Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007800.1 Hibiscus syriacus cultivar Beakdansim tig00110114_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: 4652821
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 23 of 23
Found at i:4604954 original size:21 final size:21
Alignment explanation
Indices: 4604930--4604971 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
4604920 ACTTCAAGTT
*
4604930 CGATAATTGAAACAAAGTTTA
1 CGATAATTAAAACAAAGTTTA
*
4604951 CGATAATTAAAATAAAGTTTA
1 CGATAATTAAAACAAAGTTTA
4604972 AAAATAAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.31
Consensus pattern (21 bp):
CGATAATTAAAACAAAGTTTA
Found at i:4611194 original size:31 final size:32
Alignment explanation
Indices: 4611145--4611209 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 32
4611135 AATGTAATGC
* *
4611145 TTTGGTCACTTATATTATTTATTTATAA-GTT
1 TTTGGTCACTTACATTATTGATTTATAACGTT
* * *
4611176 TTTGGTTACTTACGTTATTGATTTGTAACGTT
1 TTTGGTCACTTACATTATTGATTTATAACGTT
4611208 TT
1 TT
4611210 GATCACTAGA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 23 0.82
32 5 0.18
ACGTcount: A:0.22, C:0.08, G:0.14, T:0.57
Consensus pattern (32 bp):
TTTGGTCACTTACATTATTGATTTATAACGTT
Found at i:4611308 original size:31 final size:31
Alignment explanation
Indices: 4611273--4611346 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
4611263 ATATTAATGT
* *
4611273 TTAATTTGAA-TCTTATATTTTAGATAAAATA
1 TTAATTT-AACTCTTAAATATTAGATAAAATA
*
4611304 TTAATTTAACTTTTAAATATTAGATAAAATA
1 TTAATTTAACTCTTAAATATTAGATAAAATA
4611335 TTAATTTAACTC
1 TTAATTTAACTC
4611347 ACCAGCTCAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
30 2 0.05
31 36 0.95
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.47
Consensus pattern (31 bp):
TTAATTTAACTCTTAAATATTAGATAAAATA
Found at i:4614095 original size:23 final size:23
Alignment explanation
Indices: 4614069--4614137 Score: 56
Period size: 20 Copynumber: 3.2 Consensus size: 23
4614059 GGAAAACTGT
4614069 AAGGCTTACCCTTGCACACAGCA
1 AAGGCTTACCCTTGCACACAGCA
* * * * * *
4614092 AAGG---AACCTGGGAAACTG-T
1 AAGGCTTACCCTTGCACACAGCA
4614111 AAGGCTTACCCTTGCACACAGCA
1 AAGGCTTACCCTTGCACACAGCA
4614134 AAGG
1 AAGG
4614138 AACCTGGGAA
Statistics
Matches: 30, Mismatches: 12, Indels: 8
0.60 0.24 0.16
Matches are distributed among these distances:
19 4 0.13
20 9 0.30
22 9 0.30
23 8 0.27
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (23 bp):
AAGGCTTACCCTTGCACACAGCA
Found at i:4614165 original size:43 final size:43
Alignment explanation
Indices: 4614045--4614186 Score: 241
Period size: 43 Copynumber: 3.3 Consensus size: 43
4614035 GCTTAACCTA
* * *
4614045 AGCAGAGGAGCCTAGGAAAACTGTAAGGCTTACCCTTGCACAC
1 AGCAAAGGAACCTGGGAAAACTGTAAGGCTTACCCTTGCACAC
4614088 AGCAAAGGAACCTGGG-AAACTGTAAGGCTTACCCTTGCACAC
1 AGCAAAGGAACCTGGGAAAACTGTAAGGCTTACCCTTGCACAC
4614130 AGCAAAGGAACCTGGGAAAACTGTAAGGCTTACCCTTGCACAC
1 AGCAAAGGAACCTGGGAAAACTGTAAGGCTTACCCTTGCACAC
*
4614173 AACAAAGGAACCTG
1 AGCAAAGGAACCTG
4614187 TAATACTTCC
Statistics
Matches: 94, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
42 42 0.45
43 52 0.55
ACGTcount: A:0.35, C:0.25, G:0.24, T:0.15
Consensus pattern (43 bp):
AGCAAAGGAACCTGGGAAAACTGTAAGGCTTACCCTTGCACAC
Found at i:4614879 original size:18 final size:18
Alignment explanation
