Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002305.1 Hibiscus syriacus cultivar Beakdansim tig00004695_pilon, 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: 83125
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:163 original size:24 final size:23
Alignment explanation
Indices: 112--175 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 23
102 TGCCCTTGAA
*
112 GTGCATCGATGCATTC-T-ACAT
1 GTGCATCGATGCATCCTTAACAT
*
133 -TGTATCGATGCATCCCTTAACAT
1 GTGCATCGATGCAT-CCTTAACAT
156 GTGCATCGATGCATTCCTTA
1 GTGCATCGATGCA-TCCTTA
176 TGCATTGATG
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
20 12 0.34
21 1 0.03
22 1 0.03
23 4 0.11
24 16 0.46
25 1 0.03
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.34
Consensus pattern (23 bp):
GTGCATCGATGCATCCTTAACAT
Found at i:19028 original size:112 final size:109
Alignment explanation
Indices: 18748--19042 Score: 439
Period size: 109 Copynumber: 2.7 Consensus size: 109
18738 AACTTTCAAC
* * * *
18748 AAAGTATCGATACATTTTTATAAAAAGTATCTATACTTTCAACATATTAGGTAAATTTTACCGAT
1 AAAGTATCGAT-CCTTTTTATAAAAAGGATCGATACTTTCAACATATTAGGTAAATTTTACCGGT
*
18813 TTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTATTATAT
65 TTTGTCATAATGAAACTGCTTTTGTCATATTTTTACCTATTATAT
*
18858 -AAGTATCGATCCTTTTTTATAAAAATGATCGATACTTTCAACATATTAGGTAAATTTTACCGGT
1 AAAGTATCGATCC-TTTTTATAAAAAGGATCGATACTTTCAACATATTAGGTAAATTTTACCGGT
* *
18922 TTTGTCATAATGAAACTGCTTTTGTCATATTTTTATCTGTTATATTGT
65 TTTGTCATAATGAAACTGCTTTTGTCATATTTTTACCTATTATA---T
* * *
18970 AAAGTATCGATCCTTTTTATAAAAGGGATCGATATTTTCAACATATTAAGTAAATTTTACCGGTT
1 AAAGTATCGATCCTTTTTATAAAAAGGATCGATACTTTCAACATATTAGGTAAATTTTACCGGTT
19035 TTGTCATA
66 TTGTCATA
19043 CTTTTACATG
Statistics
Matches: 168, Mismatches: 12, Indels: 8
0.89 0.06 0.04
Matches are distributed among these distances:
108 1 0.01
109 98 0.58
112 57 0.34
113 12 0.07
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (109 bp):
AAAGTATCGATCCTTTTTATAAAAAGGATCGATACTTTCAACATATTAGGTAAATTTTACCGGTT
TTGTCATAATGAAACTGCTTTTGTCATATTTTTACCTATTATAT
Found at i:19116 original size:93 final size:92
Alignment explanation
Indices: 18941--19135 Score: 279
Period size: 93 Copynumber: 2.1 Consensus size: 92
18931 ATGAAACTGC
* * * *
18941 TTTTGTCATATTTTTATCTGTTATATTGTAAAGTATCGATCCTTTTTATAAAAGGGATCGATATT
1 TTTTGTCATACTTTTATCTGTTATATTGTAAAGTATCGATCATTTTTATAAAAAGGATCGATACT
19006 TTCAACATATTAAGTAAATTTTACCGG
66 TTCAACATATTAAGTAAATTTTACCGG
19033 TTTTGTCATACTTTTA-CATGTTATATTGTAAAGTAAT-GATACATTTTTATAAAAAGGATCGAT
1 TTTTGTCATACTTTTATC-TGTTATATTGTAAAGT-ATCGAT-CATTTTTATAAAAAGGATCGAT
* *
19096 ACTTTCAACATATCT-GGTAAATTTTACTGG
63 ACTTTCAACATAT-TAAGTAAATTTTACCGG
19126 TTTTGTCATA
1 TTTTGTCATA
19136 ATGAAACTGG
Statistics
Matches: 93, Mismatches: 6, Indels: 7
0.88 0.06 0.07
Matches are distributed among these distances:
91 1 0.01
92 34 0.37
93 57 0.61
94 1 0.01
ACGTcount: A:0.31, C:0.11, G:0.13, T:0.45
Consensus pattern (92 bp):
TTTTGTCATACTTTTATCTGTTATATTGTAAAGTATCGATCATTTTTATAAAAAGGATCGATACT
TTCAACATATTAAGTAAATTTTACCGG
Found at i:19471 original size:23 final size:23
Alignment explanation
Indices: 19445--19492 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
19435 TTAATTAACA
*
19445 TATTTTATTATATAAGCGCTACC
1 TATTATATTATATAAGCGCTACC
*
19468 TATTATGTTATATAAGCGCTACC
1 TATTATATTATATAAGCGCTACC
19491 TA
1 TA
19493 ATATGTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.42
Consensus pattern (23 bp):
TATTATATTATATAAGCGCTACC
Found at i:19497 original size:23 final size:23
Alignment explanation
Indices: 19452--19499 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
19442 ACATATTTTA
*
19452 TTATATAAGCGCTACCTATTATG
1 TTATATAAGCGCTACCTAATATG
19475 TTATATAAGCGCTACCTAATATG
1 TTATATAAGCGCTACCTAATATG
19498 TT
1 TT
19500 TTTGTGCTCG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (23 bp):
TTATATAAGCGCTACCTAATATG
Found at i:19566 original size:21 final size:23
Alignment explanation
Indices: 19538--19592 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
19528 AACTTATTTT
19538 ATTATATAAGCGCTACATATTAC
1 ATTATATAAGCGCTACATATTAC
19561 ATTATATAAGCGCTACATATTAC
1 ATTATATAAGCGCTACATATTAC
19584 ATTATATAA
1 ATTATATAA
19593 CCGGTACCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.36
