Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014402.1 Corchorus capsularis cultivar CVL-1 contig14423, 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: 53407
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:117 original size:24 final size:24
Alignment explanation
Indices: 85--253 Score: 248
Period size: 24 Copynumber: 6.8 Consensus size: 24
75 ATATGCCATG
85 TGGGGACTTGGTTGCCATGAGCCA
1 TGGGGACTTGGTTGCCATGAGCCA
109 TGGGGACTTGGTTGCCATGAGCCA
1 TGGGGACTTGGTTGCCATGAGCCA
*
133 TGTGGGATTTGGTTGCCATGAGCCA
1 TG-GGGACTTGGTTGCCATGAGCCA
*
158 TGGGGACTTGGTTGCTATGAGCCA
1 TGGGGACTTGGTTGCCATGAGCCA
*
182 TGTGGAGACTTGGTTGCCATGAGTCA
1 TG-GG-GACTTGGTTGCCATGAGCCA
*
208 TGGGGGCTTGGTTGCCATGAGCCA
1 TGGGGACTTGGTTGCCATGAGCCA
*
232 TGTGGGGACTTGGTTGCTATGA
1 --TGGGGACTTGGTTGCCATGA
254 TACGGCACAT
Statistics
Matches: 131, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
24 66 0.50
25 27 0.21
26 38 0.29
ACGTcount: A:0.16, C:0.17, G:0.38, T:0.29
Consensus pattern (24 bp):
TGGGGACTTGGTTGCCATGAGCCA
Found at i:138 original size:50 final size:50
Alignment explanation
Indices: 79--253 Score: 289
Period size: 50 Copynumber: 3.5 Consensus size: 50
69 AGTTCCATAT
79 GCCATGTGGGGACTTGGTTGCCATGAGCCATGGGGACTTGGTTGCCATGA
1 GCCATGTGGGGACTTGGTTGCCATGAGCCATGGGGACTTGGTTGCCATGA
* *
129 GCCATGT-GGGATTTGGTTGCCATGAGCCATGGGGACTTGGTTGCTATGA
1 GCCATGTGGGGACTTGGTTGCCATGAGCCATGGGGACTTGGTTGCCATGA
* * *
178 GCCATGTGGAGACTTGGTTGCCATGAGTCATGGGGGCTTGGTTGCCATGA
1 GCCATGTGGGGACTTGGTTGCCATGAGCCATGGGGACTTGGTTGCCATGA
*
228 GCCATGTGGGGACTTGGTTGCTATGA
1 GCCATGTGGGGACTTGGTTGCCATGA
254 TACGGCACAT
Statistics
Matches: 115, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
49 47 0.41
50 68 0.59
ACGTcount: A:0.16, C:0.18, G:0.38, T:0.29
Consensus pattern (50 bp):
GCCATGTGGGGACTTGGTTGCCATGAGCCATGGGGACTTGGTTGCCATGA
Found at i:2609 original size:55 final size:55
Alignment explanation
Indices: 2525--2635 Score: 213
Period size: 55 Copynumber: 2.0 Consensus size: 55
2515 ATAGTATGTG
*
2525 GTTTCCACGCCATGGTCATTGTGTGATGATGTATGGGAGCTATATAAGAGCTTTT
1 GTTTCCACGCCATGGTCATTGTATGATGATGTATGGGAGCTATATAAGAGCTTTT
2580 GTTTCCACGCCATGGTCATTGTATGATGATGTATGGGAGCTATATAAGAGCTTTT
1 GTTTCCACGCCATGGTCATTGTATGATGATGTATGGGAGCTATATAAGAGCTTTT
2635 G
1 G
2636 ATCAACTCGA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.23, C:0.14, G:0.27, T:0.36
Consensus pattern (55 bp):
GTTTCCACGCCATGGTCATTGTATGATGATGTATGGGAGCTATATAAGAGCTTTT
Found at i:3118 original size:64 final size:64
Alignment explanation
Indices: 3031--3152 Score: 154
Period size: 64 Copynumber: 1.9 Consensus size: 64
3021 GCCATAGCTC
