Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023602.1 Corchorus olitorius cultivar O-4 contig23635, 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: 26710
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.26
Found at i:8200 original size:67 final size:65
Alignment explanation
Indices: 8089--8222 Score: 214
Period size: 67 Copynumber: 2.0 Consensus size: 65
8079 AATATGTATG
* * *
8089 AACATAAATTAAAAATACATATGAGGTAATATATATGAAGGTAACTATATTGCTAATGAAGTACC
1 AACATAAATTAAAAATACATATGAGCTAATAAATATGAAGGTAAC--TATTGCCAATGAAGTACC
8154 AT
64 AT
*
8156 AACATAAATTAAAAATACATATGAGCTAATAAATATGAATGTAACTATTGCCAATGAAGTACCAT
1 AACATAAATTAAAAATACATATGAGCTAATAAATATGAAGGTAACTATTGCCAATGAAGTACCAT
8221 AA
1 AA
8223 AAGGGTCTCG
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
65 21 0.33
67 42 0.67
ACGTcount: A:0.49, C:0.10, G:0.12, T:0.28
Consensus pattern (65 bp):
AACATAAATTAAAAATACATATGAGCTAATAAATATGAAGGTAACTATTGCCAATGAAGTACCAT
Found at i:14689 original size:41 final size:41
Alignment explanation
Indices: 14585--14913 Score: 355
Period size: 41 Copynumber: 7.8 Consensus size: 41
14575 CACCCTCCCC
* *
14585 AAAGTCCCCAAACACATTTATAACACAGAGGCAATTCTCTCTCT
1 AAAGTCCCCAAACACATTTATAACACAGAGGC-A-TCTAT-ACT
*
14629 AAAGTCCTCAAACACATTTATAACACAGAGGCATCTATACT
1 AAAGTCCCCAAACACATTTATAACACAGAGGCATCTATACT
* * * *
14670 AAAGTCCCCAAACATATTTATAACACAGGGGCAATTCTCTATTCA
1 AAAGTCCCCAAACACATTTATAACACAGAGGC-A---TCTATACT
*
14715 AAAGTCCTCAAACACATTTATAACACA-A-GCATCTATA-T
1 AAAGTCCCCAAACACATTTATAACACAGAGGCATCTATACT
* *
14753 CAAAGT-CCCAAACACATTTATAACACAGGGGCAATCCTCT-CT
1 -AAAGTCCCCAAACACATTTATAACACAGAGGC-AT-CTATACT
* *
14795 AAAAGTCCTCAAACACATTTATAACACAGAGGCATCCATACT
1 -AAAGTCCCCAAACACATTTATAACACAGAGGCATCTATACT
*
14837 AAAGTCCCCAAACACATTTATAACACAGGGGCACCTCTAT-CT
1 AAAGTCCCCAAACACATTTATAACACAGAGGCA--TCTATACT
**
14879 CAAAGTCCAGAAACACATTTATAACACAGAGGCAT
1 -AAAGTCCCCAAACACATTTATAACACAGAGGCAT
14914 TTCTCTTTAT
Statistics
Matches: 243, Mismatches: 27, Indels: 33
0.80 0.09 0.11
Matches are distributed among these distances:
38 20 0.08
39 10 0.04
40 2 0.01
41 67 0.28
42 21 0.09
43 61 0.25
44 31 0.13
45 31 0.13
ACGTcount: A:0.40, C:0.27, G:0.10, T:0.23
Consensus pattern (41 bp):
AAAGTCCCCAAACACATTTATAACACAGAGGCATCTATACT
Found at i:14868 original size:167 final size:167
Alignment explanation
Indices: 14584--14906 Score: 528
Period size: 167 Copynumber: 1.9 Consensus size: 167
14574 TCACCCTCCC
14584 CAAAGTCCCCAAACACATTTATAACACAGAGGCAATTCTCTCTCTAAAGTCCTCAAACACATTTA
1 CAAAGTCCCCAAACACATTTATAACACAGAGGCAATTCTCTCTCTAAAGTCCTCAAACACATTTA
* * *
14649 TAACACAGAGGCATCTATACTAAAGTCCCCAAACATATTTATAACACAGGGGCAATTCTCTAT-T
66 TAACACAGAGGCATCCATACTAAAGTCCCCAAACACATTTATAACACAGGGGC-A-CCTCTATCT
*
14713 CAAAAGTCCTCAAACACATTTATAACACAAGCATCTATAT
129 C-AAAGTCCACAAACACATTTATAACACAAGCATCTATAT
*
14753 CAAAGT-CCCAAACACATTTATAACACAGGGGCAA-TC-CTCTCTAAAAGTCCTCAAACACATTT
