Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006523.1 Hibiscus syriacus cultivar Beakdansim tig00015898_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: 55586
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.33
Found at i:9724 original size:29 final size:31
Alignment explanation
Indices: 9657--9730 Score: 82
Period size: 29 Copynumber: 2.5 Consensus size: 31
9647 AAAATTACCC
* * *
9657 TTTTGGTCCCTAAACTTTTCTAAAGTTTATA
1 TTTTGGTCACTAAACTTTTCTAAAATTTACA
* *
9688 ATTT-GTCACAAAAC-TTTC-AAAATTTACA
1 TTTTGGTCACTAAACTTTTCTAAAATTTACA
9716 TTTTGGTCACTAAAC
1 TTTTGGTCACTAAAC
9731 AAAATTTTGG
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
28 11 0.31
29 13 0.37
30 8 0.23
31 3 0.09
ACGTcount: A:0.32, C:0.18, G:0.08, T:0.42
Consensus pattern (31 bp):
TTTTGGTCACTAAACTTTTCTAAAATTTACA
Found at i:11372 original size:46 final size:45
Alignment explanation
Indices: 11306--11477 Score: 265
Period size: 46 Copynumber: 3.8 Consensus size: 45
11296 GATAAAATCT
*
11306 CTTACCATTTATCCTATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
11351 CTTACCATTTAATCCCATAAGCTCGTAAGCTTATTATACCCAAATA
1 CTTACCATTT-ATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
*
11397 CTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTT-ATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
11443 CTTGCCA-TTATTCCATAAGCTCGTAAGCTTATTTT
1 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTT
11478 CCAGTTTATC
Statistics
Matches: 118, Mismatches: 8, Indels: 3
0.91 0.06 0.02
Matches are distributed among these distances:
44 25 0.21
45 12 0.10
46 81 0.69
ACGTcount: A:0.31, C:0.24, G:0.08, T:0.37
Consensus pattern (45 bp):
CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:15586 original size:20 final size:19
Alignment explanation
Indices: 15554--15600 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
15544 CATCTCTCAT
*
15554 TTTTTTCTCTTTTC-CTTTC
1 TTTTTTCTATTTTCTC-TTC
*
15573 TTTTTTCTAATTTTTTCTTC
1 TTTTTTCT-ATTTTCTCTTC
15593 TTTTTTCT
1 TTTTTTCT
15601 GTTTCATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 8 0.33
20 15 0.62
21 1 0.04
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTTTTCTATTTTCTCTTC
Found at i:18379 original size:44 final size:45
Alignment explanation
Indices: 18257--18382 Score: 182
Period size: 46 Copynumber: 2.8 Consensus size: 45
18247 GATAAAATTT
*
18257 CTTACCATTTATCCCATAAGCTTGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
18302 CTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTAGCAATATA
1 CTTACCATTT-ATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
** *
18348 CTTGTCA-TTATTCCATAAGCTCGTAAGCTTATTTT
1 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTT
18383 CCAGTTTATC
Statistics
Matches: 74, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
44 25 0.34
45 12 0.16
46 37 0.50
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:22782 original size:13 final size:13
Alignment explanation
Indices: 22766--22820 Score: 62
Period size: 12 Copynumber: 4.4 Consensus size: 13
22756 CATAATGAAA
*
22766 ATAAATAAATAGT
1 ATAAATAAATAAT
22779 ATAAATAAAATAAT
1 ATAAAT-AAATAAT
22793 A-AAATAAA-AAT
1 ATAAATAAATAAT
*
22804 ATATATAAA-AAT
1 ATAAATAAATAAT
22816 ATAAA
1 ATAAA
22821 AATGTATGTA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
11 4 0.11
12 16 0.43
13 10 0.27
14 7 0.19
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (13 bp):
ATAAATAAATAAT
Found at i:22806 original size:25 final size:26
Alignment explanation
Indices: 22768--22821 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
22758 TAATGAAAAT
*
22768 AAATAAATAGTATAAAT-AAAATAATA
1 AAATAAATAATATAAATAAAAAT-ATA
*
22794 AAATAAA-AATATATATAAAAATATA
1 AAATAAATAATATAAATAAAAATATA
22819 AAA
1 AAA
22822 ATGTATGTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 13 0.52
26 12 0.48
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (26 bp):
AAATAAATAATATAAATAAAAATATA