Consensus pattern (23 bp):
ATTATATAAGCGCTACATATTAC
Found at i:19574 original size:110 final size:110
Alignment explanation
Indices: 19442--19663 Score: 318
Period size: 110 Copynumber: 2.0 Consensus size: 110
19432 TAATTAATTA
** * ** * *
19442 ACATATTTTATTATATAAGCGCTACCTATTATGTTATATAAGCGCTACCTAATATGTTTTTGTGC
1 ACATATTACATTATATAAGCGCTACATATTACATTATATAACCGCTACCTAATATGTTATTGTGC
* *
19507 TCGATAATGTTTCCAATAATTAACTTATTTTATTATATAAGCGCT
66 TCGATAATGTTTCCAATAATTAACCTATTTTATTATATAAGCACT
* *
19552 ACATATTACATTATATAAGCGCTACATATTACATTATATAACCGGTACCTAATATGTTATTGTGT
1 ACATATTACATTATATAAGCGCTACATATTACATTATATAACCGCTACCTAATATGTTATTGTGC
* * *
19617 TTGATAATGTTTCTAGTAATTAACCTATTTTATTATATAAGCACT
66 TCGATAATGTTTCCAATAATTAACCTATTTTATTATATAAGCACT
19662 AC
1 AC
19664 CTTTGTGGAA
Statistics
Matches: 98, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
110 98 1.00
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.42
Consensus pattern (110 bp):
ACATATTACATTATATAAGCGCTACATATTACATTATATAACCGCTACCTAATATGTTATTGTGC
TCGATAATGTTTCCAATAATTAACCTATTTTATTATATAAGCACT
Found at i:20192 original size:112 final size:111
Alignment explanation
Indices: 19983--20434 Score: 661
Period size: 112 Copynumber: 4.0 Consensus size: 111
19973 AATTTTCAAC
*
19983 AAAGTATCGATACATTTTTATAAAAAGCATCTATACTTTCAACATATCAGGTAAATTTTACCGGT
1 AAAGTATCGAT-CATTTTTATAAAAAG-ATCGATACTTTCAACATATCAGGTAAATTTTACCGGT
* *
20048 TTTGTCATAATGAAACTGATTTTGTCATATTTTTATCTGCTATATTGT
64 TTTGTCATAATGAAACTGATTTTGTCATATTTTTACCTGTTATATTGT
* * * *
20096 AAAGTATCGATCATTTTTATAAAATGAATTGATACTTTCAACATATTAGGTAAATTTTACGGGTT
1 AAAGTATCGATCATTTTTATAAAAAG-ATCGATACTTTCAACATATCAGGTAAATTTTACCGGTT
* *
20161 TTTTCATAATGAAACTGATTTTGTCATATTTTTACCTGTTATATTAT
65 TTGTCATAATGAAACTGATTTTGTCATATTTTTACCTGTTATATTGT
* * * *
20208 AAAGTATCGATCCTTTTTATAAAAATGATCGATACTTTCAACATATTAGGTAAATCTTACCGATT
1 AAAGTATCGATCATTTTTATAAAAA-GATCGATACTTTCAACATATCAGGTAAATTTTACCGGTT
* * * *
20273 TTCTCATAATGAAACTGGTTTTATCATATTTTTACATGTTATATTGT
65 TTGTCATAATGAAACTGATTTTGTCATATTTTTACCTGTTATATTGT
* * **
20320 AAAATATCGATCCTTTTTATAAAAAGGATCGATTTTTTCAACATATCAGGTAAATTTTACCGGTT
1 AAAGTATCGATCATTTTTATAAAAA-GATCGATACTTTCAACATATCAGGTAAATTTTACCGGTT
*
20385 TTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
65 TTGTCATAATGAAACTGATTTTGTCATATTTTTACCTGTTATATTGT
20432 AAA
1 AAA
20435 AAAAGGATCG
Statistics
Matches: 307, Mismatches: 31, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
112 295 0.96
113 12 0.04
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (111 bp):
AAAGTATCGATCATTTTTATAAAAAGATCGATACTTTCAACATATCAGGTAAATTTTACCGGTTT
TGTCATAATGAAACTGATTTTGTCATATTTTTACCTGTTATATTGT
Found at i:20453 original size:94 final size:94
Alignment explanation
Indices: 20340--20528 Score: 342
Period size: 94 Copynumber: 2.0 Consensus size: 94
20330 TCCTTTTTAT
**
20340 AAAAAGGATCGATTTTTTCAACATATCAGGTAAATTTTACCGGTTTTGTCATAATGAAACTGGTT
1 AAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGGTTTTGTCATAATGAAACTGGTT
20405 TTGTCATATTTTTACCTGTTATATTGTAA
66 TTGTCATATTTTTACCTGTTATATTGTAA
* *
20434 AAAAAGGATCGATACTTTCAACATATTAGGTAAATTTTCCCGGTTTTGTCATAATGAAACTGGTT
1 AAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGGTTTTGTCATAATGAAACTGGTT
20499 TTGTCATATTTTTACCTGTTATATTGTAA
66 TTGTCATATTTTTACCTGTTATATTGTAA
20528 A
1 A
20529 GTATCAATAC
Statistics
Matches: 91, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
94 91 1.00
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.42
Consensus pattern (94 bp):
AAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGGTTTTGTCATAATGAAACTGGTT
TTGTCATATTTTTACCTGTTATATTGTAA
Found at i:20572 original size:113 final size:113
Alignment explanation
Indices: 20434--20662 Score: 350
Period size: 113 Copynumber: 2.0 Consensus size: 113
20424 TATATTGTAA
* * * * **
20434 AAAAAGGATCGATACTTTCAACATATTAGGTAAATTTTCCCGGTTTTGTCATAATGAAACTGGTT
1 AAAAAGGATCGACACTTTCAACATATCAGGTAAATTTTACCGGTTTTGTCATAATAAAACTAATT
*
20499 TTGTCATATTTTTACCTGTTATATTGTAAAGTATCAATACATTTTTAT
66 TTGTCATAGTTTTACCTGTTATATTGTAAAGTATCAATACATTTTTAT
* * *
20547 AAAAAGGATTGACACTTTCAACATATCCGGTAAATTTTATCGGTTTTGTCATAATAAAACTAATT
1 AAAAAGGATCGACACTTTCAACATATCAGGTAAATTTTACCGGTTTTGTCATAATAAAACTAATT
**
20612 TTGTCATAGTTTTACCTGTTATATTGTAAAGTATTGATACATTTTTAT
