Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005072.1 Hibiscus syriacus cultivar Beakdansim tig00011389_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: 58995
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Found at i:5555 original size:7 final size:7
Alignment explanation
Indices: 5543--5578 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
5533 TTATAAATAA
5543 TATATAT
1 TATATAT
5550 TATATAT
1 TATATAT
*
5557 TAAATAT
1 TATATAT
5564 TATATAT
1 TATATAT
*
5571 TATTTAT
1 TATATAT
5578 T
1 T
5579 TATTCGATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
TATATAT
Found at i:5560 original size:21 final size:21
Alignment explanation
Indices: 5536--5578 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
5526 TCGGAATTTA
5536 TAAATAATATATATTATATAT
1 TAAATAATATATATTATATAT
* *
5557 TAAATATTATATATTATTTAT
1 TAAATAATATATATTATATAT
5578 T
1 T
5579 TATTCGATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TAAATAATATATATTATATAT
Found at i:8534 original size:57 final size:58
Alignment explanation
Indices: 8456--8572 Score: 182
Period size: 57 Copynumber: 2.0 Consensus size: 58
8446 GCGATGTGTC
8456 GTTACATTATATTACGGTCGTAATTTAATACTATACCTTA-AGTATAGTGTAATGTAT
1 GTTACATTATATTACGGTCGTAATTTAATACTATACCTTAGAGTATAGTGTAATGTAT
* * * * *
8513 GTTATATTGTATTACGGTCGTAATTTAATACTATGCCTTAGAGTTTAGTGTAGTGTAT
1 GTTACATTATATTACGGTCGTAATTTAATACTATACCTTAGAGTATAGTGTAATGTAT
8571 GT
1 GT
8573 ATTGTAAGTA
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
57 37 0.69
58 17 0.31
ACGTcount: A:0.29, C:0.09, G:0.18, T:0.44
Consensus pattern (58 bp):
GTTACATTATATTACGGTCGTAATTTAATACTATACCTTAGAGTATAGTGTAATGTAT
Found at i:8981 original size:42 final size:42
Alignment explanation
Indices: 8922--9006 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 42
8912 GTGTTGTTAC
* * *
8922 GGATCGAGATCGAATGGTAACCATGTAGATTATAGAGCCAAT
1 GGATCGAAATAGAATGGTAACCATGGAGATTATAGAGCCAAT
* *
8964 GGATCGAAATAGAATGGTAACCTTGGAGATTATAGAGTCAAT
1 GGATCGAAATAGAATGGTAACCATGGAGATTATAGAGCCAAT
9006 G
1 G
9007 TTAATGTTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.36, C:0.12, G:0.27, T:0.25
Consensus pattern (42 bp):
GGATCGAAATAGAATGGTAACCATGGAGATTATAGAGCCAAT
Found at i:17536 original size:60 final size:57
Alignment explanation
Indices: 17436--17602 Score: 151
Period size: 58 Copynumber: 2.8 Consensus size: 57
17426 TCATATGGTA
* * * * **
17436 TTAGGCATGAAATTGGAAAATTCAAAATTTTG-GGAACTAATTTAGAACAATGATCATAA-
1 TTAGGGATGAAATT-GAATATTTAAAAGTTTGAGG-ACTAATTTA-AA-AAAAATCATAAT
*
17495 TTCGGTGATGAAATTAGAATATTTAAAAGTTTGAGGACTAATTTAAAAAAAATCATAAT
1 TTAGG-GATGAAATT-GAATATTTAAAAGTTTGAGGACTAATTTAAAAAAAATCATAAT
**
17554 TTAGGGATGAAATTGAAATAGATAAAAGTTTGAGGA-TAAAATTTAAAAA
1 TTAGGGATGAAATTG-AATATTTAAAAGTTTGAGGACT--AATTTAAAAA
17603 TATTATGATT
Statistics
Matches: 91, Mismatches: 11, Indels: 12
0.80 0.10 0.11
Matches are distributed among these distances:
57 2 0.02
58 36 0.40
59 20 0.22
60 31 0.34
61 2 0.02
ACGTcount: A:0.47, C:0.05, G:0.17, T:0.31
Consensus pattern (57 bp):
TTAGGGATGAAATTGAATATTTAAAAGTTTGAGGACTAATTTAAAAAAAATCATAAT
Found at i:18991 original size:31 final size:31
Alignment explanation
Indices: 18956--19030 Score: 132
Period size: 31 Copynumber: 2.4 Consensus size: 31
18946 TTAGGCTCAT
*
18956 GAGTTTTCAAGTCGAGTAAAGCTATATTCTA
1 GAGTTTTCAAGTCGAGTAAAGCTATATGCTA
18987 GAGTTTTCAAGTCGAGTAAAGCTATATGCTA
1 GAGTTTTCAAGTCGAGTAAAGCTATATGCTA
*
19018 GAGTTTTCGAGTC
1 GAGTTTTCAAGTC
19031 AAATTGAACT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.35
Consensus pattern (31 bp):
GAGTTTTCAAGTCGAGTAAAGCTATATGCTA
Found at i:25362 original size:20 final size:20
Alignment explanation
Indices: 25337--25388 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
25327 ACGAAGAACA
25337 AGTATCGATACTATCCCTAT
1 AGTATCGATACTATCCCTAT
*
25357 AGTATCGATATTATCCCTAT
1 AGTATCGATACTATCCCTAT
25377 AGTATCGATACT
1 AGTATCGATACT
25389 CTACCTGCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.37
Consensus pattern (20 bp):
AGTATCGATACTATCCCTAT
Found at i:30004 original size:338 final size:338
Alignment explanation
Indices: 29388--30738 Score: 2582
Period size: 338 Copynumber: 4.0 Consensus size: 338
29378 ACCCTACTCT
* *
29388 GACCTGATTCAAATTTCCGGAGTATAAATCCGGTCTAATTCGATATAAAATAAGTACTTCATTAA
1 GACCTGATTCAAATTTTCGGAGTATAAATCCGGTCTGATTCGATATAAAATAAGTACTTCATTAA
29453 AAATAATAATAAATTTTTTTAATGACATTACATGAACCTAATCTGACACGACCTCACTACCTTAA
66 AAATAATAATAAATTTTTTTAATGACATTACATGAACCTAATCTGACACGACCTCACTACCTTAA
29518 AAACCACGACCCAATTTGACCCGAACCTATTTTTCTAAAAGAAAATTGACCTTATCAAATCGGAT
131 AAACCACGACCCAATTTGACCCGAACCTATTTTTCTAAAAGAAAATTGACCTTATCAAATCGGAT
29583 CGGGTCGAAA-CCGTCGATTTCAAATTAAATTACTATCCCTACATGGTATGCTGCTGCTACGAGT
196 CGGGTC-AAAGCCGTCGATTTCAAATTAAATTACTATCCCTACATGGTATGCTGCTGCTACGAGT
29647 CAACTTGGGTCAATAATTGGCAGCCCCAATCTCCATTCGGTCCGGGACGGATCACATACTGATGG
260 CAACTTGGGTCAATAATTGGCAGCCCCAATCTCCATTCGGTCCGGGACGGATCACATACTGATGG
29712 ATCAAAAGGAAAAA
325 ATCAAAAGGAAAAA
29726 GACCTGATTCAAATTTTCGGAGTATAAATCCGGTCTGATTCGATATAAAATAAGTACTTCATTAA
1 GACCTGATTCAAATTTTCGGAGTATAAATCCGGTCTGATTCGATATAAAATAAGTACTTCATTAA
*
29791 AAATAATAATAAATTTTTTTAATGACATTACATGAACCTAATCTTACACGACCTCACTACCTTAA
66 AAATAATAATAAATTTTTTTAATGACATTACATGAACCTAATCTGACACGACCTCACTACCTTAA
29856 AAACCACGACCCAATTTGACCCGAACCTATTTTTCTAAAAGAAAATTGACCTTATCAAATCGGAT
131 AAACCACGACCCAATTTGACCCGAACCTATTTTTCTAAAAGAAAATTGACCTTATCAAATCGGAT
* *
29921 CGGGTCAAAGTCGTCGATTTCAAATTAAATTACTATCCCTACATGGTATGCTGTTGCTACGAGTC
196 CGGGTCAAAGCCGTCGATTTCAAATTAAATTACTATCCCTACATGGTATGCTGCTGCTACGAGTC
29986 AACTTGGGTCAATAATTGGCAGCCCCAATCTCCATTCGGTCCGGGACGGATCACATACTGATGGA
261 AACTTGGGTCAATAATTGGCAGCCCCAATCTCCATTCGGTCCGGGACGGATCACATACTGATGGA
30051 TCAAAAGGAAAAA
326 TCAAAAGGAAAAA
*
30064 GACCTGATTCAAATTTTCGGAGTATAAATCCGGTCTGATTCAATATAAAATAAGTACTTCATTAA