1 CAAAGTCCCCAAACACATTTATAACACAGAGGCAATTCTCTCTCT-AAAGTCCTCAAACACATTT
14815 ATAACACAGAGGCATCCATACTAAAGTCCCCAAACACATTTATAACACAGGGGCACCTCTATCTC
65 ATAACACAGAGGCATCCATACTAAAGTCCCCAAACACATTTATAACACAGGGGCACCTCTATCTC
*
14880 AAAGTCCAGAAACACATTTATAACACA
130 AAAGTCCACAAACACATTTATAACACA
14907 GAGGCATTTC
Statistics
Matches: 146, Mismatches: 6, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
165 31 0.21
166 9 0.06
167 73 0.50
168 27 0.18
169 6 0.04
ACGTcount: A:0.40, C:0.27, G:0.10, T:0.23
Consensus pattern (167 bp):
CAAAGTCCCCAAACACATTTATAACACAGAGGCAATTCTCTCTCTAAAGTCCTCAAACACATTTA
TAACACAGAGGCATCCATACTAAAGTCCCCAAACACATTTATAACACAGGGGCACCTCTATCTCA
AAGTCCACAAACACATTTATAACACAAGCATCTATAT
Found at i:14884 original size:84 final size:87
Alignment explanation
Indices: 14585--14913 Score: 486
Period size: 84 Copynumber: 3.9 Consensus size: 87
14575 CACCCTCCCC
* * *
14585 AAAGTCCCCAAACACATTTATAACACAGAGGCAAT--TCTCTCTCTAAAGTCCTCAAACACATTT
1 AAAGTCCCCAAACACATTTATAACACAGGGGCAATCCTCTATCTCAAAAGTCCTCAAACACATTT
14648 ATAACACAGAGGCATCTATACT
66 ATAACACAGAGGCATCTATACT
* *
14670 AAAGTCCCCAAACATATTTATAACACAGGGGCAATTCTCTAT-TCAAAAGTCCTCAAACACATTT
1 AAAGTCCCCAAACACATTTATAACACAGGGGCAATCCTCTATCTCAAAAGTCCTCAAACACATTT
14734 ATAACACA-A-GCATCTATA-T
66 ATAACACAGAGGCATCTATACT
14753 CAAAGT-CCCAAACACATTTATAACACAGGGGCAATCCTC--TCT-AAAAGTCCTCAAACACATT
1 -AAAGTCCCCAAACACATTTATAACACAGGGGCAATCCTCTATCTCAAAAGTCCTCAAACACATT
*
14814 TATAACACAGAGGCATCCATACT
65 TATAACACAGAGGCATCTATACT
**
14837 AAAGTCCCCAAACACATTTATAACACAGGGGC-A-CCTCTATCTC-AAAGTCCAGAAACACATTT
1 AAAGTCCCCAAACACATTTATAACACAGGGGCAATCCTCTATCTCAAAAGTCCTCAAACACATTT
14899 ATAACACAGAGGCAT
66 ATAACACAGAGGCAT
14914 TTCTCTTTAT
Statistics
Matches: 224, Mismatches: 9, Indels: 23
0.88 0.04 0.09
Matches are distributed among these distances:
81 29 0.13
82 6 0.03
83 46 0.21
84 76 0.34
85 34 0.15
86 29 0.13
87 4 0.02
ACGTcount: A:0.40, C:0.27, G:0.10, T:0.23
Consensus pattern (87 bp):
AAAGTCCCCAAACACATTTATAACACAGGGGCAATCCTCTATCTCAAAAGTCCTCAAACACATTT
ATAACACAGAGGCATCTATACT
Found at i:18489 original size:35 final size:35
Alignment explanation
Indices: 18450--18569 Score: 159
Period size: 35 Copynumber: 3.4 Consensus size: 35
18440 ATTTCATCAG
* *
18450 ATTCAGCACTTGGGGGCTACAACAACCCCTTCATC
1 ATTCAACACTTGGGGACTACAACAACCCCTTCATC
*
18485 ATTCAACACTTGGGGACTCCAACAACCCCTTCATC
1 ATTCAACACTTGGGGACTACAACAACCCCTTCATC
* * * * *
18520 ATTCAACAGTTTGGTACTCCAACAACTCCTTCATC
1 ATTCAACACTTGGGGACTACAACAACCCCTTCATC
*
18555 ATTCAACGCTTGGGG
1 ATTCAACACTTGGGG
18570 GCTATGTCAT
Statistics
Matches: 74, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 74 1.00
ACGTcount: A:0.27, C:0.33, G:0.15, T:0.26
Consensus pattern (35 bp):
ATTCAACACTTGGGGACTACAACAACCCCTTCATC
Found at i:19055 original size:72 final size:72
Alignment explanation
Indices: 18957--19429 Score: 707
Period size: 72 Copynumber: 6.6 Consensus size: 72