* *
3031 TTGGGACTTAAGCCATGGTGGCTTATGGCTCCCGCTCTTGGGACATATGCCGTAGCTCCCGTGA
1 TTGGGACTTAAGCCATGGCGGCTTATGGCTCCCGCGCTTGGGACATATGCCGTAGCTCCCGTGA
* * * * * * * *
3095 TTGGGACTTATGTCGTGGCGGCTTATGGCTTCCGCGGTTGGGACTTATGTCGTGGCTC
1 TTGGGACTTAAGCCATGGCGGCTTATGGCTCCCGCGCTTGGGACATATGCCGTAGCTC
3153 TGGGGACTTA
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
64 48 1.00
ACGTcount: A:0.12, C:0.24, G:0.33, T:0.31
Consensus pattern (64 bp):
TTGGGACTTAAGCCATGGCGGCTTATGGCTCCCGCGCTTGGGACATATGCCGTAGCTCCCGTGA
Found at i:3434 original size:45 final size:47
Alignment explanation
Indices: 3370--3496 Score: 186
Period size: 45 Copynumber: 2.7 Consensus size: 47
3360 CTCATGTATT
*
3370 ACGCCGTATCTCATGCCTTATGCCATAGACTTCTGATGCC-A-TTTG
1 ACGCCGCATCTCATGCCTTATGCCATAGACTTCTGATGCCAAGTTTG
* *
3415 ACGCCGCATCTCATGCCTTATGCCATAGAATTCTTATGCCATAATGTTTG
1 ACGCCGCATCTCATGCCTTATGCCATAGACTTCTGATGCC--AA-GTTTG
3465 ACGCCGCATCTCATGCCTTATGCCATAGACTT
1 ACGCCGCATCTCATGCCTTATGCCATAGACTT
3497 GATGCCGCAT
Statistics
Matches: 73, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
45 37 0.51
48 1 0.01
50 35 0.48
ACGTcount: A:0.22, C:0.29, G:0.17, T:0.32
Consensus pattern (47 bp):
ACGCCGCATCTCATGCCTTATGCCATAGACTTCTGATGCCAAGTTTG
Found at i:3509 original size:33 final size:33
Alignment explanation
Indices: 3462--3537 Score: 143
Period size: 33 Copynumber: 2.3 Consensus size: 33
3452 GCCATAATGT
*
3462 TTGACGCCGCATCTCATGCCTTATGCCATAGAC
1 TTGATGCCGCATCTCATGCCTTATGCCATAGAC
3495 TTGATGCCGCATCTCATGCCTTATGCCATAGAC
1 TTGATGCCGCATCTCATGCCTTATGCCATAGAC
3528 TTGATGCCGC
1 TTGATGCCGC
3538 CGCGTCTCAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.20, C:0.32, G:0.20, T:0.29
Consensus pattern (33 bp):
TTGATGCCGCATCTCATGCCTTATGCCATAGAC
Found at i:3596 original size:51 final size:51
Alignment explanation
Indices: 3535--3668 Score: 171
Period size: 52 Copynumber: 2.6 Consensus size: 51
3525 GACTTGATGC
* *
3535 CGCCGCGTCTCATGTCATTACGCCATAGACTTCTTATGCCATAATATTTGA
1 CGCCGCGTCTCATGTCATTATGCCATAGACTTATTATGCCATAATATTTGA
* * * *
3586 CGCCGCGTCTCATGTCTTTATGCCAATAGGCTTATTATGCCATGATGTTTGA
1 CGCCGCGTCTCATGTCATTATGCC-ATAGACTTATTATGCCATAATATTTGA
* * *
3638 CGCCGCATCTCATG-CCTTTTGCCATAGACTT
1 CGCCGCGTCTCATGTCATTATGCCATAGACTT
3669 GATGCCATAA
Statistics
Matches: 72, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
50 7 0.10
51 29 0.40
52 36 0.50
ACGTcount: A:0.20, C:0.28, G:0.18, T:0.34
Consensus pattern (51 bp):
CGCCGCGTCTCATGTCATTATGCCATAGACTTATTATGCCATAATATTTGA
Found at i:3645 original size:172 final size:165
Alignment explanation
Indices: 3410--4157 Score: 565