1 GACCTGATTCAAATTTTCGGAGTATAAATCCGGTCTGATTCGATATAAAATAAGTACTTCATTAA
*
30129 AAATAATAATAAA--TTTTTAATGACATTACATGAACCTAATATGACACGACCTCACTACCTTAA
66 AAATAATAATAAATTTTTTTAATGACATTACATGAACCTAATCTGACACGACCTCACTACCTTAA
30192 AAACCACGACCCAATTTGACCCGAACCTATTTTTCTAAAAGAAAATTGACCTTATCAAATCGGAT
131 AAACCACGACCCAATTTGACCCGAACCTATTTTTCTAAAAGAAAATTGACCTTATCAAATCGGAT
*
30257 CGGGTCAAAACCGTCGATTTCAAATTAAATTACTATCCCTACATGGTATGCTGCTGCTACGAGTC
196 CGGGTCAAAGCCGTCGATTTCAAATTAAATTACTATCCCTACATGGTATGCTGCTGCTACGAGTC
30322 AACTTGGGTCAATAATTGGCAGCCCCAATCTCCATTCGGTCCGGGACGGATCACATACTGATGGA
261 AACTTGGGTCAATAATTGGCAGCCCCAATCTCCATTCGGTCCGGGACGGATCACATACTGATGGA
30387 TCAAAAGGAAAAA
326 TCAAAAGGAAAAA
30400 GACCTGATTCAAATTTTCGGAGTATAAATCCGGTCTGATTCGATATAAAATAAGTACTTCATTAA
1 GACCTGATTCAAATTTTCGGAGTATAAATCCGGTCTGATTCGATATAAAATAAGTACTTCATTAA
* *
30465 AAATAATAATAAATTTTGTTAATGACATTACATGAACCTAATCTTACACGACCTCACTACCTTAA
66 AAATAATAATAAATTTTTTTAATGACATTACATGAACCTAATCTGACACGACCTCACTACCTTAA
30530 AAACCACGACCCAATTTGACCCGAACCTATTTTTCTAAAAGAAAATTGACCTTATCAAATCGGAT
131 AAACCACGACCCAATTTGACCCGAACCTATTTTTCTAAAAGAAAATTGACCTTATCAAATCGGAT
30595 CGGGTCAAAGCCGTCGATTTCAAATTAAATTACTATCCCTACATGGTATGCTGCTGCTACGAGTC
196 CGGGTCAAAGCCGTCGATTTCAAATTAAATTACTATCCCTACATGGTATGCTGCTGCTACGAGTC
30660 AACTTGGGTCAATAATTGGCAGCCCCAATCTCCATTCGGTCCGGGACGGATCACATACTGATGGA
261 AACTTGGGTCAATAATTGGCAGCCCCAATCTCCATTCGGTCCGGGACGGATCACATACTGATGGA
30725 TCAAAAGGAAAAA
326 TCAAAAGGAAAAA
30738 G
1 G
30739 TAGAATAAAC
Statistics
Matches: 994, Mismatches: 16, Indels: 6
0.98 0.02 0.01
Matches are distributed among these distances:
336 330 0.33
337 3 0.00
338 661 0.66
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.28
Consensus pattern (338 bp):
GACCTGATTCAAATTTTCGGAGTATAAATCCGGTCTGATTCGATATAAAATAAGTACTTCATTAA
AAATAATAATAAATTTTTTTAATGACATTACATGAACCTAATCTGACACGACCTCACTACCTTAA
AAACCACGACCCAATTTGACCCGAACCTATTTTTCTAAAAGAAAATTGACCTTATCAAATCGGAT
CGGGTCAAAGCCGTCGATTTCAAATTAAATTACTATCCCTACATGGTATGCTGCTGCTACGAGTC
AACTTGGGTCAATAATTGGCAGCCCCAATCTCCATTCGGTCCGGGACGGATCACATACTGATGGA
TCAAAAGGAAAAA
Found at i:30901 original size:674 final size:667
Alignment explanation
Indices: 29497--30816 Score: 2087
Period size: 674 Copynumber: 2.0 Consensus size: 667
29487 AACCTAATCT
* * * **
29497 GACACGACCTCACTACCTTAAAAACCACGACCCAATTTGACCCGAACCTATTTTTCTAAAAGAAA
1 GACACGACCTAAATACCTGAAAAACCACGACCCAATTTGAAACGAACCTATTTTTCTAAAAGAAA
*
29562 ATTGACCTTATCAAATCGGATCGGGTCGAAACCGTCGATTTCAAATTAAATTACTATCCCTACAT
66 ATTGACCTTATCAAATCGGATCGGGTCAAAACCGTCGATTTCAAATTAAATTACTATCCCTACAT
29627 GGTATGCTGCTGCTACGAGTCAACTTGGGTCAATAATTGGCAGCCCCAATCTCCATTCGGTCCGG
131 GGTATGCTGCTGCTACGAGTCAACTTGGGTCAATAATTGGCAGCCCCAATCTCCATTCGGTCCGG
29692 GACGGATCACATACTGATGGATCAAAAGGAAAAAGACCTGATTCAAATTTTCGGAGTATAAATCC
196 GACGGATCACATACTGATGGATCAAAAGGAAAAAGACCTGATTCAAATTTTCGGAGTATAAATCC