18947 CCTCTTCTTC
* *
18957 ATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGTAGTCCTTCGCACAATCCTTACATGATAAT
1 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATAAT
19022 -TTCTCAT
66 CTTC-CAT
** *
19029 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTATGTGATTAT
1 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATAAT
*
19094 CTTCCTT
66 CTTCCAT
*
19101 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACAAGATAAT
1 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATAAT
19166 CTTCCAT
66 CTTCCAT
* **
19173 ATTGTGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTATGTGATTAA
1 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGA-TAA
* *
19238 -CTTTCTT
65 TCTTCCAT
* *
19245 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGAAGTCCATCGCACAATCCTTACATGATAAT
1 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATAAT
*
19310 CTCCCAT
66 CTTCCAT
* * * ** *
19317 ATTGCGGTTGTAGCCGAGGCAATTCCCACATTTGGAAGTTCTTCGCACAATCCTTATGTGATTAT
1 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATAAT
*
19382 CTTCCTT
66 CTTCCAT
*
19389 ATTGCGGTTGTAGCTGAGGCAGTTCCCACATTTGGCAGTCC
1 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCC
19430 CCACATTTGG
Statistics
Matches: 361, Mismatches: 37, Indels: 6
0.89 0.09 0.01
Matches are distributed among these distances:
71 3 0.01
72 352 0.98
73 6 0.02
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.33
Consensus pattern (72 bp):
ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATAAT
CTTCCAT
Found at i:19209 original size:144 final size:144
Alignment explanation
Indices: 18949--19603 Score: 1008
Period size: 144 Copynumber: 4.4 Consensus size: 144
18939 TACATGGTCC
* *
18949 TCTT-CTTCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGTAGTCCTTCGCACAATCCTTA
1 TCTTCCTT-ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTA
19013 CATGATAAT-TTCTCATATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCAC
65 CATGATAATCTTC-CATATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCAC
19077 AATCCTTATGTGATTA
129 AATCCTTATGTGATTA
19093 TCTTCCTTATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTAC
1 TCTTCCTTATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTAC
* *
19158 AAGATAATCTTCCATATTGTGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAA
66 ATGATAATCTTCCATATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAA
19223 TCCTTATGTGATTA
131 TCCTTATGTGATTA
* * * *
19237 ACTTTCTTATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGAAGTCCATCGCACAATCCTTAC
1 TCTTCCTTATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTAC
* * * *
19302 ATGATAATCTCCCATATTGCGGTTGTAGCCGAGGCAATTCCCACATTTGGAAGTTCTTCGCACAA
66 ATGATAATCTTCCATATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAA
19367 TCCTTATGTGATTA
131 TCCTTATGTGATTA
*
19381 TCTTCCTTATTGCGGTTGTAGCTGAGGCAGTTCCCACATTTGGCAGTCCCCACATTTGGCAGTCC
