Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011979.1 Corchorus olitorius cultivar O-4 contig12012, 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: 11539
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Found at i:6637 original size:21 final size:21
Alignment explanation
Indices: 6611--6655 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
6601 GAATCAATCT
6611 AAAGAAAAAAAAGAAAAAGAA
1 AAAGAAAAAAAAGAAAAAGAA
*
6632 AAAGAAAAAGAAA-AGAAAGAA
1 AAAGAAAAA-AAAGAAAAAGAA
6653 AAA
1 AAA
6656 TCAAAAGGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (21 bp):
AAAGAAAAAAAAGAAAAAGAA
Found at i:6661 original size:21 final size:22
Alignment explanation
Indices: 6626--6668 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
6616 AAAAAAAGAA
6626 AAAGAAAAAGAAAAA-GAAAAG
1 AAAGAAAAAGAAAAAGGAAAAG
**
6647 AAAGAAAAATCAAAAGGAAAAG
1 AAAGAAAAAGAAAAAGGAAAAG
6669 GTTCAAATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.77, C:0.02, G:0.19, T:0.02
Consensus pattern (22 bp):
AAAGAAAAAGAAAAAGGAAAAG
Found at i:6669 original size:6 final size:6
Alignment explanation
Indices: 6618--6649 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
6608 TCTAAAGAAA
6618 AAAAAG AAAAAG AAAAAG AAAAAG -AAAAG AAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAA
6650 GAAAAATCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:6934 original size:87 final size:87
Alignment explanation
Indices: 6788--6953 Score: 233
Period size: 87 Copynumber: 1.9 Consensus size: 87
6778 TGTTTGAAGG
* * * * *
6788 TTTCTTAAGATGAGAAAATGATCCAGAAATATCAATTGAGTTGGGAATATCAATGCATGATCAAA
1 TTTCTTAAGATGAGAAAATGATCCAGAAACATCAATTGAGCTGGGAACATCAACGCATGACCAAA
6853 TTGGAGGAAGATTTGGGAAATA
66 TTGGAGGAAGATTTGGGAAATA
* * ** * *
6875 TTTCTTAAGGTGGGAAGCTGATCCAGAACCATTAATTGAGCTGGGAACATCAACGCATGACCAAA
1 TTTCTTAAGATGAGAAAATGATCCAGAAACATCAATTGAGCTGGGAACATCAACGCATGACCAAA
6940 TTGGAGGAAGATTT
66 TTGGAGGAAGATTT
6954 AGGGGCATCA
Statistics
Matches: 68, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
87 68 1.00
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (87 bp):
TTTCTTAAGATGAGAAAATGATCCAGAAACATCAATTGAGCTGGGAACATCAACGCATGACCAAA
TTGGAGGAAGATTTGGGAAATA
Found at i:7800 original size:37 final size:38
Alignment explanation
Indices: 7691--8195 Score: 442
Period size: 37 Copynumber: 13.6 Consensus size: 38
7681 AGATTCCTAG
*
7691 TTAGGTTTCTTATCAAAATCCTTATTTAAGGTCCCTGT
1 TTAGGTTTCTTATCAAAATCCTTATTTAAGGTTCCTGT
* * * * * *
7729 TTAGGTGTCTCATCAAAAT-CTTGTTCAAGATTCCTAT
1 TTAGGTTTCTTATCAAAATCCTTATTTAAGGTTCCTGT
**
7766 TTAGGTTTCTTAT-TTAATCCTTATTTAAGGTTCCTGT
1 TTAGGTTTCTTATCAAAATCCTTATTTAAGGTTCCTGT
* * * * *
7803 TTAGGTGTCTCATCAAAAT-CTTGTTTAAGATCCCTGT