Period size: 158 Copynumber: 4.6 Consensus size: 165
3400 TTCTGATGCC
* * *
3410 ATTTGACGCCGCATCTCATG-CCTTATGCCATAGAATTCTTATGCCATAATGTTTGACGCCGCAT
1 ATTTGACGCCGCGTCTCATGTCATTATGCCATAGACTTCTTATGCCATAATGTTTGACGCCGCAT
* * * *
3474 CTCATGCCTTATGCCATAGACTTGATGCCGCAT-CTCATGCCTT-ATGCCATAGACT-TGATGCC
66 CTCATGCCTTTTGCCATAGACTTGATG-C-CATAAT-ATGACTTGATGCCATA-A-TGT-ATG-A
*
3536 GCCGCGTCTCATGTCATTACGCCATAGACTTCTTATGCCATAAT
124 GCCGCGTCTCATGTCATTACGCCATAGAC-T-TGATGCCATAAT
* * * *
3580 ATTTGACGCCGCGTCTCATGTCTTTATGCCAATAGGCTTATTATGCCATGATGTTTGACGCCGCA
1 ATTTGACGCCGCGTCTCATGTCATTATGCC-ATAGACTTCTTATGCCATAATGTTTGACGCCGCA
* *
3645 TCTCATGCCTTTTGCCATAGACTTGATGCCATAATGTGACTTGATGCCATAATGTTTGAGCCGCG
65 TCTCATGCCTTTTGCCATAGACTTGATGCCATAATATGACTTGATGCCATAATGTATGAGCCGCG
*
3710 TCTCATGTCATTACGCCATAGACTTGATGTCATAAT
130 TCTCATGTCATTACGCCATAGACTTGATGCCATAAT
* * * * *
3746 GTTTGACGCCGCGTCCCATGTCATTACGCCATAGACTTCTTATGCCATAATATTTGACGCCGCGT
1 ATTTGACGCCGCGTCTCATGTCATTATGCCATAGACTTCTTATGCCATAATGTTTGACGCCGCAT
* * * * * ** *
3811 CTCATGTCTTTTTGCCATAGACTTATTATGCCAT--GATG-TTTGACGCC-GCATCTCAT--G-C
66 CTCATG-CCTTTTGCCATAGAC-T-TGATGCCATAATATGACTTGATGCCATAATGT-ATGAGCC
* *
3869 -C-T-T-ATGCCATATTATGCCATAGACTTGATGCCATAAT
127 GCGTCTCATGTC--ATTACGCCATAGACTTGATGCCATAAT
* * * *
3906 GTTTGACGCCGCGTCTCATGTCATTACGCCATAGAC-T-TGATGCCATAATGTTTGACGCCGCGT
1 ATTTGACGCCGCGTCTCATGTCATTATGCCATAGACTTCTTATGCCATAATGTTTGACGCCGCAT
* * ** * * * * *
3969 CCCATGTCATTACGCCATAGACTTCTTATGCCATAATAT---TTGACGTCGCGT-CT-CAT--G-
66 CTCATG-CCTTTTGCCATAGAC-T-TGATGCCATAATATGACTTGATG-C-CATAATGTATGAGC
** * * *
4026 C-C-T-TTTTGCCA-TA-GAC-T--TCTT-ATGCCATAAT
126 CGCGTCTCATGTCATTACGCCATAGACTTGATGCCATAAT
* * * **
4057 ATTTGACGCCGCGTCTCATGTCTTTATGCCAATAGACTTCTTATGCCATGATGTTTGACGTCGTG
1 ATTTGACGCCGCGTCTCATGTCATTATGCC-ATAGACTTCTTATGCCATAATGTTTGACGCCGCA
*
4122 TCTCATGTCTTTTTGCCATAGACTTGATGCCATAAT
65 TCTCATG-CCTTTTGCCATAGACTTGATGCCATAAT
4158 GTTTGACGCT
Statistics
Matches: 495, Mismatches: 63, Indels: 58
0.80 0.10 0.09
Matches are distributed among these distances:
151 37 0.07
152 20 0.04
153 2 0.00
154 41 0.08
155 2 0.00
156 2 0.00
157 1 0.00
158 70 0.14
159 7 0.01
160 65 0.13
161 1 0.00
162 1 0.00
163 1 0.00
164 3 0.01
165 44 0.09
166 52 0.11
167 2 0.00
168 37 0.07
169 3 0.01
170 29 0.06
171 18 0.04
172 57 0.12
ACGTcount: A:0.22, C:0.26, G:0.18, T:0.34
Consensus pattern (165 bp):
ATTTGACGCCGCGTCTCATGTCATTATGCCATAGACTTCTTATGCCATAATGTTTGACGCCGCAT
CTCATGCCTTTTGCCATAGACTTGATGCCATAATATGACTTGATGCCATAATGTATGAGCCGCGT
CTCATGTCATTACGCCATAGACTTGATGCCATAAT
Found at i:3687 original size:18 final size:18
Alignment explanation