Indices: 4614838--4614880 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
4614828 GGTCAACGAT
* *
4614838 GGGTCAGGTCATCGGGTC
1 GGGTCGGGTCAACGGGTC
4614856 GGGTCGGGTCAACGGGTC
1 GGGTCGGGTCAACGGGTC
4614874 GGGTCGG
1 GGGTCGG
4614881 TTAAACAGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.09, C:0.21, G:0.51, T:0.19
Consensus pattern (18 bp):
GGGTCGGGTCAACGGGTC
Found at i:4617300 original size:25 final size:29
Alignment explanation
Indices: 4617241--4617301 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 29
4617231 AAAATATTCG
*
4617241 AATAACATTTAAATAAAGAAATATGATGGA
1 AATAA-ATTCAAATAAAGAAATATGATGGA
4617271 AATAAATTCAAAT-AA-AAATATG-T-GA
1 AATAAATTCAAATAAAGAAATATGATGGA
4617296 AATAAA
1 AATAAA
4617302 ATATTTACAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 8 0.27
26 1 0.03
27 7 0.23
28 2 0.07
29 7 0.23
30 5 0.17
ACGTcount: A:0.61, C:0.03, G:0.10, T:0.26
Consensus pattern (29 bp):
AATAAATTCAAATAAAGAAATATGATGGA
Found at i:4617508 original size:30 final size:29
Alignment explanation
Indices: 4617439--4617536 Score: 92
Period size: 29 Copynumber: 3.3 Consensus size: 29
4617429 CAAAAACTTG
* *
4617439 AGGACAAAAATAGC-AAAA-TAGAAACTTAA
1 AGGACTAAAATAACAAAAACTA-AAA-TTAA
* *
4617468 GGGACTAAAATAACAAAAACATAAAGTTAA
1 AGGACTAAAATAACAAAAAC-TAAAATTAA
* * *
4617498 AGGATTAAAATATCAAAAACTAAAACTAA
1 AGGACTAAAATAACAAAAACTAAAATTAA
4617527 AGGACTAAAA
1 AGGACTAAAA
4617537 CTAAAATATC
Statistics
Matches: 56, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
29 27 0.48
30 25 0.45
31 2 0.04
32 2 0.04
ACGTcount: A:0.61, C:0.10, G:0.12, T:0.16
Consensus pattern (29 bp):
AGGACTAAAATAACAAAAACTAAAATTAA
Found at i:4617527 original size:29 final size:30
Alignment explanation
Indices: 4617460--4617536 Score: 93
Period size: 30 Copynumber: 2.6 Consensus size: 30
4617450 AGCAAAATAG
*
4617460 AAACTTAAGGGACTAAAATAACAAAAACATA
1 AAAC-TAAAGGACTAAAATAACAAAAACATA
** * *
4617491 AAGTTAAAGGATTAAAATATCAAAAAC-TA
1 AAACTAAAGGACTAAAATAACAAAAACATA
4617520 AAACTAAAGGACTAAAA
1 AAACTAAAGGACTAAAA
4617537 CTAAAATATC
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
29 16 0.42
30 20 0.53
31 2 0.05
ACGTcount: A:0.61, C:0.10, G:0.10, T:0.18
Consensus pattern (30 bp):
AAACTAAAGGACTAAAATAACAAAAACATA
Found at i:4617613 original size:12 final size:11
Alignment explanation
Indices: 4617575--4617616 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
4617565 ATTTGATAAT
4617575 GAAAATTG-AA
1 GAAAATTGAAA
4617585 GAAAATTGAAAA
1 GAAAATTG-AAA
*
4617597 AAAAATTGAAA
1 GAAAATTGAAA
4617608 CGAAAATTG
1 -GAAAATTG
4617617 TCATAACCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 8 0.30
11 3 0.11
12 16 0.59
ACGTcount: A:0.62, C:0.02, G:0.17, T:0.19
Consensus pattern (11 bp):
GAAAATTGAAA
Found at i:4618409 original size:25 final size:29
Alignment explanation
Indices: 4618349--4618409 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 29
4618339 AAAATATTCG
*
4618349 AATAATATTTAAATAAAGAAATATGATGGA
1 AATAA-ATTCAAATAAAGAAATATGATGGA
4618379 AATAAATTCAAAT-AA-AAATATG-T-GA
1 AATAAATTCAAATAAAGAAATATGATGGA
4618404 AATAAA
1 AATAAA
4618410 ATATTTACAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 8 0.27
26 1 0.03
27 7 0.23
28 2 0.07
29 7 0.23
30 5 0.17
ACGTcount: A:0.61, C:0.02, G:0.10, T:0.28
Consensus pattern (29 bp):
AATAAATTCAAATAAAGAAATATGATGGA
Found at i:4618613 original size:30 final size:30