Found at i:23023 original size:2 final size:2
Alignment explanation
Indices: 23018--23072 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
23008 ATAAAAAATA
23018 AT 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 AT
23060 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
23073 ATAGGAAAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:23138 original size:23 final size:23
Alignment explanation
Indices: 23104--23150 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
23094 ACGTAAAGAA
23104 AAATGAAAAAAATTATAA-TAAAT
1 AAATGAAAAAAA-TATAATTAAAT
23127 AAAT-AAATAAAATATAATTAAAT
1 AAATGAAA-AAAATATAATTAAAT
23150 A
1 A
23151 TATATATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (23 bp):
AAATGAAAAAAATATAATTAAAT
Found at i:23666 original size:37 final size:37
Alignment explanation
Indices: 23568--23669 Score: 132
Period size: 37 Copynumber: 2.8 Consensus size: 37
23558 ATGCTTATGG
* ** * *
23568 ATCCTATCTTTAGGAGTTTAAATAATAGTAGAACTAT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGCAAAACTAT
* * *
23605 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGCAAAACTAT
23642 ATCCTATTTTTAGGAGTTTAAATCCTAG
1 ATCCTATTTTTAGGAGTTTAAATCCTAG
23670 TACGACGAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATCCTAGCAAAACTAT
Found at i:24678 original size:106 final size:106
Alignment explanation
Indices: 24422--26440 Score: 3124
Period size: 106 Copynumber: 19.0 Consensus size: 106
24412 GCATTGTTCC
* * * * *
24422 GAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAATCGGGAAATTGCTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
* * * *
24486 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGGTTGTCTC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG-CGTTGTCTG
* * * * *
24529 GAGTCCAATATCATTTGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
24594 CCAGCGTTCCCTTTGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
24635 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
24700 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
24741 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
** *
24806 CCAGTAGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
24847 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTAACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
24912 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
24953 GAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
25018 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGAGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** *
25059 GAGTCCAATATCCTTCTATGTGAAGTTGAAATTGGCTCTGAAATTAGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
25124 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
25165 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
25230 CCAGCGGTTCCTTCGTCGTAAAGTTGAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
25271 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTATGAAATTGGGAAGTTCTTTATTGATAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
25336 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
25377 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
25442 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
25483 GAGTCCAATATCCTTCG-TCGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
** *
25547 ACCAGTAGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
25589 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTAACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
25654 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * **
25695 GAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTAATTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
25760 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGAGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** *
25801 GAGTCCAATATCCTTCTATGTGAAGTTGAAATTGGCTCTGAAATTAGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
25866 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