1 TTAGGTTTCTTATCAAAATCCTTATTTAAGGTTCCTGT
* *
7840 TTAGGTTTCTTATC-AAATTCTTATTTAAGGTGCCTGT
1 TTAGGTTTCTTATCAAAATCCTTATTTAAGGTTCCTGT
* ** * *
7877 TTAGGTTTCTTGTCAAAATTTTTGTTTAA-GATCCTTGT
1 TTAGGTTTCTTATCAAAATCCTTATTTAAGGTTCC-TGT
* *
7915 TTAGGTTTCTTAT-TAATTCCTTATTTAAGG-TCCTTGT
1 TTAGGTTTCTTATCAAAATCCTTATTTAAGGTTCC-TGT
* * * * **
7952 TTAGGTGTCTCATCAAAAT-CTTGTTCAAAATTCCTGT
1 TTAGGTTTCTTATCAAAATCCTTATTTAAGGTTCCTGT
*
7989 TTAGGTTTCTTAT-TAAATCCTTATTTAAGGTTCCTGT
1 TTAGGTTTCTTATCAAAATCCTTATTTAAGGTTCCTGT
* * * * ** *
8026 TTAGGTGTCTCATCAAAAT-CTTGTTCAAAATTCATGT
1 TTAGGTTTCTTATCAAAATCCTTATTTAAGGTTCCTGT
* * *
8063 TTAGGTTTCTTGTC-AAATTCTTATTTAAGGTCCCTGT
1 TTAGGTTTCTTATCAAAATCCTTATTTAAGGTTCCTGT
* * ** * * * *
8100 TTAGGTGTCTCATCAAAATTTTTGTTCAAGATCCCTGT
1 TTAGGTTTCTTATCAAAATCCTTATTTAAGGTTCCTGT
*
8138 TTAGGTTTCTTATC-AAATCCTTATTTAAGGTACCTGT
1 TTAGGTTTCTTATCAAAATCCTTATTTAAGGTTCCTGT
*
8175 TTAGGTGTCTCT-TCAAAATCC
1 TTAGGTTTCT-TATCAAAATCC
8196 CACTTTAGGT
Statistics
Matches: 367, Mismatches: 86, Indels: 28
0.76 0.18 0.06
Matches are distributed among these distances:
36 15 0.04
37 256 0.70
38 96 0.26
ACGTcount: A:0.23, C:0.16, G:0.14, T:0.46
Consensus pattern (38 bp):
TTAGGTTTCTTATCAAAATCCTTATTTAAGGTTCCTGT
Found at i:7810 original size:74 final size:74
Alignment explanation
Indices: 7665--8194 Score: 733
Period size: 74 Copynumber: 7.1 Consensus size: 74
7655 ATTCAAAACC
* *
7665 TCAAAATTTTTGTTCAAGATTCCTAG-TTAGGTTTCTTATCAAAATCCTTATTTAAGGTCCCTGT
1 TCAAAA-TCTTGTTCAAGATTCCT-GTTTAGGTTTCTTATC-AAATCCTTATTTAAGGTTCCTGT
7729 TTAGGTGTCTCA
63 TTAGGTGTCTCA
* **
7741 TCAAAATCTTGTTCAAGATTCCTATTTAGGTTTCTTATTTAATCCTTATTTAAGGTTCCTGTTTA
1 TCAAAATCTTGTTCAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTTCCTGTTTA
7806 GGTGTCTCA
66 GGTGTCTCA
* * * *
7815 TCAAAATCTTGTTTAAGATCCCTGTTTAGGTTTCTTATCAAATTCTTATTTAAGGTGCCTGTTTA
1 TCAAAATCTTGTTCAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTTCCTGTTTA
* **
7880 GGTTTCTTG
66 GGTGTCTCA
* * * *
7889 TCAAAATTTTTGTTTAAGA-TCCTTGTTTAGGTTTCTTATTAATTCCTTATTTAAGG-TCCTTGT
1 TCAAAA-TCTTGTTCAAGATTCC-TGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTTCC-TGT
7952 TTAGGTGTCTCA
63 TTAGGTGTCTCA
* *
7964 TCAAAATCTTGTTCAAAATTCCTGTTTAGGTTTCTTATTAAATCCTTATTTAAGGTTCCTGTTTA
1 TCAAAATCTTGTTCAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTTCCTGTTTA
8029 GGTGTCTCA
66 GGTGTCTCA
* * * * *
8038 TCAAAATCTTGTTCAAAATTCATGTTTAGGTTTCTTGTCAAATTCTTATTTAAGGTCCCTGTTTA
1 TCAAAATCTTGTTCAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTTCCTGTTTA
8103 GGTGTCTCA
66 GGTGTCTCA
* * *
8112 TCAAAATTTTTGTTCAAGATCCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTACCTGTTT
1 TCAAAA-TCTTGTTCAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTTCCTGTTT
*
8177 AGGTGTCTCT
65 AGGTGTCTCA
8187 TCAAAATC
1 TCAAAATC
8195 CCACTTTAGG
Statistics
Matches: 405, Mismatches: 42, Indels: 16
0.87 0.09 0.03
Matches are distributed among these distances:
74 239 0.59
75 160 0.40
76 6 0.01
ACGTcount: A:0.24, C:0.16, G:0.14, T:0.46
Consensus pattern (74 bp):
TCAAAATCTTGTTCAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTTCCTGTTTA
GGTGTCTCA
Found at i:7944 original size:149 final size:148
Alignment explanation
Indices: 7665--8194 Score: 730
Period size: 149 Copynumber: 3.6 Consensus size: 148
7655 ATTCAAAACC
* * *
7665 TCAAAATTTTTGTTCAAGATTCCTAG-TTAGGTTTCTTATCAAAATCCTTATTTAAGGTCCCTGT
1 TCAAAATTCTTGTTCAAGATCCCT-GTTTAGGTTTCTTATC-AAATCCTTATTTAAGGTACCTGT
*
7729 TTAGGTGTCTCATCAAAATCTTGTTCAAGATTCCTATTTAGGTTTCTTATTTAA-TCCTTATTTA
64 TTAGGTGTCTCATCAAAATCTTGTTCAAGA-TCCTGTTTAGGTTTCTTA-TTAATTCCTTATTTA
7793 AGGTTCCTGTTTAGGTGTCTCA
127 AGGTTCCTGTTTAGGTGTCTCA
* * *
7815 TCAAAA-TCTTGTTTAAGATCCCTGTTTAGGTTTCTTATCAAATTCTTATTTAAGGTGCCTGTTT
1 TCAAAATTCTTGTTCAAGATCCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTACCTGTTT
* ** * *
7879 AGGTTTCTTGTCAAAATTTTTGTTTAAGATCCTTGTTTAGGTTTCTTATTAATTCCTTATTTAAG
66 AGGTGTCTCATCAAAA-TCTTGTTCAAGATCC-TGTTTAGGTTTCTTATTAATTCCTTATTTAAG
7944 G-TCCTTGTTTAGGTGTCTCA
129 GTTCC-TGTTTAGGTGTCTCA
* * * *
7964 TCAAAA-TCTTGTTCAAAATTCCTGTTTAGGTTTCTTATTAAATCCTTATTTAAGGTTCCTGTTT
1 TCAAAATTCTTGTTCAAGATCCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTACCTGTTT
* * * *
8028 AGGTGTCTCATCAAAATCTTGTTCAAAATTCATGTTTAGGTTTCTTGTCAAATT-CTTATTTAAG
66 AGGTGTCTCATCAAAATCTTGTTCAAGA-TCCTGTTTAGGTTTCTTAT-TAATTCCTTATTTAAG
*
8092 GTCCCTGTTTAGGTGTCTCA
129 GTTCCTGTTTAGGTGTCTCA
*
8112 TCAAAATTTTTGTTCAAGATCCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTACCTGTTT
1 TCAAAATTCTTGTTCAAGATCCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTACCTGTTT
*
8177 AGGTGTCTCTTCAAAATC
66 AGGTGTCTCATCAAAATC
8195 CCACTTTAGG
Statistics
Matches: 338, Mismatches: 33, Indels: 19
0.87 0.08 0.05
Matches are distributed among these distances:
148 103 0.30
149 229 0.68
150 6 0.02
ACGTcount: A:0.24, C:0.16, G:0.14, T:0.46
Consensus pattern (148 bp):
TCAAAATTCTTGTTCAAGATCCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTACCTGTTT
AGGTGTCTCATCAAAATCTTGTTCAAGATCCTGTTTAGGTTTCTTATTAATTCCTTATTTAAGGT
TCCTGTTTAGGTGTCTCA
Found at i:8066 original size:223 final size:222
Alignment explanation
Indices: 7665--8194 Score: 837
Period size: 223 Copynumber: 2.4 Consensus size: 222
7655 ATTCAAAACC
*
7665 TCAAAATTTTTGTTCAAGATTCCTAG-TTAGGTTTCTTATCAAAATCCTTATTTAAGGTCCCTGT
1 TCAAAATTTTTGTTCAAGA-TCCTTGTTTAGGTTTCTTAT-AAAATCCTTATTTAAGGT-CCTGT
