTCATCCAAGCAACA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
6819 GGGG
66 GGGG
* * * * **
6823 CTTTCCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCCAGCTTTGGTTCCATCCAAACATTT
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCA-GC
6888 AGGGG
65 AGGGG
*
6893 CTTTTCCACAAGACAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
**
6958 ACGG
66 GGGG
*
6962 CTTTTCCACAAGACAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
*
7027 GCGG
66 GGGG
* * * * **
7031 CTTTCCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCCAGCTTTGGTTCCATCCAAACATTT
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCA-GC
7096 AGGGG
65 AGGGG
*
7101 CTTTTCCACAAGACAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
**
7166 ACGG
66 GGGG
*
7170 CTTTTCCACAAGACAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
*
7235 GCGG
66 GGGG
* **
7239 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCATTT
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCA-GC
7304 AGGGG
65 AGGGG
* * * ** *
7309 CTTTCCCACAAGCCAAACTCGTTTCCACACGAGTCAATT-TTGCCTTGGTTCCATCCAAGCAACA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
**
7373 AAGG
66 GGGG
* * * *
7377 CTTTTCCACTAGCCAAACTCGTTTCCATATGAGTTAGTT-TAGCCTTGGTTCCATCC-A--AGCA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
7438 GGGG
66 GGGG
* ** * *
7442 CTTTTCCATAAGCCAAGTTCATTTCCATATGAAGTCAGT
1 CTTTTCCACAAGCCAAACTCGTTTCCATACG-AGTCAGT
7481 CTTCCAAGAC
Statistics
Matches: 947, Mismatches: 115, Indels: 17
0.88 0.11 0.02
Matches are distributed among these distances:
65 31 0.03
66 6 0.01
67 1 0.00
68 235 0.25
69 511 0.54
70 163 0.17
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (69 bp):
CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
GGGG
Found at i:6511 original size:137 final size:138
Alignment explanation
Indices: 6343--7480 Score: 1536
Period size: 137 Copynumber: 8.3 Consensus size: 138
6333 AATGCTTTGA
* ** * **
6343 CTTTTCCATAAGCTTAACTCGTTTCCGTACGAGAGAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
** * * *
6408 GGGGCTTTTCCACAAGCCAAACTCGTTTCCGCACGAGTCAGTT-TAGCATTGGTTTCATCCAAGC
66 GGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGC
*
6472 AACAGGGG
131 AGCAGGGG
*
6480 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGTCTTGGTTCCATCCAAGCAGCA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
* **
6545 GCGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGAGAGTTCAAGCCTTGGTTCCATCCAAGC
66 GGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGC
6610 AGCAGGGG
131 AGCAGGGG
** * * * *
6618 CTTTTCCACAAGCCAAACTCGTTTCCGCACGAGTCAATT-TAGCCTTGGTTTCATCCAAGCAACA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
* * *
6682 GGGGCTTTTCCATAAGCCAAACTCGTTTCCATATGAGTTAGTTCAAGCCTTGGTTCCATCCAAGC
66 GGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGC
6747 AGCAGGGG
131 AGCAGGGG
* * * * *
6755 CTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAATT-TAGCCTTGGTTTCATCCAAGCAACA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
* * * *
6819 GGGGCTTTCCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCCAGCTTTGGTTCCATCCAAAC
66 GGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGC
**
6884 ATTTAGGGG
131 A-GCAGGGG
*
6893 CTTTTCCACAAGACAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
** *
6958 ACGGCTTTTCCACAAGACAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGC
66 GGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGC
*
7023 AGCAGCGG
131 AGCAGGGG
* * * * **
7031 CTTTCCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCCAGCTTTGGTTCCATCCAAACATTT
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCA-GC
*
7096 AGGGGCTTTTCCACAAGACAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAG
65 AGGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAG
**
7161 CAGCAACGG
130 CAGCAGGGG
*
7170 CTTTTCCACAAGACAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
* *
7235 GCGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGC
66 GGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGC
**
7300 ATTTAGGGG
131 A-GCAGGGG
* * * ** *
7309 CTTTCCCACAAGCCAAACTCGTTTCCACACGAGTCAATT-TTGCCTTGGTTCCATCCAAGCAACA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
** * * * *
7373 AAGGCTTTTCCACTAGCCAAACTCGTTTCCATATGAGTTAGTT-TAGCCTTGGTTCCATCC-A--
66 GGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGC
7434 AGCAGGGG
131 AGCAGGGG
* ** * *
7442 CTTTTCCATAAGCCAAGTTCATTTCCATATGAAGTCAGT
1 CTTTTCCACAAGCCAAACTCGTTTCCATACG-AGTCAGT
7481 CTTCCAAGAC
Statistics
Matches: 893, Mismatches: 102, Indels: 15
0.88 0.10 0.01
Matches are distributed among these distances:
133 29 0.03
134 7 0.01
136 1 0.00
137 322 0.36
138 287 0.32
139 247 0.28
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (138 bp):
CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
GGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGC
AGCAGGGG
Found at i:7103 original size:208 final size:208