Alignment explanation
Indices: 4618572--4618673 Score: 116
Period size: 30 Copynumber: 3.4 Consensus size: 30
4618562 AAATAGAAAC
* *
4618572 TTAAGGGACTAAAATAACAAAAACATAAAG
1 TTAAAGGACTAAAATAACAAAAACATAAAA
*
4618602 TTAAAGGACTAAAATATCAAAAAC-TAAAA
1 TTAAAGGACTAAAATAACAAAAACATAAAA
* ** * *
4618631 CTAAAGGACTAAAACGACAAAAATAGAAAA
1 TTAAAGGACTAAAATAACAAAAACATAAAA
*
4618661 TTAATGGACTAAA
1 TTAAAGGACTAAA
4618674 TTTGTAAAAA
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
29 23 0.38
30 37 0.62
ACGTcount: A:0.60, C:0.11, G:0.12, T:0.18
Consensus pattern (30 bp):
TTAAAGGACTAAAATAACAAAAACATAAAA
Found at i:4618616 original size:59 final size:59
Alignment explanation
Indices: 4618547--4618705 Score: 151
Period size: 59 Copynumber: 2.7 Consensus size: 59
4618537 CAAAAACTTG
* * *
4618547 AGGACAAAAATAGCAAAATAGAAACTTAAGGGACTAAAATAACAAAAACATAAAGTTAA
1 AGGACTAAAATAGCAAAATAGAAACTTAAGGGACTAAAATAACAAAAACAGAAAATTAA
* * ** *
4618606 AGGACTAAAATATCAAAAACTA-AAAC-TAAAGGACTAAAACGACAAAAATAGAAAATTAA
1 AGGACTAAAATAGC-AAAA-TAGAAACTTAAGGGACTAAAATAACAAAAACAGAAAATTAA
* * * * * *
4618665 TGGACTAAATTTGTAAAAACAGAAACTTAAGGAACTAAAAT
1 AGGACTAAAATAG-CAAAATAGAAACTTAAGGGACTAAAAT
4618706 GGTATTAACA
Statistics
Matches: 78, Mismatches: 17, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
58 1 0.01
59 56 0.72
60 19 0.24
61 2 0.03
ACGTcount: A:0.59, C:0.11, G:0.13, T:0.18
Consensus pattern (59 bp):
AGGACTAAAATAGCAAAATAGAAACTTAAGGGACTAAAATAACAAAAACAGAAAATTAA
Found at i:4618635 original size:29 final size:29
Alignment explanation
Indices: 4618547--4618653 Score: 101
Period size: 29 Copynumber: 3.7 Consensus size: 29
4618537 CAAAAACTTG
* *
4618547 AGGACAAAAATAGC-AAAA-TAGAAACTTAA
1 AGGACTAAAATAACAAAAACTA-AAAC-TAA
* **
4618576 GGGACTAAAATAACAAAAACATAAAGTTAA
1 AGGACTAAAATAACAAAAAC-TAAAACTAA
*
4618606 AGGACTAAAATATCAAAAACTAAAACTAA
1 AGGACTAAAATAACAAAAACTAAAACTAA
**
4618635 AGGACTAAAACGACAAAAA
1 AGGACTAAAATAACAAAAA
4618654 TAGAAAATTA
Statistics
Matches: 63, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
29 34 0.54
30 25 0.40
31 2 0.03
32 2 0.03
ACGTcount: A:0.62, C:0.12, G:0.12, T:0.14
Consensus pattern (29 bp):
AGGACTAAAATAACAAAAACTAAAACTAA
Found at i:4619944 original size:18 final size:19
Alignment explanation
Indices: 4619909--4619945 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
4619899 CACGGAATGT
4619909 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
4619929 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
4619946 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:4620113 original size:15 final size:15
Alignment explanation
Indices: 4620093--4620123 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4620083 AATTTCTAAA
4620093 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
4620108 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
4620123 T
1 T
4620124 CTATCTGTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:4622231 original size:23 final size:23
Alignment explanation
Indices: 4622205--4622273 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
4622195 CACCACAGCT
*
4622205 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
4622228 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
4622251 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