*
29757 GGTCTGATTCGATATAAAATAAGTACTTCATTAAAAATAATAATAAATTTTTTTAATGACATTAC
261 GGTCTGATTCGATATAAAATAAGTACTTCATTAAAAATAATAATAAATTTTGTTAATGACATTAC
29822 ATGAACCTAATCTTACACGACCTCACTACCTTAAAAACCACGACCCAATTTGACCCGAACCTATT
326 ATGAACCTAATCTTACACGACCTCACTACCTTAAAAACCACGACCCAATTTGACCCGAACCTATT
*
29887 TTTCTAAAAGAAAATTGACCTTATCAAATCGGATCGGGTCAAAGTCGTCGATTTCAAATTAAATT
391 TTTCTAAAAGAAAATTGACCTTATCAAATCGGATCGGGTCAAAGCCGTCGATTTCAAATTAAATT
*
29952 ACTATCCCTACATGGTATGCTGTTGCTACGAGTCAACTTGGGTCAATAATTGGCAGCCCCAATCT
456 ACTATCCCTACATGGTATGCTGCTGCTACGAGTCAACTTGGGTCAATAATTGGCAGCCCCAATCT
* **
30017 CCATTCGGTCCGGGACGGATCACATACTGATGGATCAAAAGGAAAAAGACCTGATTCAAATTTTC
521 CCATTCGGTCCGGGACGGATCACATACTGATGGATCAAAAGGAAAAAGA-C-GAATCAAACATTC
* ** * * * * * * ** * * ***
30082 GGAGTATAAATCCGGTCTGATTCAATATAAAATAAGTACTTCATTAAAAATAATAATAAATTTTT
584 GGACTATAAATAAGGCCTCATGC-ACAGAAAAT-AGGACTAAATGAAAAATAACAAT--ATTGCA
* * * * *
30147 AATGACATTACATGAACCTAATAT
645 AAAGACATGACATG-ACCGAAGAC
* * * **
30171 GACACGACCTCACTACCTTAAAAACCACGACCCAATTTGACCCGAACCTATTTTTCTAAAAGAAA
1 GACACGACCTAAATACCTGAAAAACCACGACCCAATTTGAAACGAACCTATTTTTCTAAAAGAAA
30236 ATTGACCTTATCAAATCGGATCGGGTCAAAACCGTCGATTTCAAATTAAATTACTATCCCTACAT
66 ATTGACCTTATCAAATCGGATCGGGTCAAAACCGTCGATTTCAAATTAAATTACTATCCCTACAT
30301 GGTATGCTGCTGCTACGAGTCAACTTGGGTCAATAATTGGCAGCCCCAATCTCCATTCGGTCCGG
131 GGTATGCTGCTGCTACGAGTCAACTTGGGTCAATAATTGGCAGCCCCAATCTCCATTCGGTCCGG
30366 GACGGATCACATACTGATGGATCAAAAGGAAAAAGACCTGATTCAAATTTTCGGAGTATAAATCC
196 GACGGATCACATACTGATGGATCAAAAGGAAAAAGACCTGATTCAAATTTTCGGAGTATAAATCC
30431 GGTCTGATTCGATATAAAATAAGTACTTCATTAAAAATAATAATAAATTTTGTTAATGACATTAC
261 GGTCTGATTCGATATAAAATAAGTACTTCATTAAAAATAATAATAAATTTTGTTAATGACATTAC
30496 ATGAACCTAATCTTACACGACCTCACTACCTTAAAAACCACGACCCAATTTGACCCGAACCTATT
326 ATGAACCTAATCTTACACGACCTCACTACCTTAAAAACCACGACCCAATTTGACCCGAACCTATT
30561 TTTCTAAAAGAAAATTGACCTTATCAAATCGGATCGGGTCAAAGCCGTCGATTTCAAATTAAATT
391 TTTCTAAAAGAAAATTGACCTTATCAAATCGGATCGGGTCAAAGCCGTCGATTTCAAATTAAATT
30626 ACTATCCCTACATGGTATGCTGCTGCTACGAGTCAACTTGGGTCAATAATTGGCAGCCCCAATCT
456 ACTATCCCTACATGGTATGCTGCTGCTACGAGTCAACTTGGGTCAATAATTGGCAGCCCCAATCT
30691 CCATTCGGTCCGGGACGGATCACATACTGATGGATCAAAAGGAAAAAGTA-GAAT-AAACATT-G
521 CCATTCGGTCCGGGACGGATCACATACTGATGGATCAAAAGGAAAAAG-ACGAATCAAACATTCG
* * * * ** *
30753 GCCCTTTGATTAAGGCCTCATGC-CAGCCAAT-GGAC-AAATGCAAAATACACAAT-TTAGCAAA
585 G-ACTATAAATAAGGCCTCATGCACAGAAAATAGGACTAAATGAAAAATA-ACAATATT-GCAAA
30814 AGA
647 AGA
30817 TCCGATGGCT
Statistics
Matches: 611, Mismatches: 31, Indels: 17
0.93 0.05 0.03
Matches are distributed among these distances:
664 2 0.00
665 4 0.01
666 8 0.01
667 7 0.01
669 4 0.01
670 2 0.00
671 16 0.03
672 3 0.00
674 564 0.92
675 1 0.00
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (667 bp):
GACACGACCTAAATACCTGAAAAACCACGACCCAATTTGAAACGAACCTATTTTTCTAAAAGAAA