66 TTGTCATAGTTTTACCTGTTATATTGTAAAGTATCAATACATTTTTAT
20660 AAA
1 AAA
20663 GTATCGATAC
Statistics
Matches: 104, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
113 104 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.42
Consensus pattern (113 bp):
AAAAAGGATCGACACTTTCAACATATCAGGTAAATTTTACCGGTTTTGTCATAATAAAACTAATT
TTGTCATAGTTTTACCTGTTATATTGTAAAGTATCAATACATTTTTAT
Found at i:20630 original size:207 final size:206
Alignment explanation
Indices: 20228--20641 Score: 639
Period size: 206 Copynumber: 2.0 Consensus size: 206
20218 TCCTTTTTAT
*
20228 AAAAATGATCGATACTTTCAACATATTAGGTAAATCTTACCGATTTTCTCATAATGAAACTGGTT
1 AAAAAGGATCGATACTTTCAACATATTAGGTAAATCTTACCGATTTTCTCATAATGAAACTGGTT
* * ***
20293 TTATCATATTTTTACATGTTATATTGTAAAATATCGATCCTTTTTATAAAAAGGATCGATTTTTT
66 TTATCATATTTTTACATGTTATATTGTAAAATATCAATCATTTTTATAAAAAGGATCGACACTTT
* ** *
20358 CAACATATCAGGTAAATTTTACCGGTTTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTG
131 CAACATATCAGGTAAATTTTACCGGTTTTGTCATAATAAAACTAATTTTGTCATAGTTTTACCTG
20423 TTATATTGTAA
196 TTATATTGTAA
* * * *
20434 AAAAAGGATCGATACTTTCAACATATTAGGTAAATTTTCCCGGTTTTGTCATAATGAAACTGGTT
1 AAAAAGGATCGATACTTTCAACATATTAGGTAAATCTTACCGATTTTCTCATAATGAAACTGGTT
* * * *
20499 TTGTCATATTTTTACCTGTTATATTGTAAAGTATCAATACATTTTTATAAAAAGGATTGACACTT
66 TTATCATATTTTTACATGTTATATTGTAAAATATCAAT-CATTTTTATAAAAAGGATCGACACTT
* *
20564 TCAACATATCCGGTAAATTTTATCGGTTTTGTCATAATAAAACTAATTTTGTCATAGTTTTACCT
130 TCAACATATCAGGTAAATTTTACCGGTTTTGTCATAATAAAACTAATTTTGTCATAGTTTTACCT
20629 GTTATATTGTAA
195 GTTATATTGTAA
20641 A
1 A
20642 GTATTGATAC
Statistics
Matches: 187, Mismatches: 20, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
206 94 0.50
207 93 0.50
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.42
Consensus pattern (206 bp):
AAAAAGGATCGATACTTTCAACATATTAGGTAAATCTTACCGATTTTCTCATAATGAAACTGGTT
TTATCATATTTTTACATGTTATATTGTAAAATATCAATCATTTTTATAAAAAGGATCGACACTTT
CAACATATCAGGTAAATTTTACCGGTTTTGTCATAATAAAACTAATTTTGTCATAGTTTTACCTG
TTATATTGTAA
Found at i:21018 original size:23 final size:23
Alignment explanation
Indices: 20983--21033 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
20973 TCAGTAATTA
** *
20983 ACCTATTTTATTATATAAGCGTT
1 ACCTATTACATTATATAAGCGAT
21006 ACCTATTACATTATATAAGCGAT
1 ACCTATTACATTATATAAGCGAT
21029 ACCTA
1 ACCTA
21034 ATATGTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.39
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCGAT
Found at i:21104 original size:87 final size:87
Alignment explanation
Indices: 20958--21151 Score: 343
Period size: 87 Copynumber: 2.2 Consensus size: 87
20948 AAGCGGTACT
* *
20958 TGCTTGATAATGTTTTCAGTAATTAACCTATTTTATTATATAAGCGTTACCTATTACATTATATA
1 TGCTTGATAATGTTTCCAGTAATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATATA
21023 AGCGATACCTAATATGTTATTG
66 AGCGATACCTAATATGTTATTG
*
21045 TGCTTGATAATGTTTCCAGTAATTAACCTATTTTATTATATAATCGCTACCTATTACATTATATA
1 TGCTTGATAATGTTTCCAGTAATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATATA
* *
21110 AGTGGTACCTAATATGTTATTG
66 AGCGATACCTAATATGTTATTG
21132 TGCTTGATAATGTTTCCAGT
1 TGCTTGATAATGTTTCCAGT
21152 TAAATGATAT
Statistics
Matches: 102, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 102 1.00
ACGTcount: A:0.30, C:0.13, G:0.12, T:0.44
Consensus pattern (87 bp):
TGCTTGATAATGTTTCCAGTAATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATATA
AGCGATACCTAATATGTTATTG
Found at i:21422 original size:3 final size:3
Alignment explanation
Indices: 21416--21445 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
21406 TTTTTTTTTA
21416 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
21446 TATTATTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:21450 original size:3 final size:3
Alignment explanation
Indices: 21444--21516 Score: 132
Period size: 3 Copynumber: 25.0 Consensus size: 3
21434 AATAATAATA
21444 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
21491 ATT ATT ATT ATT A-T ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
21517 TAAACATTCA
Statistics
Matches: 68, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
2 4 0.06
3 64 0.94
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:24387 original size:37 final size:37
Alignment explanation
Indices: 24305--24388 Score: 123