4622274 TATAAGGTTG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:4623179 original size:20 final size:20
Alignment explanation
Indices: 4623151--4623196 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
4623141 AAACTATAGT
*
4623151 TTCCTTTAAGTATATAAATC
1 TTCCCTTAAGTATATAAATC
4623171 TTCCCTTAAGTATATAAATC
1 TTCCCTTAAGTATATAAATC
4623191 TTCCCT
1 TTCCCT
4623197 ATAAAACTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.30, C:0.22, G:0.04, T:0.43
Consensus pattern (20 bp):
TTCCCTTAAGTATATAAATC
Found at i:4627586 original size:23 final size:23
Alignment explanation
Indices: 4627560--4627628 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
4627550 CACCACAGCT
*
4627560 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
4627583 CGTAGAATTGCACCGTAGTTCCA
1 CGTAGAAATGCACCGAAGTGCCA
* *
4627606 CATAGAAATGCACCCAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
4627629 TTAAGGTTGT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.33, C:0.28, G:0.20, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:4627905 original size:7 final size:7
Alignment explanation
Indices: 4627893--4627921 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
4627883 TTTCATATAA
4627893 ATCACAT
1 ATCACAT
4627900 ATCACAT
1 ATCACAT
4627907 ATCACAT
1 ATCACAT
4627914 AT-ACAT
1 ATCACAT
4627920 AT
1 AT
4627922 AGACACATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.31
Consensus pattern (7 bp):
ATCACAT
Found at i:4634580 original size:17 final size:17
Alignment explanation
Indices: 4634554--4634590 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
4634544 TTAATATAAT
* *
4634554 AATAATAATAAATTAAA
1 AATAAAAATAAATAAAA
4634571 AATAAAAATAAATAAAA
1 AATAAAAATAAATAAAA
4634588 AAT
1 AAT
4634591 GTTTGGACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
AATAAAAATAAATAAAA
Found at i:4636444 original size:22 final size:22
Alignment explanation
Indices: 4636401--4636447 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
4636391 ATATGCAAAG
*
4636401 AAAAAAAACGAAAATACAAATA
1 AAAAAAAAAGAAAATACAAATA
*
4636423 AAAAAAAGAAGAAAATA-TAATA
1 AAAAAAA-AAGAAAATACAAATA
4636445 AAA
1 AAA
4636448 TATAAATGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.79, C:0.04, G:0.06, T:0.11
Consensus pattern (22 bp):
AAAAAAAAAGAAAATACAAATA
Found at i:4636466 original size:19 final size:19
Alignment explanation
Indices: 4636436--4636491 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
4636426 AAAAGAAGAA
*
4636436 AATATAATAAAATATAAAT
1 AATAAAATAAAATATAAAT
* * *
4636455 GGATAAAA-AAAATACACAT
1 -AATAAAATAAAATATAAAT
4636474 AATAAAATAAAATATAAA
1 AATAAAATAAAATATAAA
4636492 GCAATGAAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
18 6 0.21
19 17 0.61
20 5 0.18
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.23
Consensus pattern (19 bp):
AATAAAATAAAATATAAAT
Found at i:4636713 original size:17 final size:19
Alignment explanation
Indices: 4636693--4636745 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
4636683 TACATATACG
*
4636693 TATATAATAATAAAAAATA
1 TATATAATAATAAATAATA
4636712 TAATATAATAGCATAAATAA-A
1 T-ATATAATA--ATAAATAATA
*
4636733 TAAATAATAATAA
1 TATATAATAATAA
4636746 TAGTAAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
18 4 0.14
19 1 0.03
20 15 0.52
21 2 0.07
22 7 0.24
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (19 bp):
TATATAATAATAAATAATA