ATTGACCTTATCAAATCGGATCGGGTCAAAACCGTCGATTTCAAATTAAATTACTATCCCTACAT
GGTATGCTGCTGCTACGAGTCAACTTGGGTCAATAATTGGCAGCCCCAATCTCCATTCGGTCCGG
GACGGATCACATACTGATGGATCAAAAGGAAAAAGACCTGATTCAAATTTTCGGAGTATAAATCC
GGTCTGATTCGATATAAAATAAGTACTTCATTAAAAATAATAATAAATTTTGTTAATGACATTAC
ATGAACCTAATCTTACACGACCTCACTACCTTAAAAACCACGACCCAATTTGACCCGAACCTATT
TTTCTAAAAGAAAATTGACCTTATCAAATCGGATCGGGTCAAAGCCGTCGATTTCAAATTAAATT
ACTATCCCTACATGGTATGCTGCTGCTACGAGTCAACTTGGGTCAATAATTGGCAGCCCCAATCT
CCATTCGGTCCGGGACGGATCACATACTGATGGATCAAAAGGAAAAAGACGAATCAAACATTCGG
ACTATAAATAAGGCCTCATGCACAGAAAATAGGACTAAATGAAAAATAACAATATTGCAAAAGAC
ATGACATGACCGAAGAC
Found at i:33234 original size:31 final size:31
Alignment explanation
Indices: 33064--33231 Score: 318
Period size: 31 Copynumber: 5.4 Consensus size: 31
33054 CTTGCTGTGC
33064 ATCAATAGCAATGGCACAACCCACCAGTTCT
1 ATCAATAGCAATGGCACAACCCACCAGTTCT
33095 ATCAATAGCAATGGCACAACCCACCAGTTCT
1 ATCAATAGCAATGGCACAACCCACCAGTTCT
33126 ATCAATAGCAATGGCACAACCCACCAGTTCT
1 ATCAATAGCAATGGCACAACCCACCAGTTCT
*
33157 ATCAATAGAAATGGCACAACCCACCAGTTCT
1 ATCAATAGCAATGGCACAACCCACCAGTTCT
*
33188 ATCAATAGCAATGCCACAACCCACCAGTTCT
1 ATCAATAGCAATGGCACAACCCACCAGTTCT
33219 ATCAATAGCAATG
1 ATCAATAGCAATG
33232 CCAATGGCAC
Statistics
Matches: 134, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 134 1.00
ACGTcount: A:0.37, C:0.31, G:0.12, T:0.20
Consensus pattern (31 bp):
ATCAATAGCAATGGCACAACCCACCAGTTCT
Found at i:35108 original size:15 final size:15
Alignment explanation
Indices: 35088--35137 Score: 82
Period size: 15 Copynumber: 3.3 Consensus size: 15
35078 AAATTAAGTT
*
35088 AATAAAATGAAATGA
1 AATAAAATGAAATAA
*
35103 AATAAAATAAAATAA
1 AATAAAATGAAATAA
35118 AATAAAATGAAATAA
1 AATAAAATGAAATAA
35133 AATAA
1 AATAA
35138 TATTAATAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.20
Consensus pattern (15 bp):
AATAAAATGAAATAA
Found at i:35136 original size:5 final size:5
Alignment explanation
Indices: 35088--35137 Score: 73
Period size: 5 Copynumber: 10.0 Consensus size: 5
35078 AAATTAAGTT
* * *
35088 AATAA AATGA AATGA AATAA AATAA AATAA AATAA AATGA AATAA AATAA
1 AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA
35138 TATTAATAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 41 1.00
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.20
Consensus pattern (5 bp):
AATAA
Found at i:35287 original size:35 final size:34
Alignment explanation
Indices: 35221--35323 Score: 102
Period size: 39 Copynumber: 2.9 Consensus size: 34
35211 TCAAAACTAT
* *
35221 ATATTATAT-AGTTTTCAAAAAATG-ATTTTAAAA
1 ATATTATATAAGTTTTC-CAAAATGTTTTTTAAAA
35254 ATATTATATAAGTTTTCCAAAATGTTTTGTTAAAACTA
1 ATATTATATAAGTTTTCCAAAATGTTTT-TT-AAA--A
*
35292 TATATTATATAAATTTTCCCAAAATGTTTTTT
1 -ATATTATATAAGTTTT-CCAAAATGTTTTTT
35324 TTAAAAAATA
Statistics
Matches: 59, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
33 15 0.25
34 9 0.15
35 2 0.03
36 3 0.05
38 1 0.02