25907 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
25972 CCAGCGGTTCCTTCGTCGTAAAGTTGAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
26013 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTATGAAATTGGGAAGTTCTTTATTGATAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
26078 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
26119 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
26184 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGAGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
26225 GAGTCCAATATCCTTCGTTGTGAAGTTGAAAATGGCTCTGAAATTGAGAAGTTGTTTGTTGAGAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
26290 CCAGCGGTCCCTTCATCATGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
26331 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATTTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* ** * * *
26396 CCAACCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
26437 GAGT
1 GAGT
26441 GGCACGATAT
Statistics
Matches: 1758, Mismatches: 151, Indels: 7
0.92 0.08 0.00
Matches are distributed among these distances:
105 1 0.00
106 1671 0.95
107 85 0.05
108 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:27431 original size:22 final size:22
Alignment explanation
Indices: 27405--27457 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
27395 GTGTTTGGTC
27405 AAAGGTTTGGCATTTGATGCTA
1 AAAGGTTTGGCATTTGATGCTA
*
27427 AAAGGTTTGGCATTTGATGCTC
1 AAAGGTTTGGCATTTGATGCTA
27449 AAAGGTTTG
1 AAAGGTTTG
27458 ATGGGGTAGC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.26, C:0.09, G:0.28, T:0.36
Consensus pattern (22 bp):
AAAGGTTTGGCATTTGATGCTA
Found at i:28086 original size:15 final size:15
Alignment explanation
Indices: 28074--28125 Score: 65
Period size: 16 Copynumber: 3.5 Consensus size: 15
28064 TTATTTTTTA
28074 TTTTTGTTC-TTT-T
1 TTTTTGTTCTTTTCT
28087 TTTTTGTT-TTCTTCT
1 TTTTTGTTCTT-TTCT
28102 TTTTTGCTTCTTTTCT
1 TTTTTG-TTCTTTTCT
28118 TTTTTGTT
1 TTTTTGTT
28126 TTTGCCCTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
13 9 0.26
14 2 0.06
15 9 0.26
16 12 0.35
17 2 0.06
ACGTcount: A:0.00, C:0.12, G:0.08, T:0.81
Consensus pattern (15 bp):
TTTTTGTTCTTTTCT
Found at i:28088 original size:18 final size:18
Alignment explanation
Indices: 28075--28129 Score: 58
Period size: 18 Copynumber: 3.0 Consensus size: 18
28065 TATTTTTTAT
*
28075 TTTTGTTCTTTTTTTTTG
1 TTTTCTTCTTTTTTTTTG
* *
28093 TTTTCTTCTTTTTTGCTTC
1 TTTTCTTCTTTTTT-TTTG
28112 TTTTCTT-TTTTGTTTTTG
1 TTTTCTTCTTTT-TTTTTG
28130 CCCTTTTTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
18 19 0.63
19 11 0.37
ACGTcount: A:0.00, C:0.11, G:0.09, T:0.80
Consensus pattern (18 bp):
TTTTCTTCTTTTTTTTTG
Found at i:32238 original size:42 final size:42
Alignment explanation
Indices: 32177--32287 Score: 159
Period size: 42 Copynumber: 2.6 Consensus size: 42
32167 GGGAGAAGGC
32177 AAAGCCATGGAATTTAATAATTAAAGCACTATGGAATAAGAA
1 AAAGCCATGGAATTTAATAATTAAAGCACTATGGAATAAGAA
* * * * * *
32219 AAAGCCATGAAATTCAATAATTAAAGTATTATGGAATAATAC
1 AAAGCCATGGAATTTAATAATTAAAGCACTATGGAATAAGAA
*
32261 AAAGCCATGGACTTTAATAATTAAAGC
1 AAAGCCATGGAATTTAATAATTAAAGC
32288 TTTATAATAG
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 59 1.00
ACGTcount: A:0.49, C:0.11, G:0.14, T:0.26
Consensus pattern (42 bp):
AAAGCCATGGAATTTAATAATTAAAGCACTATGGAATAAGAA
Found at i:34809 original size:39 final size:37
Alignment explanation
Indices: 34766--34848 Score: 96
Period size: 37 Copynumber: 2.2 Consensus size: 37
34756 GAGCAAGATG
34766 AATTTTTGTCTTTAAG-AAAACAAATCTCAAGTAAGAAAA
1 AATTTTTGTC--TAAGAAAAAC-AATCTCAAGTAAGAAAA
* * *
34805 AATTTGTGTCTAAGAAAAACAATCTCAAGTGAGATAA
1 AATTTTTGTCTAAGAAAAACAATCTCAAGTAAGAAAA
*
34842 GATTTTT
1 AATTTTT
34849 TTTACTAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
37 24 0.63
38 5 0.13
39 9 0.24
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.33
Consensus pattern (37 bp):
AATTTTTGTCTAAGAAAAACAATCTCAAGTAAGAAAA
