Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012306.1 Corchorus olitorius cultivar O-4 contig12339, 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: 17202
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Found at i:8039 original size:39 final size:38
Alignment explanation
Indices: 7949--8157 Score: 131
Period size: 39 Copynumber: 5.4 Consensus size: 38
7939 TTATCTTAGC
* * *
7949 AAACCTGCTTAGCTCCTTGTTTAGAACTTCCGTTTAA-T
1 AAACCTGCTTAGGTTCTTGTGTAGAA-TTCCGTTTAAGT
* *
7987 CAAACTTGTTTAGGTTCTTGTGTAGAATTCCCGTTTAAGT
1 -AAACCTGCTTAGGTTCTTGTGTAGAATT-CCGTTTAAGT
* * * * *
8027 GAACCTGCTTAGG-TCTACGTTTAGGAGTTTCGTTTAA-T
1 AAACCTGCTTAGGTTCT-TGTGTA-GAATTCCGTTTAAGT
* * * * *
8065 CGAACCTGCTTAGGTCCTTGTGTAAAATTTCTGTTTAAGA
1 -AAACCTGCTTAGGTTCTTGTGTAGAA-TTCCGTTTAAGT
* * *
8105 AAACCTGCTTAGG-TCTCTGCT-TAGAGTTTCTGTTTAAGA
1 AAACCTGCTTAGGTTCT-TG-TGTAGA-ATTCCGTTTAAGT
8144 AAACCTGCTTAGGT
1 AAACCTGCTTAGGT
8158 CCCCGCTTAG
Statistics
Matches: 134, Mismatches: 24, Indels: 23
0.74 0.13 0.13
Matches are distributed among these distances:
38 9 0.07
39 117 0.87
40 8 0.06
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.39
Consensus pattern (38 bp):
AAACCTGCTTAGGTTCTTGTGTAGAATTCCGTTTAAGT
Found at i:8050 original size:78 final size:77
Alignment explanation
Indices: 7949--8159 Score: 215
Period size: 78 Copynumber: 2.7 Consensus size: 77
7939 TTATCTTAGC
* * * * * *
7949 AAACCTGCTTAGCTCCTTGTTTAGAACTTCCGTTTAATCAAACTTGTTTAGGTTCTTGTGTAGAA
1 AAACCTGCTTAGGT-CTCGTTTAGAACTTCCGTTTAATCAAACCTGCTTAGGTCCTTGTGTAAAA
*
8014 TTCCCGTTTAAGT
65 TTCCCGTTTAAGA
* * * * *
8027 GAACCTGCTTAGGTCTACGTTTAGGAGTTTCGTTTAATCGAACCTGCTTAGGTCCTTGTGTAAAA
1 AAACCTGCTTAGGTCT-CGTTTAGAACTTCCGTTTAATCAAACCTGCTTAGGTCCTTGTGTAAAA
* *
8092 TTTCTGTTTAAGA
65 TTCCCGTTTAAGA
* ** * **
8105 AAACCTGCTTAGGTCTCTGCTTAGAGTTTCTGTTTAAGAAAACCTGCTTAGGTCC
1 AAACCTGCTTAGGTCTC-GTTTAGAACTTCCGTTTAATCAAACCTGCTTAGGTCC
8160 CCGCTTAGAA
Statistics
Matches: 107, Mismatches: 24, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
77 3 0.03
78 104 0.97
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (77 bp):
AAACCTGCTTAGGTCTCGTTTAGAACTTCCGTTTAATCAAACCTGCTTAGGTCCTTGTGTAAAAT
TCCCGTTTAAGA
Found at i:8158 original size:39 final size:38
Alignment explanation
Indices: 8018--8504 Score: 372