Alignment explanation
Indices: 6343--7480 Score: 1639
Period size: 208 Copynumber: 5.5 Consensus size: 208
6333 AATGCTTTGA
* ** * **
6343 CTTTTCCATAAGCTTAACTCGTTTCCGTACGAGAGAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
** * * *
6408 GGGGCTTTTCCACAAGCCAAACTCGTTTCCGCACGAGTCAGTT-TAGCATTGGTTTCATCCAAGC
66 GGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCCAGCTTTGGTTCCATCCAAGC
** *
6472 A-ACAGGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGTCTTGGTTCCATC
131 ATTTAGGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATC
*
6536 CAAGCAGCAGCGG
196 CAAGCAGCAACGG
**
6549 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGAGAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
** * * * *
6614 GGGGCTTTTCCACAAGCCAAACTCGTTTCCGCACGAGTCAATT-TAGCCTTGGTTTCATCCAAGC
66 GGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCCAGCTTTGGTTCCATCCAAGC
** * * *
6678 A-ACAGGGGCTTTTCCATAAGCCAAACTCGTTTCCATATGAGTTAGTTCAAGCCTTGGTTCCATC
131 ATTTAGGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATC
**
6742 CAAGCAGCAGGGG
196 CAAGCAGCAACGG
* * * * *
6755 CTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAATT-TAGCCTTGGTTTCATCCAAGCAACA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
* *
6819 GGGGCTTTCCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCCAGCTTTGGTTCCATCCAAAC
66 GGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCCAGCTTTGGTTCCATCCAAGC
*
6884 ATTTAGGGGCTTTTCCACAAGACAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATC
131 ATTTAGGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATC
6949 CAAGCAGCAACGG
196 CAAGCAGCAACGG
*
6962 CTTTTCCACAAGACAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
* * *
7027 GCGGCTTTCCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCCAGCTTTGGTTCCATCCAAAC
66 GGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCCAGCTTTGGTTCCATCCAAGC
*
7092 ATTTAGGGGCTTTTCCACAAGACAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATC
131 ATTTAGGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATC
7157 CAAGCAGCAACGG
196 CAAGCAGCAACGG
*
7170 CTTTTCCACAAGACAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
* *
7235 GCGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGC
66 GGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCCAGCTTTGGTTCCATCCAAGC
* * * **
7300 ATTTAGGGGCTTTCCCACAAGCCAAACTCGTTTCCACACGAGTCAATT-TTGCCTTGGTTCCATC
131 ATTTAGGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATC
* *
7364 CAAGCAACAAAGG
196 CAAGCAGCAACGG
* * * *
7377 CTTTTCCACTAGCCAAACTCGTTTCCATATGAGTTAGTT-TAGCCTTGGTTCCATCC-A--AGCA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
* ** * *
7438 GGGGCTTTTCCATAAGCCAAGTTCATTTCCATATGAAGTCAGT
66 GGGGCTTTTCCACAAGCCAAACTCGTTTCCATACG-AGTCAGT
7481 CTTCCAAGAC
Statistics
Matches: 865, Mismatches: 63, Indels: 10
0.92 0.07 0.01
Matches are distributed among these distances:
203 33 0.04
204 7 0.01
205 62 0.07
206 264 0.31
207 164 0.19
208 335 0.39
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (208 bp):
CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCA
GGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCCAGCTTTGGTTCCATCCAAGC
ATTTAGGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATC
CAAGCAGCAACGG
Found at i:7896 original size:27 final size:27
Alignment explanation
Indices: 7838--7910 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 27
7828 TAGGGTCACA
*
7838 TAGGGGCATTTTGGTCATTTTCACGTT
1 TAGGGGCATTTTGGTCATTTTCACATT
* * **
7865 CAGGGGCATTTTGGTCTTTTTTGCATT
1 TAGGGGCATTTTGGTCATTTTCACATT
* *
7892 TAGGGGTATTGTGGTCATT
1 TAGGGGCATTTTGGTCATT
7911 GTAAGTTCAC
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.14, C:0.12, G:0.29, T:0.45
Consensus pattern (27 bp):
TAGGGGCATTTTGGTCATTTTCACATT
Found at i:8256 original size:14 final size:14
Alignment explanation
Indices: 8237--8270 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
8227 GTATATTAAC
8237 TTTAGTCCATTTAG
1 TTTAGTCCATTTAG
8251 TTTAGTCCATTTAG
1 TTTAGTCCATTTAG
*
8265 ATTAGT
1 TTTAGT
8271 ATCATAGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.12, G:0.15, T:0.50
Consensus pattern (14 bp):
TTTAGTCCATTTAG
Found at i:8447 original size:20 final size:20
Alignment explanation
Indices: 8411--8449 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
8401 AAATACAAGG
*
8411 CATTTGATTTACGAATTGGA
1 CATTTGATTTACAAATTGGA
*
8431 CATTTGATTTGCAAATTGG
1 CATTTGATTTACAAATTGG
8450 TGCTATTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41
Consensus pattern (20 bp):
CATTTGATTTACAAATTGGA
Found at i:10287 original size:2 final size:2
Alignment explanation
Indices: 10273--10305 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
10263 ATGTTGATTT
10273 TA TA TA -A TA -A 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 TA TA TA TA T
10306 GATGGTTCCT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Done.