Found at i:35216 original size:116 final size:116
Alignment explanation
Indices: 35033--35333 Score: 354
Period size: 116 Copynumber: 2.6 Consensus size: 116
35023 ATTGAAAAAG
** * ** * * * * * **
35033 TTCTCATTATAAACTTCTTATCCATTATTGGACTAGTTTTTCTCATTATGAACCCATCTGTTGGA
1 TTCTCATTAGGAACTTCTTCTCCCGTATCGGACGAGTTCTTCTCATTATGAATCCTTCCATTGGA
* * * *
35098 AAT-TCTAAACGACCTTCTTCTGTGATGGACGTGTCAAAGTTGAACAAGTTC
66 AATGT-TAAACCACCTCCTTCTGTGATGGACGAGTCAAAGATGAACAAGTTC
* *
35149 TTCTTATTAGGAACTTCTTCTCCC-TAATCGGACGAGTTCTTCTCATTTTGAATCCTTCCATTGG
1 TTCTCATTAGGAACTTCTTCTCCCGT-ATCGGACGAGTTCTTCTCATTATGAATCCTTCCATTGG
* * *
35213 AAATGTTGATCCACCTCCTTCTGTGATGGACGAGTCAAGGATGAACAAGTTC
65 AAATGTTAAACCACCTCCTTCTGTGATGGACGAGTCAAAGATGAACAAGTTC
* * *
35265 TTCTCATTAGGAACTTTTTCTCCCGTATCGGATGAGTTGTTCTCATTATGAATCCTTCCATTGGA
1 TTCTCATTAGGAACTTCTTCTCCCGTATCGGACGAGTTCTTCTCATTATGAATCCTTCCATTGGA
35330 AATG
66 AATG
35334 ATTGGTCTAT
Statistics
Matches: 157, Mismatches: 25, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
115 1 0.01
116 154 0.98
117 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (116 bp):
TTCTCATTAGGAACTTCTTCTCCCGTATCGGACGAGTTCTTCTCATTATGAATCCTTCCATTGGA
AATGTTAAACCACCTCCTTCTGTGATGGACGAGTCAAAGATGAACAAGTTC
Found at i:36216 original size:20 final size:20
Alignment explanation
Indices: 36191--36236 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
36181 ACCTGGACCG
*
36191 TTGATCGTTGACCATTGACT
1 TTGATCGTTGACCATTAACT
* *
36211 TTGATCGTTGATCGTTAACT
1 TTGATCGTTGACCATTAACT
36231 TTGATC
1 TTGATC
36237 TTTAACTGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (20 bp):
TTGATCGTTGACCATTAACT
Found at i:38446 original size:17 final size:17
Alignment explanation
Indices: 38407--38447 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
38397 TCTAAAGATG
38407 TGAAGGTTTGAAAGTCT
1 TGAAGGTTTGAAAGTCT
* * *
38424 TAAAGGTTTGAAGGTTT
1 TGAAGGTTTGAAAGTCT
38441 TGAAGGT
1 TGAAGGT
38448 CGTGCATTGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.29, C:0.02, G:0.32, T:0.37
Consensus pattern (17 bp):
TGAAGGTTTGAAAGTCT
Found at i:40846 original size:6 final size:6
Alignment explanation
Indices: 40826--40875 Score: 64
Period size: 6 Copynumber: 8.2 Consensus size: 6
40816 GACACGTATT
* **
40826 ACCACG ACCACCG ACCACG ACCTCG ACCTTG ACCACG ACCACG ACCACG
1 ACCACG ACCA-CG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
40875 A
1 A
40876 GCCGAGCCAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
6 33 0.85
7 6 0.15
ACGTcount: A:0.30, C:0.48, G:0.16, T:0.06
Consensus pattern (6 bp):
ACCACG
Found at i:46747 original size:5 final size:5
Alignment explanation
Indices: 46737--46815 Score: 70
Period size: 5 Copynumber: 15.8 Consensus size: 5
46727 ACCACGACCA
* * * *
46737 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CAAGC CAAGC CGTA-C CGTGT
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CG-AGC CGAGC
* * * *
46787 CGTGC CGTGC CGAGC CGAGA CGAGA CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
46816 ACGGACGGAC
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
5 64 0.98
6 1 0.02
ACGTcount: A:0.22, C:0.35, G:0.37, T:0.06
Consensus pattern (5 bp):
CGAGC
Found at i:48416 original size:6 final size:6
Alignment explanation
Indices: 48405--48435 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
48395 TCCATTGCTC
48405 ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG A
48436 GCCGAGCCGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.35, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:48443 original size:5 final size:5
Alignment explanation
Indices: 48433--48471 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
48423 ACCACGACCA
* * *
48433 CGAGC CGAGC CGAGC CGTGC CGAGC CGAGA CGAGA CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
48472 GACGGACGGC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.23, C:0.33, G:0.41, T:0.03
Consensus pattern (5 bp):
CGAGC
Done.