Period size: 39 Copynumber: 12.6 Consensus size: 38
8008 GTAGAATTCC
** *
8018 CGTTTAAGTGAACCTGCTTAGGTCTAC-GTTTAGGAGTTT
1 CGTTTAAGAAAACCTGCTTAGGTCT-CTGCTTA-GAGTTT
*** * *
8057 CGTTTAATCGAACCTGCTTAGGTC-CTTG-TGTAAAATTT
1 CGTTTAAGAAAACCTGCTTAGGTCTC-TGCT-TAGAGTTT
8095 CTGTTTAAGAAAACCTGCTTAGGTCTCTGCTTAGAGTTT
1 C-GTTTAAGAAAACCTGCTTAGGTCTCTGCTTAGAGTTT
* * * *
8134 CTGTTTAAGAAAACCTGCTTAGGTCCCCGCTTAGAATCT
1 C-GTTTAAGAAAACCTGCTTAGGTCTCTGCTTAGAGTTT
* ** ** * *
8173 CGTTTGATTAATTCTGCTTAGGACCTCTACTTAGAGTTT
1 CGTTTAAGAAAACCTGCTTAGG-TCTCTGCTTAGAGTTT
* * * * * *
8212 CGTTTAAGTAAACCTACTTAGATCTTTGTTTAGAATTTT
1 CGTTTAAGAAAACCTGCTTAGGTCTCTGCTTAG-AGTTT
* *
8251 CGTTTAAGAAAACTTGCTTAGGTCTCTGCTTAGAGTTG
1 CGTTTAAGAAAACCTGCTTAGGTCTCTGCTTAGAGTTT
* * * * *
8289 CCTTTAAGTAAACCTGCTCAAGCCTCTGCTTAGAGTTT
1 CGTTTAAGAAAACCTGCTTAGGTCTCTGCTTAGAGTTT
* * *
8327 CGTTCAAGAAAAACCTGCTTAGGATTTCTGCTTAGAATTT
1 CGTTTAAG-AAAACCTGCTTAGG-TCTCTGCTTAGAGTTT
* * * * *
8367 -TTATTCAAGTAAACCTGTTTAGGCCTCTGCTTGGAGTTT
1 CGT-TT-AAGAAAACCTGCTTAGGTCTCTGCTTAGAGTTT
*
8406 CGTTTAAGAAAAAACTGCTTAGGTCTCTGCTTAGAGTTT
1 CGTTTAAG-AAAACCTGCTTAGGTCTCTGCTTAGAGTTT
** * * *
8445 CGGCTGAGTAAAA-CTGTTTAGGTCTCTGCTTAGAGTTC
1 CGTTTAAG-AAAACCTGCTTAGGTCTCTGCTTAGAGTTT
* *
8483 CTGTTTAAGTAAACCCGCTTAG
1 C-GTTTAAGAAAACCTGCTTAG
8505 CTCCTTCTGT
Statistics
Matches: 348, Mismatches: 84, Indels: 32
0.75 0.18 0.07
Matches are distributed among these distances:
37 1 0.00
38 99 0.28
39 216 0.62
40 29 0.08
41 3 0.01
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Consensus pattern (38 bp):
CGTTTAAGAAAACCTGCTTAGGTCTCTGCTTAGAGTTT
Found at i:8225 original size:116 final size:113
Alignment explanation
Indices: 8092--8504 Score: 355
Period size: 116 Copynumber: 3.6 Consensus size: 113
8082 TTGTGTAAAA
*
8092 TTTCTGTTTAAGAAAACCTGCTTAGGTCTCTGCTTAGAGTTTCTGTTTAAGAAAACCTGCTTAGG
1 TTTC-GTTTAAGAAAACCTGCTTAGGTCTCTGCTTAGAATTTCTGTTTAAGAAAACCTGCTTAGG
* * ** *
8157 TCCCCGCTTAGAATCTCGTTTGATTAATTCTGCTTAGGACCTCTACTTAGAG
65 TCCCTGCTTAGAGT-TCGTTTGA-TAAAACTGCTTAGG-CCTCTGCTTAGAG
* * * * * *
8209 TTTCGTTTAAGTAAACCTACTTAGATCTTTGTTTAGAATTT-TCGTTTAAGAAAACTTGCTTAGG
1 TTTCGTTTAAGAAAACCTGCTTAGGTCTCTGCTTAGAATTTCT-GTTTAAGAAAACCTGCTTAGG
* * * * * *
8273 TCTCTGCTTAGAGTTGCCTTTAAGTAAACCTGCTCAAGCCTCTGCTTAGAG
65 TCCCTGCTTAGAGTT-CGTTTGA-TAAAACTGCTTAGGCCTCTGCTTAGAG