1 TCTTCCTTATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGT---C-C---T-----T-C
*
19446 TTTGCACAATCCTTACATGATAATCTTCCATATTGCGGTTGTAGCCGAGGCAGTCCCCACATTTG
53 ---GCACAATCCTTACATGATAATCTTCCATATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTG
19511 GCAGTCCTTCGCACAATCCTTATGTGATTA
115 GCAGTCCTTCGCACAATCCTTATGTGATTA
19541 TCTTCCTTATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTT
1 TCTTCCTTATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTT
19604 GCTACTAATC
Statistics
Matches: 468, Mismatches: 25, Indels: 36
0.88 0.05 0.07
Matches are distributed among these distances:
144 320 0.68
145 6 0.01
147 2 0.00
148 2 0.00
153 1 0.00
156 2 0.00
157 2 0.00
160 133 0.28
ACGTcount: A:0.21, C:0.27, G:0.20, T:0.33
Consensus pattern (144 bp):
TCTTCCTTATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTAC
ATGATAATCTTCCATATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAA
TCCTTATGTGATTA
Found at i:19345 original size:216 final size:215
Alignment explanation
Indices: 18957--19603 Score: 891
Period size: 216 Copynumber: 2.9 Consensus size: 215
18947 CCTCTTCTTC
* *
18957 ATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGTAGTCCTTCGCACAATCCTTACATGATAA-
1 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATAAC
19021 TTTCTCATATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTAT
66 TTTCT--TATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTAT
19086 GTGATTATCTTCCTTATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAA
129 GTGATTATCTTCCTTATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAA
19151 TCCTTACAAGATAATCTTCCAT
194 TCCTTACAAGATAATCTTCCAT
* **
19173 ATTGTGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTATGTGATTAA
1 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGA-TAA
* * **
19238 CTTTCTTATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGAAGTCCATCGCACAATCCTTACA
65 CTTTCTTATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTATG
* * * * * *
19303 TGATAATCTCCCATATTGCGGTTGTAGCCGAGGCAATTCCCACATTTGGAAGTTCTTCGCACAAT
130 TGATTATCTTCCTTATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAAT
*** * *
19368 CCTTATGTGATTATCTTCCTT
195 CCTTACAAGATAATCTTCCAT
*
19389 ATTGCGGTTGTAGCTGAGGCAGTTCCCACATTTGGCAGTCCCCACATTTGGCAGTCCTTTGCACA
1 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGT---C-C---T-----T-C---GCACA
* * *
19454 ATCCTTACATGATAATCTTCCATATTGCGGTTGTAGCCGAGGCAGTCCCCACATTTGGCAGTCCT
50 ATCCTTACATGATAA-CTTTCTTATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCT
19519 TCGCACAATCCTTATGTGATTATCTTCCTTATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGG
114 TCGCACAATCCTTATGTGATTATCTTCCTTATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGG
19584 CAGTCCTTCGCACAATCCTT
179 CAGTCCTTCGCACAATCCTT
19604 GCTACTAATC
Statistics
Matches: 375, Mismatches: 37, Indels: 22
0.86 0.09 0.05
Matches are distributed among these distances:
216 223 0.59
217 3 0.01
218 5 0.01
219 1 0.00
220 1 0.00