Indices: 3664--3699 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
3654 TTTTGCCATA
3664 GACTTGATGCCATAATGT
1 GACTTGATGCCATAATGT
3682 GACTTGATGCCATAATGT
1 GACTTGATGCCATAATGT
3700 TTGAGCCGCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (18 bp):
GACTTGATGCCATAATGT
Found at i:3728 original size:66 final size:66
Alignment explanation
Indices: 3622--3747 Score: 182
Period size: 66 Copynumber: 1.9 Consensus size: 66
3612 TAGGCTTATT
* * **
3622 ATGCCATGATGTTTGACGCCGCATCTCATGCCTTTTGCCATAGACTTGATGCCATAATGTGACTT
1 ATGCCATAATGTTTGACGCCGCATCTCATGCATTACGCCATAGACTTGATGCCATAATGTGACTT
3687 G
66 G
* *
3688 ATGCCATAATGTTTGA-GCCGCGTCTCATGTCATTACGCCATAGACTTGATGTCATAATGT
1 ATGCCATAATGTTTGACGCCGCATCTCATG-CATTACGCCATAGACTTGATGCCATAATGT
3748 TTGACGCCGC
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
65 12 0.23
66 41 0.77
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (66 bp):
ATGCCATAATGTTTGACGCCGCATCTCATGCATTACGCCATAGACTTGATGCCATAATGTGACTT
G
Found at i:3774 original size:49 final size:51
Alignment explanation
Indices: 3686--4279 Score: 594
Period size: 51 Copynumber: 11.8 Consensus size: 51
3676 TAATGTGACT
3686 TGATGCCATAATGTTTGA-GCCGCGTCTCATGTCATTACGCCATAGAC-T-
1 TGATGCCATAATGTTTGACGCCGCGTCTCATGTCATTACGCCATAGACTTA
* * *
3734 TGATGTCATAATGTTTGACGCCGCGTCCCATGTCATTACGCCATAGACTTC
1 TGATGCCATAATGTTTGACGCCGCGTCTCATGTCATTACGCCATAGACTTA
* * * **
3785 TTATGCCATAATATTTGACGCCGCGTCTCATGTCTTTTTGCCATAGACTTA
1 TGATGCCATAATGTTTGACGCCGCGTCTCATGTCATTACGCCATAGACTTA
* * * *
3836 TTATGCCATGATGTTTGACGCCGCATCTCATGCCTTATGCCATATTATGCCATAGAC-T-
1 TGATGCCATAATGTTTGACGCCGCGTCTCATG-----T--C--ATTACGCCATAGACTTA
3894 TGATGCCATAATGTTTGACGCCGCGTCTCATGTCATTACGCCATAGAC-T-
1 TGATGCCATAATGTTTGACGCCGCGTCTCATGTCATTACGCCATAGACTTA
* *
3943 TGATGCCATAATGTTTGACGCCGCGTCCCATGTCATTACGCCATAGACTTC
1 TGATGCCATAATGTTTGACGCCGCGTCTCATGTCATTACGCCATAGACTTA
* * * * * ** *
3994 TTATGCCATAATATTTGACGTCGCGTCTCATGCCTTTTTGCCATAGACTTC
1 TGATGCCATAATGTTTGACGCCGCGTCTCATGTCATTACGCCATAGACTTA
* * * * *
4045 TTATGCCATAATATTTGACGCCGCGTCTCATGTCTTTATGCCAATAGACTTC
1 TGATGCCATAATGTTTGACGCCGCGTCTCATGTCATTACGCC-ATAGACTTA
* * * * * **
4097 TTATGCCATGATGTTTGACGTCGTGTCTCATGTCTTTTTGCCATAGAC-T-
1 TGATGCCATAATGTTTGACGCCGCGTCTCATGTCATTACGCCATAGACTTA
* *
4146 TGATGCCATAATGTTTGACGCTGCG-----TGTC-TT-TGCCATAGAC-T-
1 TGATGCCATAATGTTTGACGCCGCGTCTCATGTCATTACGCCATAGACTTA
* *
4188 TGATGCCATAATGTTTGACGCCGCGTCTCATGTCATTACGCCATAAACTTC
1 TGATGCCATAATGTTTGACGCCGCGTCTCATGTCATTACGCCATAGACTTA
* * * *
4239 TTATGCCATAATATTTGACACCGCGTCTCATGTCTTTACGC
1 TGATGCCATAATGTTTGACGCCGCGTCTCATGTCATTACGC