* * * * * * *
8324 TTTCGTTCAAGAAAAACCTGCTTAGGATTTCTGCTTAGAATTTTTATTCAAGTAAACCTGTTTAG
1 TTTCGTTTAAG-AAAACCTGCTTAGG-TCTCTGCTTAGAATTTCTGTTTAAGAAAACCTGCTTAG
* * *
8389 G-CCTCTGCTTGGAGTTTCGTTTAAGAAAAAACTGCTTAGGTCTCTGCTTAGAG
64 GTCC-CTGCTTAGAG-TTCGTTT--GATAAAACTGCTTAGGCCTCTGCTTAGAG
** * * * * * *
8442 TTTCGGCTGAGTAAAA-CTGTTTAGGTCTCTGCTTAGAGTTCCTGTTTAAGTAAACCCGCTTAG
1 TTTCGTTTAAG-AAAACCTGCTTAGGTCTCTGCTTAGAATTTCTGTTTAAGAAAACCTGCTTAG
8505 CTCCTTCTGT
Statistics
Matches: 234, Mismatches: 53, Indels: 19
0.76 0.17 0.06
Matches are distributed among these distances:
115 24 0.10
116 119 0.51
117 54 0.23
118 36 0.15
119 1 0.00
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (113 bp):
TTTCGTTTAAGAAAACCTGCTTAGGTCTCTGCTTAGAATTTCTGTTTAAGAAAACCTGCTTAGGT
CCCTGCTTAGAGTTCGTTTGATAAAACTGCTTAGGCCTCTGCTTAGAG
Found at i:8322 original size:77 final size:78
Alignment explanation
Indices: 8018--8504 Score: 338
Period size: 77 Copynumber: 6.3 Consensus size: 78
8008 GTAGAATTCC
** * * * *
8018 CGTTTAAGTGAACCTGCTTAGGTCTAC-GTTTAGGAGTTTCGTTTAA-TCGAACCTGCTTAGGTC
1 CGTTTAAGAAAACCTGCTTAGGTCT-CTGCTTA-GAGTTTCGTTTAAGT-AAACCTGCTTAAGAC
*
8081 CT-TG-TGTA-AAATTT
63 CTCTGCT-TAGAAGTTT
* * *
8095 CTGTTTAAGAAAACCTGCTTAGGTCTCTGCTTAGAGTTTCTGTTTAAGAAAACCTGCTTAGGTCC
1 C-GTTTAAGAAAACCTGCTTAGGTCTCTGCTTAGAGTTTC-GTTTAAGTAAACCTGCTTAAGACC
* *
8160 -CCGCTTAGAA-TCT
64 TCTGCTTAGAAGTTT
* ** ** * * * *
8173 CGTTTGATTAATTCTGCTTAGGACCTCTACTTAGAGTTTCGTTTAAGTAAACCTACTT-AGATCT
1 CGTTTAAGAAAACCTGCTTAGG-TCTCTGCTTAGAGTTTCGTTTAAGTAAACCTGCTTAAGACCT
* * *
8237 TTGTTTAGAATTTT
65 CTGCTTAGAAGTTT
* * * *
8251 CGTTTAAGAAAACTTGCTTAGGTCTCTGCTTAGAGTTGCCTTTAAGTAAACCTGCTCAAG-CCTC
1 CGTTTAAGAAAACCTGCTTAGGTCTCTGCTTAGAGTTTCGTTTAAGTAAACCTGCTTAAGACCTC
8315 TGCTTAG-AGTTT
66 TGCTTAGAAGTTT
* * * * * *
8327 CGTTCAAGAAAAACCTGCTTAGGATTTCTGCTTAGAATTT-TTATTCAAGTAAACCTG-TTTAGG
1 CGTTTAAG-AAAACCTGCTTAGG-TCTCTGCTTAGAGTTTCGT-TT-AAGTAAACCTGCTTAAGA
*
8390 CCTCTGCTT-GGAGTTT
62 CCTCTGCTTAGAAGTTT
* ** * * * **
8406 CGTTTAAGAAAAAACTGCTTAGGTCTCTGCTTAGAGTTTCGGCTGAGTAAAACTG-TTTAGGTCT
1 CGTTTAAG-AAAACCTGCTTAGGTCTCTGCTTAGAGTTTCGTTTAAGTAAACCTGCTTAAGACCT
*
8470 CTGCTTAG-AGTTC
65 CTGCTTAGAAGTTT
* *
8483 CTGTTTAAGTAAACCCGCTTAG
1 C-GTTTAAGAAAACCTGCTTAG
8505 CTCCTTCTGT
Statistics
Matches: 329, Mismatches: 61, Indels: 40