39 17 0.29
40 12 0.20
ACGTcount: A:0.41, C:0.07, G:0.06, T:0.47
Consensus pattern (34 bp):
ATATTATATAAGTTTTCCAAAATGTTTTTTAAAA
Found at i:35335 original size:40 final size:38
Alignment explanation
Indices: 35250--35353 Score: 117
Period size: 39 Copynumber: 2.8 Consensus size: 38
35240 AAATGATTTT
*
35250 AAAA-ATATTATATAAGTTTTCCAAAATGTTTTGTTAA
1 AAAATATATTATATAAATTTTCCAAAATGTTTTGTTAA
* *
35287 AACTATATATTATATAAATTTTCCCAAAATGTTTTTTTTAA
1 AA-AATATATTATATAAATTTT-CCAAAATG-TTTTGTTAA
*
35328 AAAATATA-TAT-TATATTTT-CAAAATG
1 AAAATATATTATATAAATTTTCCAAAATG
35354 ATTTCAAAAC
Statistics
Matches: 58, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
36 7 0.12
37 2 0.03
38 8 0.14
39 18 0.31
40 13 0.22
41 10 0.17
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (38 bp):
AAAATATATTATATAAATTTTCCAAAATGTTTTGTTAA
Found at i:36296 original size:84 final size:84
Alignment explanation
Indices: 36183--36589 Score: 454
Period size: 84 Copynumber: 4.9 Consensus size: 84
36173 CGACTTAAAC
* **
36183 TATGCTGCAAAATGATGTGCCTTGGAGCTGAGCGGAGTCGAACTCGAAGGTCTTTTGGTCACAGA
1 TATGCTGC-AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGGCAGA
*
36248 TAACCCTTCTAGCTTTGAGT
65 TAACCCTTCTAGCTTTAAGT
* * * * *
36268 TATGCTGTAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGAC
1 TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGGCAGAT
36333 AACCCTTCTAG-TCTTAAGT
66 AACCCTTCTAGCT-TTAAGT
* ** * *
36352 TGTATTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGAT
1 TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGGCAGAT
*
36417 AACCCTTCTCGAC-TTAAGT
66 AACCCTTCTAG-CTTTAAGT
* * * * * **
36436 TATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTTGGGGGTC--TT--TGGCAGA
1 TATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGGCAGA
* * * *
36497 TAGCCCTTCTCGATTTAAGC
65 TAACCCTTCTAGCTTTAAGT
36517 TATGCTGCAAATGATGTGCCGTT-GAGCTGAGCGTAGTCGAACTCGAAGGTC--TTGGTGGGCAG
1 TATGCTGCAAATGATGTGCC-TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGT-GGCAG
*
36579 ATAGCCCTTCT
64 ATAACCCTTCT
36590 GGCCTTGAGC
Statistics
Matches: 274, Mismatches: 39, Indels: 20
0.82 0.12 0.06
Matches are distributed among these distances:
80 26 0.09
81 42 0.15
82 1 0.00
83 19 0.07
84 153 0.56
85 33 0.12
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (84 bp):
TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGGCAGAT
AACCCTTCTAGCTTTAAGT
Found at i:36377 original size:168 final size:165
Alignment explanation
Indices: 36136--36569 Score: 489
Period size: 168 Copynumber: 2.6 Consensus size: 165
36126 AAGTTGAATA
* * * * * * * *
36136 TAATCGAACTCGAAGGTCTTTAGCAGATAGCCCTTCTCGACTTAAACTATGCTGCAAAATGATGT
1 TAATCGAACTCAAAGGTCTTTGGCAGACAACCCTTCTAGATTTAAGCTATACTGC-AAATGATGT
* *
36201 GCCTTGGAGCTGAGCGGAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAG-CTTTG
65 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGAC-TTA
* * *