4280 TGCGTAGGCT
Statistics
Matches: 474, Mismatches: 48, Indels: 45
0.84 0.08 0.08
Matches are distributed among these distances:
42 35 0.07
43 2 0.00
44 4 0.01
47 4 0.01
48 19 0.04
49 117 0.25
50 4 0.01
51 198 0.42
52 46 0.10
53 1 0.00
56 1 0.00
58 30 0.06
59 1 0.00
60 12 0.03
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.35
Consensus pattern (51 bp):
TGATGCCATAATGTTTGACGCCGCGTCTCATGTCATTACGCCATAGACTTA
Found at i:3796 original size:117 final size:118
Alignment explanation
Indices: 3570--3783 Score: 283
Period size: 114 Copynumber: 1.8 Consensus size: 118
3560 TAGACTTCTT
* * * * *
3570 ATGCCATAATATTTGACGCCGCGTCTCATGTCTTTATGCCAATAGGCTTATTATGCCATGATGTT
1 ATGCCATAATATTTGACGCCGCGTCTCATGTCATTACGCCAATAGACTTATGATGCCATAATGTT
* * **
3635 TGACGCCGCATCTCATGCCTTTTGCCATAGACTTGATGCCATAATGTGACTTG
66 TGACGCCGCATCCCATGCATTACGCCATAGACTTGATGCCATAATGTGACTTG
* *
3688 ATGCCATAATGTTTGA-GCCGCGTCTCATGTCATTACGCC-ATAGAC-T-TGATGTCATAATGTT
1 ATGCCATAATATTTGACGCCGCGTCTCATGTCATTACGCCAATAGACTTATGATGCCATAATGTT
*
3749 TGACGCCGCGTCCCATGTCATTACGCCATAGACTT
66 TGACGCCGCATCCCATG-CATTACGCCATAGACTT
3784 CTTATGCCAT
Statistics
Matches: 83, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
114 27 0.33
115 15 0.18
116 5 0.06
117 21 0.25
118 15 0.18
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.33
Consensus pattern (118 bp):
ATGCCATAATATTTGACGCCGCGTCTCATGTCATTACGCCAATAGACTTATGATGCCATAATGTT
TGACGCCGCATCCCATGCATTACGCCATAGACTTGATGCCATAATGTGACTTG
Found at i:3977 original size:209 final size:209
Alignment explanation
Indices: 3535--4270 Score: 966
Period size: 209 Copynumber: 3.6 Consensus size: 209
3525 GACTTGATGC
*
3535 CGCCGCGTCTCATGTCATTACGCCATAGACTTCTTATGCCATAATATTTGACGCCGCGTCTCATG
1 CGCCGCGTCCCATGTCATTACGCCATAGACTTCTTATGCCATAATATTTGACGCCGCGTCTCATG
* * * *
3600 TCTTTATGCCAATAGGCTTATTATGCCATGATGTTTGACGCCGCATCTCATGCCTTTTGCCATAG
66 TCTTTATGCC-ATAGACTTATTATGCCATAATATTTGACGCCGCATCTCATGCCTTATGCCAT--
3665 ACTTGATGCCATAATGTGACTTGATGCCATAATGTTTGA-GCCGCGTCTCATGTCATTACGCCAT
128 A-TT-ATGCCAT-A---GACTTGATGCCATAATGTTTGACGCCGCGTCTCATGTCATTACGCCAT
*
3729 AGACTTGATGTCATAATGTTTGA
187 AGACTTGATGCCATAATGTTTGA
3752 CGCCGCGTCCCATGTCATTACGCCATAGACTTCTTATGCCATAATATTTGACGCCGCGTCTCATG
1 CGCCGCGTCCCATGTCATTACGCCATAGACTTCTTATGCCATAATATTTGACGCCGCGTCTCATG
* * *
3817 TCTTTTTGCCATAGACTTATTATGCCATGATGTTTGACGCCGCATCTCATGCCTTATGCCATATT
66 TCTTTATGCCATAGACTTATTATGCCATAATATTTGACGCCGCATCTCATGCCTTATGCCATATT
3882 ATGCCATAGACTTGATGCCATAATGTTTGACGCCGCGTCTCATGTCATTACGCCATAGACTTGAT
131 ATGCCATAGACTTGATGCCATAATGTTTGACGCCGCGTCTCATGTCATTACGCCATAGACTTGAT
3947 GCCATAATGTTTGA
196 GCCATAATGTTTGA