Period size: 37 Copynumber: 2.3 Consensus size: 37
24295 TTTATTTTAT
* *
24305 TCGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGG
1 TCGGGTCGGGCCGGATTTTTTAAGTGTGATATTCGGG
** *
24342 TCAAGTCGGGCCTGATTTTTTAAGTGTGATATTCGGG
1 TCGGGTCGGGCCGGATTTTTTAAGTGTGATATTCGGG
24379 TCGGGTCGGG
1 TCGGGTCGGG
24389 TTCGGGTTTA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.13, C:0.13, G:0.38, T:0.36
Consensus pattern (37 bp):
TCGGGTCGGGCCGGATTTTTTAAGTGTGATATTCGGG
Found at i:24537 original size:22 final size:21
Alignment explanation
Indices: 24485--24541 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
24475 TCCTCTATAT
*
24485 ATAATTTTTTT-TTCAATTAA
1 ATAATTTTTTTATTCAATAAA
* *
24505 ATCAATGTTTTTATTGAATAAAA
1 AT-AATTTTTTTATTCAAT-AAA
24528 ATAATTTTTTTATT
1 ATAATTTTTTTATT
24542 ATTTCGTGTC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 2 0.07
21 8 0.27
22 16 0.53
23 4 0.13
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.56
Consensus pattern (21 bp):
ATAATTTTTTTATTCAATAAA
Found at i:25098 original size:55 final size:55
Alignment explanation
Indices: 24967--25099 Score: 239
Period size: 55 Copynumber: 2.4 Consensus size: 55
24957 TTGGTATATT
* *
24967 TTTTGATAACTAATTAACATACTCCAATTGGAATGTATAAAAATATTGCTCTATC
1 TTTTGATAACTTATTAACATATTCCAATTGGAATGTATAAAAATATTGCTCTATC
*
25022 TTTTGATAACTTATTAACATATTCCAATTGGAATGTATGAAAATATTGCTCTATC
1 TTTTGATAACTTATTAACATATTCCAATTGGAATGTATAAAAATATTGCTCTATC
25077 TTTTGATAACTTATTAACATATT
1 TTTTGATAACTTATTAACATATT
25100 TTGATTGCGA
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 75 1.00
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.42
Consensus pattern (55 bp):
TTTTGATAACTTATTAACATATTCCAATTGGAATGTATAAAAATATTGCTCTATC
Found at i:25183 original size:420 final size:420
Alignment explanation
Indices: 24602--25782 Score: 2272
Period size: 420 Copynumber: 2.8 Consensus size: 420
24592 TTGGTATATT
* * *
24602 TTTTGGTAACTAATTAACATACTCCAATTGGAATGTATGAAAATATTGCTCTATCTTTTGATAAC
1 TTTTGATAACTTATTAACATATTCCAATTGGAATGTATGAAAATATTGCTCTATCTTTTGATAAC
24667 TTATTAACATATTTTGATTGCGATGATTTTAACTTATGATGTTTATTAGCATGATTTTTATAATT
66 TTATTAACATATTTTGATTGCGATGATTTTAACTTATGATGTTTATTAGCATGATTTTTATAATT
24732 TATTGAAATGAATAATCAATCAATAAAATGAAAATTTAATATTTTTTAATTTTTTATAATATATT
131 TATTGAAATGAATAATCAATCAATAAAATGAAAATTTAATATTTTTTAATTTTTTATAATATATT
24797 ACTACATGTAAGTTGTAAAATAAACTAAAAAAAAGCAAAAAAAATAAGGGCAATTCTGTCATTTT
196 ACTACATGTAAGTTGTAAAATAAACTAAAAAAAAGCAAAAAAAATAAGGGCAATTCTGTCATTTT
*
24862 ACATTACTGAAATCAAATTCATCTGACATGTCTGCGAACCAAACAGAATATGGAATTATATTTCA
261 ACATTACTGAAATCAAATTCATCTGACATGTCTGCGAACCAAACAGAATATGGAATTAGATTTCA
24927 ATTCCTTCACAAATTGGATAAAAATAATTTTTGGTATATTTTTTGATAACTAATTAACATACTCC
326 ATTCCTTCACAAATTGGATAAAAATAATTTTTGGTATATTTTTTGATAACTAATTAACATACTCC
24992 AATTGGAATGTATAAAAATATTGCTCTATC
391 AATTGGAATGTATAAAAATATTGCTCTATC
25022 TTTTGATAACTTATTAACATATTCCAATTGGAATGTATGAAAATATTGCTCTATCTTTTGATAAC
1 TTTTGATAACTTATTAACATATTCCAATTGGAATGTATGAAAATATTGCTCTATCTTTTGATAAC
25087 TTATTAACATATTTTGATTGCGATGATTTTAACTTATGATGTTTATTAGCATGATTTTTATAATT
66 TTATTAACATATTTTGATTGCGATGATTTTAACTTATGATGTTTATTAGCATGATTTTTATAATT
25152 TATTGAAATGAATAATCAATCAATAAAATGAAAATTTAATATTTTTTAATTTTTTATAATATATT
131 TATTGAAATGAATAATCAATCAATAAAATGAAAATTTAATATTTTTTAATTTTTTATAATATATT
25217 ACTACATGTAAGTTGTAAAATAAACTAAAAAAAAGCAAAAAAAATAAGGGCAATTCTGTCATTTT
196 ACTACATGTAAGTTGTAAAATAAACTAAAAAAAAGCAAAAAAAATAAGGGCAATTCTGTCATTTT
25282 ACATTACTGAAATCAAATTCATCTGACATGTCTGCGAACCAAACAGAATATGGAATTAGATTTCA
261 ACATTACTGAAATCAAATTCATCTGACATGTCTGCGAACCAAACAGAATATGGAATTAGATTTCA
25347 ATTCCTTCACAAATTGGATAAAAATAATTTTTGGTATATTTTTTGATAACTAATTAACATACTCC
326 ATTCCTTCACAAATTGGATAAAAATAATTTTTGGTATATTTTTTGATAACTAATTAACATACTCC
*
25412 AATTGGAATGTATGAAAATATTGCTCTATC
391 AATTGGAATGTATAAAAATATTGCTCTATC
25442 TTTTGATAACTTATTAACATATTCCAATTGGAATGTATGAAAATATTGCTCTATCTTTTGATAAC
1 TTTTGATAACTTATTAACATATTCCAATTGGAATGTATGAAAATATTGCTCTATCTTTTGATAAC
25507 TTATTAACATATTTTGATTGCGATGATTTTAACTTATGATGTTTATTAGCATGATTTTTATAATT
66 TTATTAACATATTTTGATTGCGATGATTTTAACTTATGATGTTTATTAGCATGATTTTTATAATT
*
25572 TATTGAAATTAATAATCAATCAATAAAATGAAAATTTAATATTTTTTAATTTTTTATAATATATT
131 TATTGAAATGAATAATCAATCAATAAAATGAAAATTTAATATTTTTTAATTTTTTATAATATATT
*