0.77 0.14 0.09
Matches are distributed among these distances:
76 13 0.04
77 137 0.42
78 130 0.40
79 49 0.15
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Consensus pattern (78 bp):
CGTTTAAGAAAACCTGCTTAGGTCTCTGCTTAGAGTTTCGTTTAAGTAAACCTGCTTAAGACCTC
TGCTTAGAAGTTT
Found at i:8345 original size:155 final size:154
Alignment explanation
Indices: 8051--8443 Score: 377
Period size: 155 Copynumber: 2.5 Consensus size: 154
8041 CTACGTTTAG
* * *
8051 GAGTTTCGTTTAA-TCGAACCTGCTTAGGTCCTTGTGTA-AAATTTCTGTTTAAGAAAACCTGCT
1 GAGTTTCGTTTAAGT-AAACCTGCTTAGGTCTTTGTTTAGAAATTTC-GTTTAAGAAAA-CTGCT
* * * * *
8114 TAGGTCTCTGCTTAGAGTTTCTGTTTAAGAAAACCTGCTTAGGTCCCCGCTTAGAATCTCGTTTG
63 TAGGTCTCTGCTTAGAGTTGCTCTTTAAGAAAACCTGCTCAAGTCCCCGCTTAGAATCTCGTTAG
* **
8179 ATTAATTCTGCTTAGGACCTCTACTTA
128 ATAAAACCTGCTTAGGACCTCTACTTA
* * *
8206 GAGTTTCGTTTAAGTAAACCTACTTAGATCTTTGTTTAGAATTTTCGTTTAAGAAAACTTGCTTA
1 GAGTTTCGTTTAAGTAAACCTGCTTAGGTCTTTGTTTAGAAATTTCGTTTAAGAAAAC-TGCTTA
* * * *
8271 GGTCTCTGCTTAGAGTTGC-CTTTAAGTAAACCTGCTCAAG-CCTCTGCTTAGAGTTTCGTTCAA
65 GGTCTCTGCTTAGAGTTGCTCTTTAAGAAAACCTGCTCAAGTCC-CCGCTTAGAATCTCGTT--A
** *
8334 GA-AAAACCTGCTTAGGATTTCTGCTTA
127 GATAAAACCTGCTTAGGACCTCTACTTA
* * * * * * * *
8361 GAATTT-TTATTCAAGTAAACCTGTTTAGGCCTCTGCTT-GGAGTTTCGTTTAAGAAAAAACTGC
1 GAGTTTCGT-TT-AAGTAAACCTGCTTAGGTCTTTGTTTAGAAATTTCGTTTAAG--AAAACTGC
8424 TTAGGTCTCTGCTTAGAGTT
62 TTAGGTCTCTGCTTAGAGTT
8444 TCGGCTGAGT
Statistics
Matches: 197, Mismatches: 31, Indels: 19
0.80 0.13 0.08
Matches are distributed among these distances:
153 2 0.01
154 33 0.17
155 105 0.53
156 52 0.26
157 5 0.03
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.38
Consensus pattern (154 bp):
GAGTTTCGTTTAAGTAAACCTGCTTAGGTCTTTGTTTAGAAATTTCGTTTAAGAAAACTGCTTAG
GTCTCTGCTTAGAGTTGCTCTTTAAGAAAACCTGCTCAAGTCCCCGCTTAGAATCTCGTTAGATA
AAACCTGCTTAGGACCTCTACTTA
Found at i:8467 original size:38 final size:38
Alignment explanation
Indices: 8255--8481 Score: 143
Period size: 38 Copynumber: 5.9 Consensus size: 38
8245 AATTTTCGTT
* * ***
8255 TAAG-AAAACTTGCTTAGGTCTCTGCTTAGAGTTGCCTT
1 TAAGTAAAAC-TGTTTAGGTCTCTGCTTAGAGTTTCGGC
* * * * * *
8293 TAAGTAAACCTGCTCAAGCCTCTGCTTAGAGTTTC-GT
1 TAAGTAAAACTGTTTAGGTCTCTGCTTAGAGTTTCGGC
* * * * ****
8330 TCAAGAAAAACCTGCTTAGGATTTCTGCTTAGAATTTTTAT