223 1 0.00
228 1 0.00
229 1 0.00
231 3 0.01
232 136 0.36
ACGTcount: A:0.21, C:0.26, G:0.20, T:0.32
Consensus pattern (215 bp):
ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATAAC
TTTCTTATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTATGT
GATTATCTTCCTTATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATC
CTTACAAGATAATCTTCCAT
Found at i:19427 original size:16 final size:16
Alignment explanation
Indices: 19406--19445 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
19396 TTGTAGCTGA
*
19406 GGCAGTTCCCACATTT
1 GGCAGTCCCCACATTT
19422 GGCAGTCCCCACATTT
1 GGCAGTCCCCACATTT
19438 GGCAGTCC
1 GGCAGTCC
19446 TTTGCACAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.17, C:0.35, G:0.23, T:0.25
Consensus pattern (16 bp):
GGCAGTCCCCACATTT
Found at i:19490 original size:88 final size:88
Alignment explanation
Indices: 19341--19517 Score: 273
Period size: 88 Copynumber: 2.0 Consensus size: 88
19331 CGAGGCAATT
* ** * * *
19341 CCCACATTTGGAAGTTCTTCGCACAATCCTTATGTGATTATCTTCCTTATTGCGGTTGTAGCTGA
1 CCCACATTTGGAAGTCCTTCGCACAATCCTTACATGATAATCTTCCATATTGCGGTTGTAGCCGA
*
19406 GGCAGTTCCCACATTTGGCAGTC
66 GGCAGTCCCCACATTTGGCAGTC
* *
19429 CCCACATTTGGCAGTCCTTTGCACAATCCTTACATGATAATCTTCCATATTGCGGTTGTAGCCGA
1 CCCACATTTGGAAGTCCTTCGCACAATCCTTACATGATAATCTTCCATATTGCGGTTGTAGCCGA
19494 GGCAGTCCCCACATTTGGCAGTC
66 GGCAGTCCCCACATTTGGCAGTC
19517 C
1 C
19518 TTCGCACAAT
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
88 80 1.00
ACGTcount: A:0.20, C:0.28, G:0.20, T:0.32
Consensus pattern (88 bp):
CCCACATTTGGAAGTCCTTCGCACAATCCTTACATGATAATCTTCCATATTGCGGTTGTAGCCGA
GGCAGTCCCCACATTTGGCAGTC
Found at i:19507 original size:72 final size:72
Alignment explanation
Indices: 19422--19603 Score: 310
Period size: 72 Copynumber: 2.5 Consensus size: 72
19412 TCCCACATTT
*
19422 GGCAGTCCCCACATTTGGCAGTCCTTTGCACAATCCTTACATGATAATCTTCCATATTGCGGTTG
1 GGCAGTCCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATAATCTTCCATATTGCGGTTG
19487 TAGCCGA
66 TAGCCGA
** * *
19494 GGCAGTCCCCACATTTGGCAGTCCTTCGCACAATCCTTATGTGATTATCTTCCTTATTGCGGTTG
1 GGCAGTCCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATAATCTTCCATATTGCGGTTG
19559 TAGCCGA
66 TAGCCGA
*
19566 GGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTT
1 GGCAGTCCCCACATTTGGCAGTCCTTCGCACAATCCTT
19604 GCTACTAATC
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
72 104 1.00
ACGTcount: A:0.20, C:0.29, G:0.20, T:0.31
Consensus pattern (72 bp):
GGCAGTCCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATAATCTTCCATATTGCGGTTG
TAGCCGA
Found at i:19533 original size:160 final size:160
Alignment explanation
Indices: 19262--19589 Score: 566
Period size: 160 Copynumber: 2.0 Consensus size: 160
19252 TTGTAGCCGA
*
19262 GGCAGTTCCCACATTTGGAAGTCCATCGCACAATCCTTACATGATAATCTCCCATATTGCGGTTG
1 GGCAGTCCCCACATTTGGAAGTCCATCGCACAATCCTTACATGATAATCTCCCATATTGCGGTTG
* *