36265 AGTTATGCTGTAAATGATGTGCCTTTG-AGCTGAGCG
129 AGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGCG
* * * *
36301 TAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAG-TCTTAAGTTGTATTGCAAATG
1 TAATCGAACTCAAAGGTC---T-TTGGCAGACAACCCTTCTAGAT-TTAAGCTATACTGCAAATG
* * ** *
36365 ATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGAC
61 ATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGAC
*
36430 TTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTG
126 TTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGCG
**** * * * *
36470 TAATCGAACTTGGGGGTCTTTGGCAGATAGCCCTTCTCGATTTAAGCTATGCTGCAAATGATGTG
1 TAATCGAACTCAAAGGTCTTTGGCAGACAACCCTTCTAGATTTAAGCTATACTGCAAATGATGTG
36535 CCGTT-GAGCTGAGCGTAGTCGAACTCGAAGGTCTT
66 CC-TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTT
36570 GGTGGGCAGA
Statistics
Matches: 224, Mismatches: 36, Indels: 18
0.81 0.13 0.06
Matches are distributed among these distances:
165 84 0.38
166 4 0.02
168 89 0.40
169 47 0.21
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.30
Consensus pattern (165 bp):
TAATCGAACTCAAAGGTCTTTGGCAGACAACCCTTCTAGATTTAAGCTATACTGCAAATGATGTG
CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGACTTAAG
TTATGCTGCAAATGATGTGCCCTCGAAGCTGAGCG
Found at i:43079 original size:10 final size:10
Alignment explanation
Indices: 43062--43112 Score: 75
Period size: 10 Copynumber: 5.1 Consensus size: 10
43052 AAATTAAGTT
*
43062 AATAAAATGA
1 AATAAAATAA
*
43072 AATGAAATAA
1 AATAAAATAA
43082 AATAAAATAA
1 AATAAAATAA
*
43092 AATAAAATGA
1 AATAAAATAA
43102 AATAAAATAA
1 AATAAAATAA
43112 A
1 A
43113 TATTAATAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 36 1.00
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.20
Consensus pattern (10 bp):
AATAAAATAA
Found at i:43121 original size:15 final size:15
Alignment explanation
Indices: 43062--43112 Score: 84
Period size: 15 Copynumber: 3.4 Consensus size: 15
43052 AAATTAAGTT
*
43062 AATAAAATGAAATGA
1 AATAAAATGAAATAA
*
43077 AATAAAATAAAATAA
1 AATAAAATGAAATAA
43092 AATAAAATGAAATAA
1 AATAAAATGAAATAA
43107 AATAAA
1 AATAAA
43113 TATTAATAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.20
Consensus pattern (15 bp):
AATAAAATGAAATAA
Found at i:43265 original size:35 final size:34
Alignment explanation
Indices: 43199--43301 Score: 102
Period size: 39 Copynumber: 2.9 Consensus size: 34
43189 TCAAAACTAT
* *
43199 ATATTATAT-AGTTTTCAAAAAATG-ATTTTAAAA
1 ATATTATATAAGTTTTC-CAAAATGTTTTTTAAAA
43232 ATATTATATAAGTTTTCCAAAATGTTTTGTTAAAACTA
1 ATATTATATAAGTTTTCCAAAATGTTTT-TT-AAA--A
*
43270 TATATTATATAAATTTTCCCAAAATGTTTTTT
1 -ATATTATATAAGTTTT-CCAAAATGTTTTTT
43302 TTAAAAAATA
Statistics
Matches: 59, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
33 15 0.25
34 9 0.15
35 2 0.03
36 3 0.05
38 1 0.02
39 17 0.29
40 12 0.20
ACGTcount: A:0.41, C:0.07, G:0.06, T:0.47
Consensus pattern (34 bp):