1 T-AAGTAAAA-CTGTTTAGG-TCTCTGCTTAGAGTTTCGGC
* * * **
8371 TCAAGTAAACCTGTTTAGGCCTCTGCTTGGAGTTTCGTT
1 T-AAGTAAAACTGTTTAGGTCTCTGCTTAGAGTTTCGGC
* *
8410 TAAGAAAAAACTGCTTAGGTCTCTGCTTAGAGTTTCGGC
1 TAAG-TAAAACTGTTTAGGTCTCTGCTTAGAGTTTCGGC
*
8449 TGAGTAAAACTGTTTAGGTCTCTGCTTAGAGTT
1 TAAGTAAAACTGTTTAGGTCTCTGCTTAGAGTT
8482 CCTGTTTAAG
Statistics
Matches: 148, Mismatches: 35, Indels: 12
0.76 0.18 0.06
Matches are distributed among these distances:
37 2 0.01
38 61 0.41
39 55 0.37
40 21 0.14
41 9 0.06
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (38 bp):
TAAGTAAAACTGTTTAGGTCTCTGCTTAGAGTTTCGGC
Found at i:10339 original size:38 final size:38
Alignment explanation
Indices: 10294--10371 Score: 138
Period size: 38 Copynumber: 2.1 Consensus size: 38
10284 GGACACCTGT
*
10294 TGTCGGTCTCAATTCATCGTTCCTAGACTTGGAACATC
1 TGTCGGTCTAAATTCATCGTTCCTAGACTTGGAACATC
*
10332 TGTCGGTCTAAATTCATCGTTCCTAGGCTTGGAACATC
1 TGTCGGTCTAAATTCATCGTTCCTAGACTTGGAACATC
10370 TG
1 TG
10372 GACGGGGGTC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.35
Consensus pattern (38 bp):
TGTCGGTCTAAATTCATCGTTCCTAGACTTGGAACATC
Found at i:12869 original size:1 final size:1
Alignment explanation
Indices: 12863--12941 Score: 50
Period size: 1 Copynumber: 79.0 Consensus size: 1
12853 AGCTCGCAAT
* * * * * * * * **
12863 AAAAAAATAAAAACAAAAAAAACAAAAAAAGAACAAACAAAAAAACAAAAAAAGAACGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
12928 AACAAAAAAGAAAA
1 AAAAAAAAAAAAAA
12942 GAAGAATAGT
Statistics
Matches: 55, Mismatches: 23, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 55 1.00
ACGTcount: A:0.85, C:0.09, G:0.05, T:0.01
Consensus pattern (1 bp):
A
Found at i:12873 original size:8 final size:8
Alignment explanation
Indices: 12871--12936 Score: 57
Period size: 8 Copynumber: 8.5 Consensus size: 8
12861 ATAAAAAAAT
12871 AAAAACAAA
1 AAAAAC-AA
12880 AAAAACAA
1 AAAAACAA
*
12888 AAAAA-GA
1 AAAAACAA
*
12895 ACAAACAA
1 AAAAACAA
12903 AAAAACAA
1 AAAAACAA
*
12911 AAAAA-GA
1 AAAAACAA
**
12918 ACGAA-AA
1 AAAAACAA
12925 AAAAACAA
1 AAAAACAA
12933 AAAA
1 AAAA
12937 GAAAAGAAGA
Statistics
Matches: 45, Mismatches: 10, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
7 13 0.29
8 26 0.58
9 6 0.13
ACGTcount: A:0.85, C:0.11, G:0.05, T:0.00
Consensus pattern (8 bp):
AAAAACAA
Found at i:12889 original size:23 final size:23