* *
7729 TTAGGTGTCTCATCAAAATCTTGTTCAAGATTCCTATTTAGGTTTCTTATTTAATCCTTATTTAA
63 TTAGGTGTCTCATCAAAATCTTGTTCAAAATTCCTATTTAGGTTTCTTATTAAATCCTTATTTAA
* * *
7794 GGTTCCTGTTTAGGTGTCTCATCAAAATCTTGTTTAAGATCCCTGTTTAGGTTTCTTATCAAATT
128 GGTTCCTGTTTAGGTGTCTCATCAAAATCTTGTTCAAAATCCATGTTTAGGTTTCTTATCAAATT
* * **
7859 CTTATTTAAGGTGCCTGTTTAGGTTTCTTG
193 CTTATTTAAGGTCCCTGTTTAGGTGTCTCA
* * *
7889 TCAAAATTTTTGTTTAAGATCCTTGTTTAGGTTTCTTATTAATTCCTTATTTAAGGTCCTTGTTT
1 TCAAAATTTTTGTTCAAGATCCTTGTTTAGGTTTCTTATAAAATCCTTATTTAAGGTCC-TGTTT
*
7954 AGGTGTCTCATCAAAATCTTGTTCAAAATTCCTGTTTAGGTTTCTTATTAAATCCTTATTTAAGG
65 AGGTGTCTCATCAAAATCTTGTTCAAAATTCCTATTTAGGTTTCTTATTAAATCCTTATTTAAGG
* *
8019 TTCCTGTTTAGGTGTCTCATCAAAATCTTGTTCAAAATTCATGTTTAGGTTTCTTGTCAAATTCT
130 TTCCTGTTTAGGTGTCTCATCAAAATCTTGTTCAAAATCCATGTTTAGGTTTCTTATCAAATTCT
8084 TATTTAAGGTCCCTGTTTAGGTGTCTCA
195 TATTTAAGGTCCCTGTTTAGGTGTCTCA
* *
8112 TCAAAATTTTTGTTCAAGATCCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTACCTGTTT
1 TCAAAATTTTTGTTCAAGATCCTTGTTTAGGTTTCTTATAAAATCCTTATTTAAGGT-CCTGTTT
*
8177 AGGTGTCTCTTCAAAATC
65 AGGTGTCTCATCAAAATC
8195 CCACTTTAGG
Statistics
Matches: 282, Mismatches: 21, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
222 2 0.01
223 247 0.88
224 33 0.12
ACGTcount: A:0.24, C:0.16, G:0.14, T:0.46
Consensus pattern (222 bp):
TCAAAATTTTTGTTCAAGATCCTTGTTTAGGTTTCTTATAAAATCCTTATTTAAGGTCCTGTTTA
GGTGTCTCATCAAAATCTTGTTCAAAATTCCTATTTAGGTTTCTTATTAAATCCTTATTTAAGGT
TCCTGTTTAGGTGTCTCATCAAAATCTTGTTCAAAATCCATGTTTAGGTTTCTTATCAAATTCTT
ATTTAAGGTCCCTGTTTAGGTGTCTCA
Found at i:8259 original size:18 final size:19
Alignment explanation
Indices: 8217--8259 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
8207 TCTTATCAAA
8217 ATTTTGTTCAAAATCCATT
1 ATTTTGTTCAAAATCCATT
* *
8236 -TCTTGTTCAAAATTC-TT
1 ATTTTGTTCAAAATCCATT
8253 ATTTTGT
1 ATTTTGT
8260 GTTTTAAATG
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.26, C:0.14, G:0.07, T:0.53
Consensus pattern (19 bp):
ATTTTGTTCAAAATCCATT
Found at i:8932 original size:54 final size:54
Alignment explanation
Indices: 8285--8952 Score: 900
Period size: 54 Copynumber: 12.3 Consensus size: 54
8275 GTGTGGTCTC
* * *
8285 TCTTAAGTTGATCCAGTGTGGTCTTTCATAGAAGTTTTCAGAAATCTAAGTTGA
1 TCTTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTTGA
* * * * *
8339 TCTTGAGATGACCTAGTGTGGTCTTTCATAGAAGTTTTCAAATATATCTACGTTGA
1 TCTTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTC--AGAGATCTAAGTTGA
* * * *
8395 TATTAAAATGA-CCAGTGTGGTCTTCCCTAGAAGTTTTCAGAGATCTAAGTTGA
1 TCTTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTTGA
* * * *
8448 TCTAAAGTTGATCCAGTGTGGTCTTTCATATAAGTTTTCAGAGATCTAAGTTGA
1 TCTTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTTGA
* *
8502 TCTTAAGTTGATCCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTTGA
1 TCTTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTTGA
*
8556 TCTTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAAAGATCTAAGTTGA
1 TCTTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTTGA
* *
8610 TCTTAAGGTGACCTAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTTGA
1 TCTTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTTGA
*
8664 TCTTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCTGAGTTGA
1 TCTTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTTGA
*
8718 TCTTAAGATGTCCCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTTGA
1 TCTTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTTGA
* * *
8772 TCTTAAGATGACCCAGTGTGGTCTTTCATAGAAGCTTTCAAAGGTCTAAGTTGA
1 TCTTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTTGA
* * * *
8826 TCTTCAGATGA-CCATGTTTGGTCTTCCATAGAAGTTTTCA-ATAATCTAAGTTGA
1 TCTTAAGATGACCCA-GTGTGGTCTTTCATAGAAGTTTTCAGA-GATCTAAGTTGA
* * * *
8880 TCTTAAGTTGAACCAGTGTGGTCATTCCA-AGAAGTTTAC-GATGATC-AGAGTTGA
1 TCTTAAGATGACCCAGTGTGGTC-TTTCATAGAAGTTTTCAGA-GATCTA-AGTTGA
8934 TCTCTAA-ACTGACCCAGTG
1 TCT-TAAGA-TGACCCAGTG
8953 CGATCATTCC
Statistics
Matches: 550, Mismatches: 53, Indels: 21
0.88 0.08 0.03
Matches are distributed among these distances:
53 24 0.04
54 462 0.84
55 44 0.08
56 20 0.04
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (54 bp):
TCTTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTTGA
Found at i:9062 original size:33 final size:33
Alignment explanation
Indices: 9020--9097 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
9010 ATTAATTAAG
* * * *
9020 AAGTTCAAAATTTGCATTTCATTTCAAAATTCA
1 AAGTTCAAAATCTGCATATCATATCAAAACTCA
9053 AAGTTCAAAATCTGCATATCATATCAAAACTCA
1 AAGTTCAAAATCTGCATATCATATCAAAACTCA
9086 AAGTTCAAAATC
1 AAGTTCAAAATC
9098 CACAATTTCT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.44, C:0.18, G:0.06, T:0.32
Consensus pattern (33 bp):
AAGTTCAAAATCTGCATATCATATCAAAACTCA
Found at i:9234 original size:23 final size:23
Alignment explanation
Indices: 9208--9254 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
9198 TTCCTTTGCA
9208 TTTCATTACTCAAAATTCAAAAT
1 TTTCATTACTCAAAATTCAAAAT
*
9231 TTTCATTGCTCAAAATTCAAAAT
1 TTTCATTACTCAAAATTCAAAAT
9254 T
1 T
9255 CAAAATTCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.40, C:0.17, G:0.02, T:0.40
Consensus pattern (23 bp):
TTTCATTACTCAAAATTCAAAAT
Found at i:9264 original size:21 final size:21
Alignment explanation
Indices: 9239--9323 Score: 98
Period size: 21 Copynumber: 4.0 Consensus size: 21
9229 ATTTTCATTG
*
9239 CTCAAAATTCAAAATTCAAAA
1 CTCAAAACTCAAAATTCAAAA