ATATTATATAAGTTTTCCAAAATGTTTTTTAAAA
Found at i:43313 original size:40 final size:38
Alignment explanation
Indices: 43228--43331 Score: 117
Period size: 39 Copynumber: 2.8 Consensus size: 38
43218 AAATGATTTT
*
43228 AAAA-ATATTATATAAGTTTTCCAAAATGTTTTGTTAA
1 AAAATATATTATATAAATTTTCCAAAATGTTTTGTTAA
* *
43265 AACTATATATTATATAAATTTTCCCAAAATGTTTTTTTTAA
1 AA-AATATATTATATAAATTTT-CCAAAATG-TTTTGTTAA
*
43306 AAAATATA-TAT-TATATTTT-CAAAATG
1 AAAATATATTATATAAATTTTCCAAAATG
43332 ATTTCAAAAC
Statistics
Matches: 58, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
36 7 0.12
37 2 0.03
38 8 0.14
39 18 0.31
40 13 0.22
41 10 0.17
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (38 bp):
AAAATATATTATATAAATTTTCCAAAATGTTTTGTTAA
Found at i:45705 original size:104 final size:104
Alignment explanation
Indices: 45525--45730 Score: 412
Period size: 104 Copynumber: 2.0 Consensus size: 104
45515 ATATATATAT
45525 ATATATATATCAAGTTAAGATGATTATAAAATTGTATTCATTCGAAATATTATTAATCATTTGAT
1 ATATATATATCAAGTTAAGATGATTATAAAATTGTATTCATTCGAAATATTATTAATCATTTGAT
45590 AATGAACGTTCAATCATCTTGTTGTAGTCGTTGGTGTAC
66 AATGAACGTTCAATCATCTTGTTGTAGTCGTTGGTGTAC
45629 ATATATATATCAAGTTAAGATGATTATAAAATTGTATTCATTCGAAATATTATTAATCATTTGAT
1 ATATATATATCAAGTTAAGATGATTATAAAATTGTATTCATTCGAAATATTATTAATCATTTGAT
45694 AATGAACGTTCAATCATCTTGTTGTAGTCGTTGGTGT
66 AATGAACGTTCAATCATCTTGTTGTAGTCGTTGGTGT
45731 TTGAACCCTT
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
104 102 1.00
ACGTcount: A:0.34, C:0.09, G:0.15, T:0.42
Consensus pattern (104 bp):
ATATATATATCAAGTTAAGATGATTATAAAATTGTATTCATTCGAAATATTATTAATCATTTGAT
AATGAACGTTCAATCATCTTGTTGTAGTCGTTGGTGTAC
Found at i:47903 original size:19 final size:19
Alignment explanation
Indices: 47865--47906 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
47855 TCTATTATGT
*
47865 TCATATCATATATCTTATA
1 TCATATCATATATCTCATA
47884 TCATATCATATAAT-TCATA
1 TCATATCATAT-ATCTCATA
47903 TCAT
1 TCAT
47907 TAACATTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 19 0.90
20 2 0.10
ACGTcount: A:0.38, C:0.17, G:0.00, T:0.45
Consensus pattern (19 bp):
TCATATCATATATCTCATA
Found at i:49719 original size:2 final size:2
Alignment explanation
Indices: 49712--49751 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
49702 CCCAAAGGCC
49712 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
49752 GTGTGTGTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52674 original size:35 final size:35
Alignment explanation
Indices: 52647--52716 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
52637 TGTTTATCTC
52647 CTTTTGATCTACTAATGTTTGGAATTGTCGTAGTT
1 CTTTTGATCTACTAATGTTTGGAATTGTCGTAGTT
52682 CTTTTGATCTACTAATGTTTGGAATTGTCGTAGTT
1 CTTTTGATCTACTAATGTTTGGAATTGTCGTAGTT
52717 GTTCTTGGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.20, C:0.11, G:0.20, T:0.49
Consensus pattern (35 bp):
CTTTTGATCTACTAATGTTTGGAATTGTCGTAGTT
Done.