25637 ACTACATGTAAATTGTAAAATAAACTAAAAAAAAGCAAAAAAAAATAAGGGCAATTCTGTCATTT
196 ACTACATGTAAGTTGTAAAATAAACTAAAAAAAAGC-AAAAAAAATAAGGGCAATTCTGTCATTT
25702 TACATTACTGAAATCAAATTCATCTGACATGTCTGCGAACCAAACAGAATATGGAATTAGATTTC
260 TACATTACTGAAATCAAATTCATCTGACATGTCTGCGAACCAAACAGAATATGGAATTAGATTTC
**
25767 AATTGGTTCACAAATT
325 AATTCCTTCACAAATT
25783 CCAATTCCCT
Statistics
Matches: 751, Mismatches: 9, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
420 644 0.86
421 107 0.14
ACGTcount: A:0.40, C:0.11, G:0.10, T:0.39
Consensus pattern (420 bp):
TTTTGATAACTTATTAACATATTCCAATTGGAATGTATGAAAATATTGCTCTATCTTTTGATAAC
TTATTAACATATTTTGATTGCGATGATTTTAACTTATGATGTTTATTAGCATGATTTTTATAATT
TATTGAAATGAATAATCAATCAATAAAATGAAAATTTAATATTTTTTAATTTTTTATAATATATT
ACTACATGTAAGTTGTAAAATAAACTAAAAAAAAGCAAAAAAAATAAGGGCAATTCTGTCATTTT
ACATTACTGAAATCAAATTCATCTGACATGTCTGCGAACCAAACAGAATATGGAATTAGATTTCA
ATTCCTTCACAAATTGGATAAAAATAATTTTTGGTATATTTTTTGATAACTAATTAACATACTCC
AATTGGAATGTATAAAAATATTGCTCTATC
Found at i:25518 original size:55 final size:55
Alignment explanation
Indices: 25387--25519 Score: 248
Period size: 55 Copynumber: 2.4 Consensus size: 55
25377 TTGGTATATT
* *
25387 TTTTGATAACTAATTAACATACTCCAATTGGAATGTATGAAAATATTGCTCTATC
1 TTTTGATAACTTATTAACATATTCCAATTGGAATGTATGAAAATATTGCTCTATC
25442 TTTTGATAACTTATTAACATATTCCAATTGGAATGTATGAAAATATTGCTCTATC
1 TTTTGATAACTTATTAACATATTCCAATTGGAATGTATGAAAATATTGCTCTATC
25497 TTTTGATAACTTATTAACATATT
1 TTTTGATAACTTATTAACATATT
25520 TTGATTGCGA
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
55 76 1.00
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (55 bp):
TTTTGATAACTTATTAACATATTCCAATTGGAATGTATGAAAATATTGCTCTATC
Found at i:30135 original size:19 final size:19
Alignment explanation
Indices: 30113--30169 Score: 53
Period size: 23 Copynumber: 2.8 Consensus size: 19
30103 GTTTGTTTCC
30113 TACAGCTTGTTTTCTACTA
1 TACAGCTTGTTTTCTACTA
*
30132 TACAGTCTGTTTTCTTTCTACTA
1 TACAG-C--TTGT-TTTCTACTA
30155 TACAG-TCTGTTTTCT
1 TACAGCT-TGTTTTCT
30170 TTCTACAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
19 11 0.35
20 3 0.10
22 3 0.10
23 14 0.45
ACGTcount: A:0.18, C:0.21, G:0.11, T:0.51
Consensus pattern (19 bp):
TACAGCTTGTTTTCTACTA
Found at i:30153 original size:23 final size:23
Alignment explanation
Indices: 30123--30175 Score: 106
Period size: 23 Copynumber: 2.3 Consensus size: 23
30113 TACAGCTTGT
30123 TTTCTACTATACAGTCTGTTTTC
1 TTTCTACTATACAGTCTGTTTTC
30146 TTTCTACTATACAGTCTGTTTTC
1 TTTCTACTATACAGTCTGTTTTC
30169 TTTCTAC
1 TTTCTAC
30176 AATCTGTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.17, C:0.23, G:0.08, T:0.53
Consensus pattern (23 bp):
TTTCTACTATACAGTCTGTTTTC
Found at i:30181 original size:18 final size:18
Alignment explanation
Indices: 30132--30185 Score: 54
Period size: 23 Copynumber: 2.7 Consensus size: 18
30122 TTTTCTACTA
*
30132 TACAGTCTGTTTTCTTTC
1 TACAATCTGTTTTCTTTC
30150 TACTATACAGTCTGTTTTCTTTC
1 TAC---A-A-TCTGTTTTCTTTC
30173 TACAATCTGTTTT
1 TACAATCTGTTTT
30186 TCTACATGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 10
0.73 0.02 0.24
Matches are distributed among these distances:
18 11 0.37
19 1 0.03
20 1 0.03
21 1 0.03
23 16 0.53
ACGTcount: A:0.17, C:0.20, G:0.09, T:0.54
Consensus pattern (18 bp):
TACAATCTGTTTTCTTTC
Found at i:32294 original size:36 final size:36
Alignment explanation
Indices: 32254--32324 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
32244 CTAGCATTCG
*
32254 CCAAGAACCAGATTCGGATCCAGTTGCCTCTGAAAA
1 CCAAGAACCAGATTCGGATCCAGTTGCATCTGAAAA
* *
32290 CCAAGAACTAGATTCGGATCCTGTTGCATCTGAAA
1 CCAAGAACCAGATTCGGATCCAGTTGCATCTGAAA
32325 CAGAAGGTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (36 bp):
CCAAGAACCAGATTCGGATCCAGTTGCATCTGAAAA
Found at i:34304 original size:15 final size:17
Alignment explanation
Indices: 34270--34306 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
34260 TTTTCTACTA
34270 TACAGTCTGCTTTCTTTC
1 TACAGTCTGC-TTCTTTC
34288 TACAGTCTG-TT-TTTC
1 TACAGTCTGCTTCTTTC
34303 TACA
1 TACA
34307 ATAAAGAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 8 0.42
16 2 0.11
18 9 0.47
ACGTcount: A:0.16, C:0.24, G:0.11, T:0.49
Consensus pattern (17 bp):
TACAGTCTGCTTCTTTC
Found at i:35285 original size:14 final size:14
Alignment explanation
Indices: 35266--35293 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