Alignment explanation
Indices: 12863--12941 Score: 101
Period size: 23 Copynumber: 3.5 Consensus size: 23
12853 AGCTCGCAAT
*
12863 AAAAAAATAAAAACAAAAAAAAC
1 AAAAAAAGAAAAACAAAAAAAAC
12886 AAAAAAAGAACAAAC-AAAAAAAC
1 AAAAAAAGAA-AAACAAAAAAAAC
**
12909 AAAAAAAGAACGA-AAAAAAAAC
1 AAAAAAAGAAAAACAAAAAAAAC
12931 -AAAAAAGAAAA
1 AAAAAAAGAAAA
12942 GAAGAATAGT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
21 9 0.18
22 9 0.18
23 27 0.55
24 4 0.08
ACGTcount: A:0.85, C:0.09, G:0.05, T:0.01
Consensus pattern (23 bp):
AAAAAAAGAAAAACAAAAAAAAC
Found at i:13420 original size:10 final size:10
Alignment explanation
Indices: 13405--13437 Score: 50
Period size: 9 Copynumber: 3.3 Consensus size: 10
13395 TACTACACTT
13405 AAACAAAAAA
1 AAACAAAAAA
13415 AAAC-AAAAA
1 AAACAAAAAA
13424 AAACAAAAACA
1 AAACAAAAA-A
13435 AAA
1 AAA
13438 ACACTCGGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.43
10 8 0.38
11 4 0.19
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (10 bp):
AAACAAAAAA
Found at i:13433 original size:15 final size:14
Alignment explanation
Indices: 13409--13438 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
13399 ACACTTAAAC
13409 AAAAAAAAACAAAA
1 AAAAAAAAACAAAA
13423 AAAACAAAAACAAAA
1 AAAA-AAAAACAAAA
13438 A
1 A
13439 CACTCGGCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAAAAAACAAAA
Found at i:14740 original size:69 final size:69
Alignment explanation
Indices: 14649--14820 Score: 265
Period size: 69 Copynumber: 2.5 Consensus size: 69
14639 CGAATGCTTT
*
14649 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAG
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAACCTTGGTTCCATCCAAGCAG
14714 CAT-
66 CATA
* * *
14717 GTGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAACCTTGGTTCCGTCCAGGCA
1 G-GCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAACCTTGGTTCCATCCAAGCA
14782 GCATA
65 GCATA
**
14787 GGCTTTTCCACAAGCCACAGTTCGTTTCCATACG
1 GGCTTTTCCACAAGCCA-AACTCGTTTCCATACG
14821 GTGCATTACC
Statistics
Matches: 94, Mismatches: 7, Indels: 4
0.90 0.07 0.04
Matches are distributed among these distances:
68 1 0.01
69 78 0.83
70 15 0.16
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.28
Consensus pattern (69 bp):
GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAACCTTGGTTCCATCCAAGCAG
CATA
Found at i:14882 original size:35 final size:35
Alignment explanation
Indices: 14836--15312 Score: 486
Period size: 35 Copynumber: 13.8 Consensus size: 35
14826 TTACCATCTT
*
14836 CTCAGATGACTCGGTTTAGCATCTTCAAAGTTGAA
1 CTCAGATGACTCGGTGTAGCATCTTCAAAGTTGAA
*
14871 CTCAGATGACTCGGTGTAGCATCTTCAAAGTCGAA
1 CTCAGATGACTCGGTGTAGCATCTTCAAAGTTGAA
*
14906 -TCCAGATGACTCGGTGTAGCATCTTCAAAGATGAA
1 CT-CAGATGACTCGGTGTAGCATCTTCAAAGTTGAA
*
14941 CTCAGATGACTCGGTGTAGCATCTTCAAAGTCGAA
1 CTCAGATGACTCGGTGTAGCATCTTCAAAGTTGAA
*
14976 -TCCAGATGACTCGGTGTAGCATCTTCAAAGATGAA
1 CT-CAGATGACTCGGTGTAGCATCTTCAAAGTTGAA
*
15011 CTCAGATGACTCGGTGTATCATCTTCAAAGTTGAA
1 CTCAGATGACTCGGTGTAGCATCTTCAAAGTTGAA
* * *
15046 TTCAGATGACTC--AGTAGCATCTTCAAAGATGAA
1 CTCAGATGACTCGGTGTAGCATCTTCAAAGTTGAA
*
15079 CTCAGATCACTCGGTGTAGCATCTTCAAAGTTGAA
1 CTCAGATGACTCGGTGTAGCATCTTCAAAGTTGAA
* * * *
15114 TTCAGATGACTC--AGTAACATCTTCAAAGATGAA
1 CTCAGATGACTCGGTGTAGCATCTTCAAAGTTGAA
* *
15147 TTCAGATGACTCGGTGTAGCATCTTC-AA-TATGGA
1 CTCAGATGACTCGGTGTAGCATCTTCAAAGT-TGAA
* * *
15181 CTCAG-TAGGCTCGGTGCAGCAAATCTTCAAA-TAG-A
1 CTCAGAT-GACTCGGTGTAGC--ATCTTCAAAGTTGAA
* * *
15216 -TCAAAATGACTCGGGGTAGCATCTTC-AA-TATGGA
1 CTC-AGATGACTCGGTGTAGCATCTTCAAAGT-TGAA
* * * *
15250 CTCAG-TGGGCTCGATGCAGCAAATCTTCAAA--TGGA
1 CTCAGAT-GACTCGGTGTAGC--ATCTTCAAAGTTGAA
15285 -TCAGAATGACTCGGTGTAGCATCTTCAA
1 CTCAG-ATGACTCGGTGTAGCATCTTCAA
15313 TATGGACTCA
Statistics
Matches: 374, Mismatches: 44, Indels: 50
0.80 0.09 0.11
Matches are distributed among these distances:
32 3 0.01
33 75 0.20
34 39 0.10
35 235 0.63
36 17 0.05
37 5 0.01
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.27
Consensus pattern (35 bp):
CTCAGATGACTCGGTGTAGCATCTTCAAAGTTGAA
Found at i:14951 original size:70 final size:70
Alignment explanation
Indices: 14838--15174 Score: 538
Period size: 70 Copynumber: 4.9 Consensus size: 70
14828 ACCATCTTCT
* *
14838 CAGATGACTCGGTTTAGCATCTTCAAAGTTGAACTCAGATGACTCGGTGTAGCATCTTCAAAGTC
1 CAGATGACTCGGTGTAGCATCTTCAAAGATGAACTCAGATGACTCGGTGTAGCATCTTCAAAGTC
14903 GAATC
66 GAATC
14908 CAGATGACTCGGTGTAGCATCTTCAAAGATGAACTCAGATGACTCGGTGTAGCATCTTCAAAGTC
1 CAGATGACTCGGTGTAGCATCTTCAAAGATGAACTCAGATGACTCGGTGTAGCATCTTCAAAGTC
14973 GAATC
66 GAATC
* *
14978 CAGATGACTCGGTGTAGCATCTTCAAAGATGAACTCAGATGACTCGGTGTATCATCTTCAAAGTT