*
3961 CGCCGCGTCCCATGTCATTACGCCATAGACTTCTTATGCCATAATATTTGACGTCGCGTCTCATG
1 CGCCGCGTCCCATGTCATTACGCCATAGACTTCTTATGCCATAATATTTGACGCCGCGTCTCATG
* * * * *
4026 CCTTTTTGCCATAGACTTCTTATGCCATAATATTTGACGCCGCGTCTCATGTCTTTATGCCA-A-
66 TCTTTATGCCATAGACTTATTATGCCATAATATTTGACGCCGCATCTCATG-CCTTATGCCATAT
* * * * * * **
4089 TA-GAC-T--TCTT-ATGCCATGATGTTTGACGTCGTGTCTCATGTCTTTTTGCCATAGACTTGA
130 TATGCCATAGACTTGATGCCATAATGTTTGACGCCGCGTCTCATGTCATTACGCCATAGACTTGA
4149 TGCCATAATGTTTGA
195 TGCCATAATGTTTGA
* * * *
4164 CGCTGCG-----TGTC-TT-TGCCATAGAC-T-TGATGCCATAATGTTTGACGCCGCGTCTCATG
1 CGCCGCGTCCCATGTCATTACGCCATAGACTTCTTATGCCATAATATTTGACGCCGCGTCTCATG
* * * * * *
4220 TCATTACGCCATAAACTTCTTATGCCATAATATTTGACACCGCGTCTCATG
66 TCTTTATGCCATAGACTTATTATGCCATAATATTTGACGCCGCATCTCATG
4271 TCTTTACGCT
Statistics
Matches: 486, Mismatches: 31, Indels: 27
0.89 0.06 0.05
Matches are distributed among these distances:
194 74 0.15
195 1 0.00
196 9 0.02
197 2 0.00
198 4 0.01
203 65 0.13
204 3 0.01
206 1 0.00
207 2 0.00
208 24 0.05
209 158 0.33
210 9 0.02
211 1 0.00
212 7 0.01
213 2 0.00
214 1 0.00
216 50 0.10
217 73 0.15
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.35
Consensus pattern (209 bp):
CGCCGCGTCCCATGTCATTACGCCATAGACTTCTTATGCCATAATATTTGACGCCGCGTCTCATG
TCTTTATGCCATAGACTTATTATGCCATAATATTTGACGCCGCATCTCATGCCTTATGCCATATT
ATGCCATAGACTTGATGCCATAATGTTTGACGCCGCGTCTCATGTCATTACGCCATAGACTTGAT
GCCATAATGTTTGA
Found at i:4026 original size:27 final size:27
Alignment explanation
Indices: 3996--4076 Score: 71
Period size: 27 Copynumber: 3.1 Consensus size: 27
3986 TAGACTTCTT
3996 ATGCCATAATATTTGACGTCGCGTCTC
1 ATGCCATAATATTTGACGTCGCGTCTC
* * * * *
4023 ATGCC-T--T-TTTGCCATAGACTTCTT
1 ATGCCATAATATTTGACGTCG-CGTCTC
*
4047 ATGCCATAATATTTGACGCCGCGTCTC
1 ATGCCATAATATTTGACGTCGCGTCTC
4074 ATG
1 ATG
4077 TCTTTATGCC
Statistics
Matches: 38, Mismatches: 11, Indels: 10
0.64 0.19 0.17
Matches are distributed among these distances:
23 7 0.18
24 10 0.26
25 1 0.03
26 1 0.03
27 13 0.34
28 6 0.16
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.36
Consensus pattern (27 bp):
ATGCCATAATATTTGACGTCGCGTCTC
Found at i:4181 original size:42 final size:42
Alignment explanation
Indices: 4133--4213 Score: 153
Period size: 42 Copynumber: 1.9 Consensus size: 42
4123 CTCATGTCTT
*
4133 TTTGCCATAGACTTGATGCCATAATGTTTGACGCTGCGTGTC
1 TTTGCCATAGACTTGATGCCATAATGTTTGACGCCGCGTGTC
4175 TTTGCCATAGACTTGATGCCATAATGTTTGACGCCGCGT
1 TTTGCCATAGACTTGATGCCATAATGTTTGACGCCGCGT
4214 CTCATGTCAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.35
Consensus pattern (42 bp):