35256 GAAATGCATT
35266 TAGAAAACGAAAAG
1 TAGAAAACGAAAAG
35280 TAGAAAACGAAAAG
1 TAGAAAACGAAAAG
35294 CAAAAGTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.07, G:0.21, T:0.07
Consensus pattern (14 bp):
TAGAAAACGAAAAG
Found at i:37178 original size:19 final size:19
Alignment explanation
Indices: 37155--37250 Score: 138
Period size: 19 Copynumber: 5.1 Consensus size: 19
37145 TGCATTGGAC
*
37155 TATGAATTTGAAAATAAGC
1 TATGAATTTGAAAATAAGT
37174 TATGAATTTGAAAATAAGT
1 TATGAATTTGAAAATAAGT
* *
37193 TATGAATTTGACAGTAAGT
1 TATGAATTTGAAAATAAGT
*
37212 TATGAGTTTGAAAATAAGT
1 TATGAATTTGAAAATAAGT
* *
37231 TATGAATCTGGAAATAAGT
1 TATGAATTTGAAAATAAGT
37250 T
1 T
37251 CTGATTCAGA
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 68 1.00
ACGTcount: A:0.43, C:0.03, G:0.19, T:0.35
Consensus pattern (19 bp):
TATGAATTTGAAAATAAGT
Found at i:37263 original size:38 final size:38
Alignment explanation
Indices: 37155--37266 Score: 111
Period size: 38 Copynumber: 2.9 Consensus size: 38
37145 TGCATTGGAC
* * * * *
37155 TATGAATTTGAAAATAAGCTATGAATTTGAAAATAAGT
1 TATGAATTGGACAATAAGTTATGAGTTAGAAAATAAGT
* * *
37193 TATGAATTTGACAGTAAGTTATGAGTTTGAAAATAAGT
1 TATGAATTGGACAATAAGTTATGAGTTAGAAAATAAGT
*
37231 TATGAATCTGGA-AATAAGTTCTGA-TTCAGAAAATAA
1 TATGAAT-TGGACAATAAGTTATGAGTT-AGAAAATAA
37267 ATTCTAAAAT
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
37 2 0.03
38 59 0.92
39 3 0.05
ACGTcount: A:0.44, C:0.04, G:0.18, T:0.34
Consensus pattern (38 bp):
TATGAATTGGACAATAAGTTATGAGTTAGAAAATAAGT
Found at i:37264 original size:19 final size:19
Alignment explanation
Indices: 37221--37271 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 19
37211 TTATGAGTTT
* *
37221 GAAAATAAGTTATGAATCT
1 GAAAATAAGTTCTGAATCA
* *
37240 GGAAATAAGTTCTGATTCA
1 GAAAATAAGTTCTGAATCA
*
37259 GAAAATAAATTCT
1 GAAAATAAGTTCT
37272 AAAATGTGAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.45, C:0.08, G:0.16, T:0.31
Consensus pattern (19 bp):
GAAAATAAGTTCTGAATCA
Found at i:39222 original size:24 final size:24
Alignment explanation
Indices: 39190--39280 Score: 103
Period size: 24 Copynumber: 3.8 Consensus size: 24
39180 TAGGTCGAAT
* * *
39190 ATAAACGAATGAACATACATGGAC
1 ATAAACGAACGAACATAAATGAAC
39214 ATAAACGAACGAACATAAATGAAC
1 ATAAACGAACGAACATAAATGAAC
* * *
39238 ATACACAAAC-ATAAATAAATGAAC
1 ATAAACGAACGA-ACATAAATGAAC
*
39262 ATAAATGAACGAACATAAA
1 ATAAACGAACGAACATAAA
39281 CGAAAGGATT
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
23 1 0.02
24 53 0.96
25 1 0.02
ACGTcount: A:0.58, C:0.15, G:0.11, T:0.15
Consensus pattern (24 bp):
ATAAACGAACGAACATAAATGAAC
Found at i:39237 original size:34 final size:34
Alignment explanation
Indices: 39197--39271 Score: 96
Period size: 34 Copynumber: 2.2 Consensus size: 34
39187 AATATAAACG
*** *
39197 AATGAACATACATGGACATAAACGAACGAACATA
1 AATGAACATACACAAACATAAACAAACGAACATA
* *
39231 AATGAACATACACAAACATAAATAAATGAACATA
1 AATGAACATACACAAACATAAACAAACGAACATA
39265 AATGAAC
1 AATGAAC
39272 GAACATAAAC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.57, C:0.16, G:0.11, T:0.16
Consensus pattern (34 bp):
AATGAACATACACAAACATAAACAAACGAACATA
Found at i:39264 original size:14 final size:14
Alignment explanation
Indices: 39245--39280 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
39235 AACATACACA
*
39245 AACATAAATAAATG
1 AACATAAATAAACG
*
39259 AACATAAATGAACG
1 AACATAAATAAACG
39273 AACATAAA
1 AACATAAA
39281 CGAAAGGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.64, C:0.11, G:0.08, T:0.17
Consensus pattern (14 bp):
AACATAAATAAACG
Found at i:41095 original size:21 final size:21
Alignment explanation
Indices: 41071--41137 Score: 58
Period size: 21 Copynumber: 3.5 Consensus size: 21
41061 AACTTTGAAA
41071 AAATGGTTTTTAAAGTTTGGT
1 AAATGGTTTTTAAAGTTTGGT
*
41092 AAAT-G-TTTT----TTT-GA
1 AAATGGTTTTTAAAGTTTGGT
*
41106 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTTAAAGTTTGGT
*
41127 AAATGTTTTTT
1 AAATGGTTTTT
41138 TGAAAAATAG
Statistics
Matches: 34, Mismatches: 5, Indels: 14
0.64 0.09 0.26
Matches are distributed among these distances:
14 5 0.15
15 4 0.12
16 3 0.09
19 4 0.12
20 4 0.12
21 14 0.41
ACGTcount: A:0.28, C:0.01, G:0.19, T:0.51
Consensus pattern (21 bp):
AAATGGTTTTTAAAGTTTGGT