1 CAGATGACTCGGTGTAGCATCTTCAAAGATGAACTCAGATGACTCGGTGTAGCATCTTCAAAGTC
*
15043 GAATT
66 GAATC
* * *
15048 CAGATGACTC--AGTAGCATCTTCAAAGATGAACTCAGATCACTCGGTGTAGCATCTTCAAAGTT
1 CAGATGACTCGGTGTAGCATCTTCAAAGATGAACTCAGATGACTCGGTGTAGCATCTTCAAAGTC
*
15111 GAATT
66 GAATC
* * *
15116 CAGATGACTC--AGTAACATCTTCAAAGATGAATTCAGATGACTCGGTGTAGCATCTTCAA
1 CAGATGACTCGGTGTAGCATCTTCAAAGATGAACTCAGATGACTCGGTGTAGCATCTTCAA
15175 TATGGACTCA
Statistics
Matches: 256, Mismatches: 11, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
68 111 0.43
70 145 0.57
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (70 bp):
CAGATGACTCGGTGTAGCATCTTCAAAGATGAACTCAGATGACTCGGTGTAGCATCTTCAAAGTC
GAATC
Found at i:15369 original size:69 final size:69
Alignment explanation
Indices: 15148--15357 Score: 359
Period size: 69 Copynumber: 3.1 Consensus size: 69
15138 AAAGATGAAT
* *
15148 TCAG-ATGACTCGGTGTAGCATCTTCAATATGGACTCAGTAGGCTCGGTGCAGCAAATCTTCAAA
1 TCAGAATGACTCGGTGTAGCATCTTCAATATGGACTCAGTGGGCTCGATGCAGCAAATCTTCAAA
15212 TAGA
66 TAGA
* *
15216 TCAAAATGACTCGGGGTAGCATCTTCAATATGGACTCAGTGGGCTCGATGCAGCAAATCTTCAAA
1 TCAGAATGACTCGGTGTAGCATCTTCAATATGGACTCAGTGGGCTCGATGCAGCAAATCTTCAAA
*
15281 TGGA
66 TAGA
*
15285 TCAGAATGACTCGGTGTAGCATCTTCAATATGGACTCAATGGGCTCGATGCAGCAAATCTTCAAA
1 TCAGAATGACTCGGTGTAGCATCTTCAATATGGACTCAGTGGGCTCGATGCAGCAAATCTTCAAA
15350 TAGA
66 TAGA
15354 TCAG
1 TCAG
15358 GCTGATTCGG
Statistics
Matches: 132, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
68 3 0.02
69 129 0.98
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.26
Consensus pattern (69 bp):
TCAGAATGACTCGGTGTAGCATCTTCAATATGGACTCAGTGGGCTCGATGCAGCAAATCTTCAAA
TAGA
Found at i:15811 original size:26 final size:26
Alignment explanation
Indices: 15706--15803 Score: 133
Period size: 26 Copynumber: 3.7 Consensus size: 26
15696 AGGATCATCT
* * **
15706 AGGGGGATTTTGGTCATTTTTACACC
1 AGGGGCATTTTGGTCATTTGTACTTC
15732 TAGGGGCATTTTGGTCATTTGTACTTC
1 -AGGGGCATTTTGGTCATTTGTACTTC
*
15759 AGGGGTATTTTGGTCATTTGTACTTC
1 AGGGGCATTTTGGTCATTTGTACTTC
*
15785 AGGGGCATTTTGATCATTT
1 AGGGGCATTTTGGTCATTT
15804 TAAGTTCACA
Statistics
Matches: 64, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
26 42 0.66
27 22 0.34
ACGTcount: A:0.17, C:0.13, G:0.27, T:0.43
Consensus pattern (26 bp):
AGGGGCATTTTGGTCATTTGTACTTC
Done.