TTTGCCATAGACTTGATGCCATAATGTTTGACGCCGCGTGTC
Found at i:5731 original size:24 final size:24
Alignment explanation
Indices: 5699--5868 Score: 241
Period size: 24 Copynumber: 6.8 Consensus size: 24
5689 ATATGCCATG
5699 TGGGGACTTGGTTGCCATGAGCCA
1 TGGGGACTTGGTTGCCATGAGCCA
5723 TGGGGACTTGGTTGCCATGAGCCA
1 TGGGGACTTGGTTGCCATGAGCCA
*
5747 TGTGGGGATTTGGTTGCCATGAGCCA
1 --TGGGGACTTGGTTGCCATGAGCCA
*
5773 TGGGGACTTGGTTGCTATGAGCCA
1 TGGGGACTTGGTTGCCATGAGCCA
*
5797 TGTGGAGACTTGGTTGCCATGAGTCA
1 TG-GG-GACTTGGTTGCCATGAGCCA
*
5823 TGGGGGCTTGGTTGCCATGAGCCA
1 TGGGGACTTGGTTGCCATGAGCCA
*
5847 TGTGGGGACTTGGTTGCTATGA
1 --TGGGGACTTGGTTGCCATGA
5869 TACGGCACAT
Statistics
Matches: 131, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
24 66 0.50
25 4 0.03
26 61 0.47
ACGTcount: A:0.16, C:0.17, G:0.38, T:0.29
Consensus pattern (24 bp):
TGGGGACTTGGTTGCCATGAGCCA
Found at i:5752 original size:50 final size:50
Alignment explanation
Indices: 5693--5868 Score: 298
Period size: 50 Copynumber: 3.5 Consensus size: 50
5683 AGTTCCATAT
5693 GCCATGTGGGGACTTGGTTGCCATGAGCCATGGGGACTTGGTTGCCATGA
1 GCCATGTGGGGACTTGGTTGCCATGAGCCATGGGGACTTGGTTGCCATGA
* *
5743 GCCATGTGGGGATTTGGTTGCCATGAGCCATGGGGACTTGGTTGCTATGA
1 GCCATGTGGGGACTTGGTTGCCATGAGCCATGGGGACTTGGTTGCCATGA
* * *
5793 GCCATGTGGAGACTTGGTTGCCATGAGTCATGGGGGCTTGGTTGCCATGA
1 GCCATGTGGGGACTTGGTTGCCATGAGCCATGGGGACTTGGTTGCCATGA
*
5843 GCCATGTGGGGACTTGGTTGCTATGA
1 GCCATGTGGGGACTTGGTTGCCATGA
5869 TACGGCACAT
Statistics
Matches: 117, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 117 1.00
ACGTcount: A:0.16, C:0.18, G:0.38, T:0.28
Consensus pattern (50 bp):
GCCATGTGGGGACTTGGTTGCCATGAGCCATGGGGACTTGGTTGCCATGA
Found at i:10782 original size:6 final size:6
Alignment explanation
Indices: 10771--10816 Score: 74
Period size: 6 Copynumber: 7.7 Consensus size: 6
10761 GAATATTTGT
* *
10771 AAGGGG AAGGGG AAGGGA AAGGGG AAGGGG AAGGGA AAGGGG AAGG
1 AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG AAGG
10817 AAACCCAGTC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.39, C:0.00, G:0.61, T:0.00
Consensus pattern (6 bp):
AAGGGG
Found at i:10794 original size:18 final size:18
Alignment explanation
Indices: 10771--10816 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
10761 GAATATTTGT
10771 AAGGGGAAGGGGAAGGGA
1 AAGGGGAAGGGGAAGGGA
10789 AAGGGGAAGGGGAAGGGA
1 AAGGGGAAGGGGAAGGGA
10807 AAGGGGAAGG
1 AAGGGGAAGG
10817 AAACCCAGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.39, C:0.00, G:0.61, T:0.00
Consensus pattern (18 bp):
AAGGGGAAGGGGAAGGGA
Found at i:21917 original size:17 final size:17
Alignment explanation