Found at i:41108 original size:37 final size:36
Alignment explanation
Indices: 41064--41182 Score: 170
Period size: 35 Copynumber: 3.3 Consensus size: 36
41054 GATAACTAAC
41064 TTTGAAAAAATGGTTTTTAAAGTTTGGTAAATGTTTT
1 TTTG-AAAAATGGTTTTTAAAGTTTGGTAAATGTTTT
*
41101 TTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTTT
1 TTTGAAAAATGGTTTTTAAAGTTTGGTAAATGTTTT
* *
41136 TTTGAAAAATAGTTTTTCAAAGTTTGGTAGATG-TTT
1 TTTGAAAAATGGTTTTT-AAAGTTTGGTAAATGTTTT
*
41172 GTTGAAAAATG
1 TTTGAAAAATG
41183 ATAATGGGAT
Statistics
Matches: 74, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
35 34 0.46
36 22 0.30
37 18 0.24
ACGTcount: A:0.32, C:0.02, G:0.20, T:0.46
Consensus pattern (36 bp):
TTTGAAAAATGGTTTTTAAAGTTTGGTAAATGTTTT
Found at i:45729 original size:37 final size:38
Alignment explanation
Indices: 45674--45757 Score: 120
Period size: 37 Copynumber: 2.3 Consensus size: 38
45664 TGGTAACCAA
45674 CTTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATATGGTTTTCAAAGTTTGGTAAATGTTT
* *
45711 CTTTGAAAAATA-GTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATATGGTTTTCAAAGTTTGGTAAATGTTT
*
45748 -GTTGAAAAAT
1 CTTTGAAAAAT
45758 GATAATGGGA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
36 9 0.21
37 33 0.77
38 1 0.02
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (38 bp):
CTTTGAAAAATATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:48261 original size:93 final size:92
Alignment explanation
Indices: 48098--48364 Score: 390
Period size: 93 Copynumber: 2.9 Consensus size: 92
48088 AGGGTACTTG
* * * *
48098 CACTCCGCAAATGTCCCCCAGTTTGAGCTATGAAATTGGAAAGCAGTCAGTTGATCAAGATGCGA
1 CACTCCG-AAATGTCTCCCAGTTTGAACTATGAAATTAGACAGCAGTCAGTTGATCAAGATGCGA
*
48163 AGCTTAATAACAATTCCGATGGTTCTTA
65 TGCTTAATAACAATTCCGATGGTTCTTA
*
48191 CACTCCTGAAATGTCTCCCAGTTTGAACTATGAAATTAGACAGCAGTCAGTTGATCAAGATGTGA
1 CACTCC-GAAATGTCTCCCAGTTTGAACTATGAAATTAGACAGCAGTCAGTTGATCAAGATGCGA
*
48256 TGCTTAAGAACAATTCCGATGGTTCTTA
65 TGCTTAATAACAATTCCGATGGTTCTTA
* * * * *
48284 CGCTCCACAAATGTCTCCCAGTTTGAACTATGAAATTAGACAGCAGTCATTTGATCAATATGCCA
1 CACTCC-GAAATGTCTCCCAGTTTGAACTATGAAATTAGACAGCAGTCAGTTGATCAAGATGCGA
*
48349 TGATTAATAACAATTC
65 TGCTTAATAACAATTC
48365 TGAAGGCATT
Statistics
Matches: 157, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
93 156 0.99
94 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (92 bp):
CACTCCGAAATGTCTCCCAGTTTGAACTATGAAATTAGACAGCAGTCAGTTGATCAAGATGCGAT
GCTTAATAACAATTCCGATGGTTCTTA
Found at i:49582 original size:31 final size:31
Alignment explanation
Indices: 49529--49625 Score: 106
Period size: 31 Copynumber: 3.1 Consensus size: 31
49519 ATTTTGACTG
* * *
49529 AATTGAATGATTAAATTTATATTTTATTTAA
1 AATTTAATAATTAAATTAATATTTTATTTAA
* *
49560 AATTTAATAATTATATTAATATTTTATCTAAA
1 AATTTAATAATTAAATTAATATTTTAT-TTAA
* * *
49592 AATTTAA-AGTTAAATTAATAATTTATCTAA
1 AATTTAATAATTAAATTAATATTTTATTTAA
49622 AATT
1 AATT
49626 AAAGGATGAA
Statistics
Matches: 55, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
30 6 0.11
31 39 0.71
32 10 0.18
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.48
Consensus pattern (31 bp):
AATTTAATAATTAAATTAATATTTTATTTAA
Found at i:61954 original size:20 final size:20
Alignment explanation
Indices: 61929--61983 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
61919 GGCCATCCGA
*
61929 CCGAGGCCATCTGAAAGCAT
1 CCGAGGCCATCCGAAAGCAT
*
61949 CCGAGGCCATCCGAGAGCAT
1 CCGAGGCCATCCGAAAGCAT
61969 CCGAGGCCATCCGAA
1 CCGAGGCCATCCGAA
61984 CGAGCTATGC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.27, C:0.35, G:0.27, T:0.11
Consensus pattern (20 bp):
CCGAGGCCATCCGAAAGCAT
Found at i:61959 original size:10 final size:10
Alignment explanation
Indices: 61946--61982 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
61936 CATCTGAAAG
61946 CATCCGAGGC
1 CATCCGAGGC
61956 CATCCGAGAG-
1 CATCCGAG-GC
61966 CATCCGAGGC
1 CATCCGAGGC
61976 CATCCGA
1 CATCCGA
61983 ACGAGCTATG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 1 0.04
10 23 0.92
11 1 0.04
ACGTcount: A:0.24, C:0.38, G:0.27, T:0.11
Consensus pattern (10 bp):
CATCCGAGGC
Found at i:62073 original size:14 final size:14
Alignment explanation
Indices: 62054--62114 Score: 104
Period size: 14 Copynumber: 4.4 Consensus size: 14
62044 CCTCGCATAG
*