* *
9260 TTCAAAACTCAAAACTCAAAA
1 CTCAAAACTCAAAATTCAAAA
***
9281 CTCAAAACTCAAAATTCATGT
1 CTCAAAACTCAAAATTCAAAA
* *
9302 CTCAAAAATCAAATTTCAAAA
1 CTCAAAACTCAAAATTCAAAA
9323 C
1 C
9324 CTGCATTTCA
Statistics
Matches: 51, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.53, C:0.22, G:0.01, T:0.24
Consensus pattern (21 bp):
CTCAAAACTCAAAATTCAAAA
Found at i:9313 original size:7 final size:7
Alignment explanation
Indices: 9239--9294 Score: 85
Period size: 7 Copynumber: 8.0 Consensus size: 7
9229 ATTTTCATTG
9239 CTCAAAA
1 CTCAAAA
*
9246 TTCAAAA
1 CTCAAAA
*
9253 TTCAAAA
1 CTCAAAA
*
9260 TTCAAAA
1 CTCAAAA
9267 CTCAAAA
1 CTCAAAA
9274 CTCAAAA
1 CTCAAAA
9281 CTCAAAA
1 CTCAAAA
9288 CTCAAAA
1 CTCAAAA
9295 TTCATGTCTC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 47 1.00
ACGTcount: A:0.57, C:0.23, G:0.00, T:0.20
Consensus pattern (7 bp):
CTCAAAA
Found at i:9356 original size:7 final size:7
Alignment explanation
Indices: 9346--9371 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
9336 ATTTCATTCT
9346 TCAAAAG
1 TCAAAAG
9353 TCAAAAG
1 TCAAAAG
9360 TCAAAAG
1 TCAAAAG
9367 TCAAA
1 TCAAA
9372 TTTCAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.15, G:0.12, T:0.15
Consensus pattern (7 bp):
TCAAAAG
Found at i:9377 original size:14 final size:14
Alignment explanation
Indices: 9345--9379 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
9335 CATTTCATTC
9345 TTCAAAAGTCAAAA
1 TTCAAAAGTCAAAA
* *
9359 GTCAAAAGTCAAAT
1 TTCAAAAGTCAAAA
9373 TTCAAAA
1 TTCAAAA
9380 TTTGCATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.54, C:0.14, G:0.09, T:0.23
Consensus pattern (14 bp):
TTCAAAAGTCAAAA
Found at i:10821 original size:7 final size:7
Alignment explanation
Indices: 10806--10847 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
10796 AAATTCAATT
10806 ATAAATA
1 ATAAATA
*
10813 ATAATTA
1 ATAAATA
10820 ATAAATA
1 ATAAATA
10827 ATAAATA
1 ATAAATA
10834 ATTAAATA
1 A-TAAATA
*
10842 CTAAAT
1 ATAAAT
10848 TTTTCCAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
7 25 0.81
8 6 0.19
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (7 bp):
ATAAATA
Found at i:11319 original size:31 final size:29
Alignment explanation
Indices: 11284--11363 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
11274 GCTAAATACC
* *
11284 CAAAAAAATCCCTTATGTTTTGCTTTTGGGA
1 CAAAATAATCCCTTATGTTTT--TTTCGGGA
11315 CAAAATAATCCCTTATGTTTTTTTCGGGA
1 CAAAATAATCCCTTATGTTTTTTTCGGGA
* *
11344 CAAATTAATCCCTTACGTTT
1 CAAAATAATCCCTTATGTTT
11364 CAAAAATGAG
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 25 0.56
31 20 0.44
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (29 bp):
CAAAATAATCCCTTATGTTTTTTTCGGGA
Done.