19327 TAGCCGAGGCAATTCCCACATTTGGAAGTTCTTCGCACAATCCTTATGTGATTATCTTCCTTATT
66 TAGCCGAGGCAATCCCCACATTTGGAAGTCCTTCGCACAATCCTTATGTGATTATCTTCCTTATT
*
19392 GCGGTTGTAGCTGAGGCAGTTCCCACATTT
131 GCGGTTGTAGCCGAGGCAGTTCCCACATTT
* * * *
19422 GGCAGTCCCCACATTTGGCAGTCCTTTGCACAATCCTTACATGATAATCTTCCATATTGCGGTTG
1 GGCAGTCCCCACATTTGGAAGTCCATCGCACAATCCTTACATGATAATCTCCCATATTGCGGTTG
* *
19487 TAGCCGAGGCAGTCCCCACATTTGGCAGTCCTTCGCACAATCCTTATGTGATTATCTTCCTTATT
66 TAGCCGAGGCAATCCCCACATTTGGAAGTCCTTCGCACAATCCTTATGTGATTATCTTCCTTATT
19552 GCGGTTGTAGCCGAGGCAGTTCCCACATTT
131 GCGGTTGTAGCCGAGGCAGTTCCCACATTT
19582 GGCAGTCC
1 GGCAGTCC
19590 TTCGCACAAT
Statistics
Matches: 158, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
160 158 1.00
ACGTcount: A:0.21, C:0.27, G:0.20, T:0.32
Consensus pattern (160 bp):
GGCAGTCCCCACATTTGGAAGTCCATCGCACAATCCTTACATGATAATCTCCCATATTGCGGTTG
TAGCCGAGGCAATCCCCACATTTGGAAGTCCTTCGCACAATCCTTATGTGATTATCTTCCTTATT
GCGGTTGTAGCCGAGGCAGTTCCCACATTT
Found at i:20168 original size:59 final size:59
Alignment explanation
Indices: 20103--20223 Score: 215
Period size: 59 Copynumber: 2.1 Consensus size: 59
20093 CCCAGAAAGC
* *
20103 CTTCCACAACTGTCATTATCAACTCCAAGTAATCAACAAAGAAAACGATTCAAGCAAGT
1 CTTCCACAACTATCATTATCAACTCCAAGTAATCAACAAAGAAAACAATTCAAGCAAGT
*
20162 CTTCCACAACTATCATTATCAACTCCAAGTAATCAACAAAGAAGACAATTCAAGCAAGT
1 CTTCCACAACTATCATTATCAACTCCAAGTAATCAACAAAGAAAACAATTCAAGCAAGT
20221 CTT
1 CTT
20224 GCAATATTCA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.42, C:0.26, G:0.09, T:0.23
Consensus pattern (59 bp):
CTTCCACAACTATCATTATCAACTCCAAGTAATCAACAAAGAAAACAATTCAAGCAAGT
Found at i:20808 original size:20 final size:20
Alignment explanation
Indices: 20773--20810 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
20763 TTCGAATTGT
*
20773 CATAGTTGCGGCAGAGACGA
1 CATAGTTGCAGCAGAGACGA
*
20793 CATAGTTGCAGTAGAGAC
1 CATAGTTGCAGCAGAGAC
20811 AAGCATGGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.18, G:0.32, T:0.18
Consensus pattern (20 bp):
CATAGTTGCAGCAGAGACGA
Found at i:23046 original size:41 final size:41
Alignment explanation
Indices: 22945--23278 Score: 386
Period size: 41 Copynumber: 7.9 Consensus size: 41
22935 TTCTCCATCC
* * *
22945 CTAAAGTCCCCAAACACATTTATAACACAGGGGCAATTCTCTCT
1 CTAAAGTCCCCAAACACATTTATAACACAGAGGC-A-TCTAT-A
* *
22989 CTAAAGTCCTCAAACACATTTATAACACATAGGCATCTATA
1 CTAAAGTCCCCAAACACATTTATAACACAGAGGCATCTATA
* *
23030 CTAAAGTCCCCAAACACATTTATAACACAGGGGCAATTCTCTATT
1 CTAAAGTCCCCAAACACATTTATAACACAGAGGC-A---TCTATA
* *
23075 CCAAAGTCCTCAAACACATTTATAACACAGAGGCATCTATA
1 CTAAAGTCCCCAAACACATTTATAACACAGAGGCATCTATA
* *
23116 -TCAAAGTCCCCAAACACATTTATAACACAGGGGCAATCCTCT-
1 CT-AAAGTCCCCAAACACATTTATAACACAGAGGC-AT-CTATA
* *
23158 CTAAAAGTCCCCATACACATTTATAACACAGAGGCATCCATA
1 CT-AAAGTCCCCAAACACATTTATAACACAGAGGCATCTATA
*
23200 CTAAAGTCCCCAAACACATTTATAACACAGGGGCACCTCTAT-
1 CTAAAGTCCCCAAACACATTTATAACACAGAGGCA--TCTATA
*