Indices: 21895--21930 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
21885 AGATAGTACA
21895 TAGTAATATAGAGAAAG
1 TAGTAATATAGAGAAAG
21912 TAGTAATATAGAGAAAG
1 TAGTAATATAGAGAAAG
21929 TA
1 TA
21931 TATGAAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.22, T:0.25
Consensus pattern (17 bp):
TAGTAATATAGAGAAAG
Found at i:26854 original size:2 final size:2
Alignment explanation
Indices: 26849--26877 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
26839 GTGTGCGCGC
26849 GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
26878 AGAGAGAGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:27317 original size:24 final size:24
Alignment explanation
Indices: 27289--27334 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
27279 CAAAATTCAA
27289 GATATAATTCCATAGACTTGTAAT
1 GATATAATTCCATAGACTTGTAAT
27313 GATATAATTCCATAGACTTGTA
1 GATATAATTCCATAGACTTGTA
27335 CAAATATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (24 bp):
GATATAATTCCATAGACTTGTAAT
Found at i:27341 original size:24 final size:24
Alignment explanation
Indices: 27290--27344 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
27280 AAAATTCAAG
*
27290 ATATAATTCCATAGACTTGTAATG
1 ATATAATTCCATAGACTTGTAATA
27314 ATATAATTCCATAGACTTGTACA-A
1 ATATAATTCCATAGACTTGTA-ATA
27338 ATATAAT
1 ATATAAT
27345 CTATGGAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 28 0.97
25 1 0.03
ACGTcount: A:0.42, C:0.13, G:0.09, T:0.36
Consensus pattern (24 bp):
ATATAATTCCATAGACTTGTAATA
Found at i:29493 original size:17 final size:18
Alignment explanation
Indices: 29471--29504 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
29461 ACGGACACGC
*
29471 TTTT-CCGGCTATTTTCG
1 TTTTCCCGGCAATTTTCG
29488 TTTTCCCGGCAATTTTC
1 TTTTCCCGGCAATTTTC
29505 TTTCCCCGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.09, C:0.26, G:0.15, T:0.50
Consensus pattern (18 bp):
TTTTCCCGGCAATTTTCG
Found at i:29512 original size:17 final size:18
Alignment explanation
Indices: 29475--29512 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
29465 ACACGCTTTT
* *
29475 CCGGCTATTTTCGTTTTC
1 CCGGCAATTTTCGTTTCC
29493 CCGGCAATTTTC-TTTCC
1 CCGGCAATTTTCGTTTCC
29510 CCG
1 CCG
29513 ATTGCGATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.08, C:0.34, G:0.16, T:0.42
Consensus pattern (18 bp):
CCGGCAATTTTCGTTTCC
Found at i:39985 original size:1 final size:1
Alignment explanation
Indices: 39979--40005 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
39969 GTCTATTGCC
39979 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
40006 CTATTGGGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Done.