62054 CTCGTTCGGATGGC
1 CTCGGTCGGATGGC
*
62068 CTCGTTCGGATGGC
1 CTCGGTCGGATGGC
62082 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
62096 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
62110 CTCGG
1 CTCGG
62115 ATGCCCAGCG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
14 46 1.00
ACGTcount: A:0.07, C:0.30, G:0.39, T:0.25
Consensus pattern (14 bp):
CTCGGTCGGATGGC
Found at i:63132 original size:20 final size:20
Alignment explanation
Indices: 63091--63132 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
63081 TTATAATTAA
* **
63091 TATAGAATAGTAATTATGTT
1 TATAGAATAATAATTAACTT
63111 TATAGAATAATAATTAACTT
1 TATAGAATAATAATTAACTT
63131 TA
1 TA
63133 AAACATAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.02, G:0.10, T:0.43
Consensus pattern (20 bp):
TATAGAATAATAATTAACTT
Found at i:71992 original size:143 final size:143
Alignment explanation
Indices: 71734--72023 Score: 571
Period size: 143 Copynumber: 2.0 Consensus size: 143
71724 TACGGACAAA
71734 ACTAAATTACAAGACCGGTTTAAGATTAGCAAATGTTTAAAAGGAGGGAAATAAACCATTTAATA
1 ACTAAATTACAAGACCGGTTTAAGATTAGCAAATGTTTAAAAGGAGGGAAATAAACCATTTAATA
*
71799 CTATCTCGGATAAATTGATTTGTCAAGTATTCTTACCTTATTCATTTGGTTGACAAAATCTAAGG
66 CTATCTCGGATAAATTGATTTGTCAAGTATTCTTAACTTATTCATTTGGTTGACAAAATCTAAGG
71864 GCAAGGGATGCAC
131 GCAAGGGATGCAC
71877 ACTAAATTACAAGACCGGTTTAAGATTAGCAAATGTTTAAAAGGAGGGAAATAAACCATTTAATA
1 ACTAAATTACAAGACCGGTTTAAGATTAGCAAATGTTTAAAAGGAGGGAAATAAACCATTTAATA
71942 CTATCTCGGATAAATTGATTTGTCAAGTATTCTTAACTTATTCATTTGGTTGACAAAATCTAAGG
66 CTATCTCGGATAAATTGATTTGTCAAGTATTCTTAACTTATTCATTTGGTTGACAAAATCTAAGG
72007 GCAAGGGATGCAC
131 GCAAGGGATGCAC
72020 ACTA
1 ACTA
72024 GGAAGTGGAG
Statistics
Matches: 146, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
143 146 1.00
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.31
Consensus pattern (143 bp):
ACTAAATTACAAGACCGGTTTAAGATTAGCAAATGTTTAAAAGGAGGGAAATAAACCATTTAATA
CTATCTCGGATAAATTGATTTGTCAAGTATTCTTAACTTATTCATTTGGTTGACAAAATCTAAGG
GCAAGGGATGCAC
Found at i:76871 original size:5 final size:5
Alignment explanation
Indices: 76861--76920 Score: 77
Period size: 5 Copynumber: 11.8 Consensus size: 5
76851 GGAAGTTAAC
* *
76861 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTC- AGTCG GGTCG GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG
76912 GGTCG GGTC
1 GGTCG GGTC
76921 AGACCGGTCA
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
4 3 0.06
5 41 0.85
7 4 0.08
ACGTcount: A:0.05, C:0.22, G:0.53, T:0.20
Consensus pattern (5 bp):
GGTCG
Found at i:76929 original size:24 final size:24
Alignment explanation
Indices: 76883--76929 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
76873 TCGGGTCAAC
* *
76883 GGTCGGGTCGGGTCAGTCGGGTCG
1 GGTCGGGTCGGGTCAGACCGGTCG
76907 GGTCGGGTCGGGTCAGACCGGTC
1 GGTCGGGTCGGGTCAGACCGGTC
76930 AAATCGGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.06, C:0.23, G:0.51, T:0.19
Consensus pattern (24 bp):
GGTCGGGTCGGGTCAGACCGGTCG
Found at i:76936 original size:19 final size:19
Alignment explanation
Indices: 76914--76951 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
76904 TCGGGTCGGG
76914 TCGGGTCAGACCGGTCAAA
1 TCGGGTCAGACCGGTCAAA
*
76933 TCGGTTCAGACCGGTCAAA
1 TCGGGTCAGACCGGTCAAA
76952 CCAGTTCGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.26, G:0.29, T:0.18
Consensus pattern (19 bp):
TCGGGTCAGACCGGTCAAA
Found at i:76936 original size:24 final size:24
Alignment explanation
Indices: 76885--76936 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
76875 GGGTCAACGG
* * ***
76885 TCGGGTCGGGTCAGTCGGGTCGGG
1 TCGGGTCGGGTCAGACCGGTCAAA
76909 TCGGGTCGGGTCAGACCGGTCAAA
1 TCGGGTCGGGTCAGACCGGTCAAA
76933 TCGG
1 TCGG
76937 TTCAGACCGG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.12, C:0.23, G:0.46, T:0.19
Consensus pattern (24 bp):
TCGGGTCGGGTCAGACCGGTCAAA
Found at i:76964 original size:19 final size:19
Alignment explanation
Indices: 76919--76958 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
76909 TCGGGTCGGG
* *
76919 TCAGACCGGTCAAATCGGT
1 TCAGACCGGTCAAACCAGT
76938 TCAGACCGGTCAAACCAGT
1 TCAGACCGGTCAAACCAGT
76957 TC
1 TC
76959 GAACCGATCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.30, G:0.23, T:0.20
Consensus pattern (19 bp):
TCAGACCGGTCAAACCAGT
Done.