23242 CTCAAAGTCCTCAAACACATTTATAACACAGAGGCAT
1 CT-AAAGTCCCCAAACACATTTATAACACAGAGGCAT
23279 TTCTCTTTGA
Statistics
Matches: 251, Mismatches: 27, Indels: 27
0.82 0.09 0.09
Matches are distributed among these distances:
41 100 0.40
42 13 0.05
43 70 0.28
44 32 0.13
45 36 0.14
ACGTcount: A:0.38, C:0.28, G:0.10, T:0.23
Consensus pattern (41 bp):
CTAAAGTCCCCAAACACATTTATAACACAGAGGCATCTATA
Found at i:23122 original size:86 final size:85
Alignment explanation
Indices: 22945--23278 Score: 523
Period size: 84 Copynumber: 3.9 Consensus size: 85
22935 TTCTCCATCC
* *
22945 CTAAAGTCCCCAAACACATTTATAACACAGGGGCAATTCTCTCTCTAAAGTCCTCAAACACATTT
1 CTAAAGTCCCCAAACACATTTATAACACAGGGGCAATCCTCTCTCCAAAGTCCTCAAACACATTT
*
23010 ATAACACATAGGCATCTATA
66 ATAACACAGAGGCATCTATA
* *
23030 CTAAAGTCCCCAAACACATTTATAACACAGGGGCAATTCTCTATTCCAAAGTCCTCAAACACATT
1 CTAAAGTCCCCAAACACATTTATAACACAGGGGCAATCCTCT-CTCCAAAGTCCTCAAACACATT
23095 TATAACACAGAGGCATCTATA
65 TATAACACAGAGGCATCTATA
* * *
23116 -TCAAAGTCCCCAAACACATTTATAACACAGGGGCAATCCTCTCT-AAAAGTCCCCATACACATT
1 CT-AAAGTCCCCAAACACATTTATAACACAGGGGCAATCCTCTCTCCAAAGTCCTCAAACACATT
*
23179 TATAACACAGAGGCATCCATA
65 TATAACACAGAGGCATCTATA
*
23200 CTAAAGTCCCCAAACACATTTATAACACAGGGGC-A-CCTCTATCTCAAAGTCCTCAAACACATT
1 CTAAAGTCCCCAAACACATTTATAACACAGGGGCAATCCTCTCTC-CAAAGTCCTCAAACACATT
23263 TATAACACAGAGGCAT
65 TATAACACAGAGGCAT
23279 TTCTCTTTGA
Statistics
Matches: 231, Mismatches: 13, Indels: 11
0.91 0.05 0.04
Matches are distributed among these distances:
82 6 0.03
83 1 0.00
84 100 0.43
85 45 0.19
86 79 0.34
ACGTcount: A:0.38, C:0.28, G:0.10, T:0.23
Consensus pattern (85 bp):
CTAAAGTCCCCAAACACATTTATAACACAGGGGCAATCCTCTCTCCAAAGTCCTCAAACACATTT
ATAACACAGAGGCATCTATA
Found at i:24833 original size:76 final size:76
Alignment explanation
Indices: 24683--24825 Score: 173
Period size: 76 Copynumber: 1.9 Consensus size: 76
24673 CAAGGGCCCT
* * *
24683 GACTCCACCTGGGCGCCCACATGGTTGCCTTGAACACCCATGTAGTTTGCTTAAGGACCCAGGTG
1 GACTCCACCTGGGCGCCCACATGGTTGCCTTGAACACCCATGTAGTTTGCCTAAGCACCCAGATG
24748 GGCGGTGTCAC
66 GGCGGTGTCAC
* * * * * *
24759 GACTCCAGCTGGGTGCCCACATGGTTTG-TTTGAAGACCCATGT-GTTTCGCCTGATCACCCAGA
1 GACTCCACCTGGGCGCCCACATGG-TTGCCTTGAACACCCATGTAGTTT-GCCTAAGCACCCAGA
24822 TGGG
64 TGGG
24826 TTGTGTCATA
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
75 4 0.07
76 49 0.88
77 3 0.05
ACGTcount: A:0.18, C:0.29, G:0.29, T:0.24
Consensus pattern (76 bp):
GACTCCACCTGGGCGCCCACATGGTTGCCTTGAACACCCATGTAGTTTGCCTAAGCACCCAGATG
GGCGGTGTCAC
Found at i:26561 original size:20 final size:21
Alignment explanation
Indices: 26536--26574 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
26526 TCTATAAAAA
*
26536 CAAACAGAA-TCAAATCAAAT
1 CAAACAGAAGTAAAATCAAAT
26556 CAAACAGAAGTAAAATCAA
1 CAAACAGAAGTAAAATCAA
26575 GACTAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.62, C:0.18, G:0.08, T:0.13
Consensus pattern (21 bp):
CAAACAGAAGTAAAATCAAAT
Done.