Found at i:4636717 original size:20 final size:20
Alignment explanation
Indices: 4636694--4636747 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 20
4636684 ACATATACGT
4636694 ATATAATAATAAA-AAATATA
1 ATATAATAATAAATAAATA-A
4636714 ATATAATAGCATAAATAAATAA
1 ATATAATA--ATAAATAAATAA
4636736 ATAATAATAATA
1 AT-ATAATAATA
4636748 GTAAAAAGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
20 8 0.27
21 3 0.10
22 8 0.27
23 11 0.37
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (20 bp):
ATATAATAATAAATAAATAA
Found at i:4638950 original size:105 final size:105
Alignment explanation
Indices: 4638827--4639286 Score: 911
Period size: 105 Copynumber: 4.4 Consensus size: 105
4638817 GTATTGTTCA
4638827 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
4638892 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
4638932 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
4638997 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
4639037 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
4639102 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
4639142 TAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
4639207 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
4639247 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
4639287 GGTAAAACCT
Statistics
Matches: 353, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
105 353 1.00
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:4640073 original size:53 final size:53
Alignment explanation
Indices: 4640014--4640115 Score: 150
Period size: 53 Copynumber: 1.9 Consensus size: 53
4640004 TCTTTTTTCC
* ** *
4640014 TCTTTTTTCTTTTTTCAATTTAGGGTGCCCTTTCGGGTTTTCACCCTAAACGT
1 TCTTTTTTCTTTTTTCAACTTAGGACGCCCTCTCGGGTTTTCACCCTAAACGT
* *
4640067 TCTTTTTTTTTTTTTCAACTTAGGACGCCCTCTCGGGTTTTCATCCTAA
1 TCTTTTTTCTTTTTTCAACTTAGGACGCCCTCTCGGGTTTTCACCCTAA
4640116 GCGAAGTATT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 43 1.00
ACGTcount: A:0.14, C:0.24, G:0.14, T:0.49
Consensus pattern (53 bp):
TCTTTTTTCTTTTTTCAACTTAGGACGCCCTCTCGGGTTTTCACCCTAAACGT
Found at i:4649483 original size:20 final size:20
Alignment explanation
Indices: 4649445--4649488 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
4649435 ATGGTTAGTA
*
4649445 AAATAAAAATAAATGGAAAT
1 AAATAAAAATAAATAGAAAT
4649465 AAATAAAAATAACA-AGAAAT
1 AAATAAAAATAA-ATAGAAAT
4649485 AAAT
1 AAAT
4649489 GGCAATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 21 0.95
21 1 0.05
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.18
Consensus pattern (20 bp):
AAATAAAAATAAATAGAAAT
Found at i:4650577 original size:19 final size:19
Alignment explanation
Indices: 4650547--4650602 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
4650537 AAAAGAAGAA
*
4650547 AATATAATAAAATATAAAT
1 AATAAAATAAAATATAAAT
* * *
4650566 GGATAAAA-AAAATACACAT
1 -AATAAAATAAAATATAAAT
4650585 AATAAAATAAAATATAAA
1 AATAAAATAAAATATAAA
4650603 GCAATGAAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
18 6 0.21
19 17 0.61
20 5 0.18
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.23
Consensus pattern (19 bp):
AATAAAATAAAATATAAAT
Found at i:4650631 original size:14 final size:14
Alignment explanation
Indices: 4650609--4650638 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
4650599 TAAAGCAATG
*
4650609 AAAATGAAAAAAAA
1 AAAAAGAAAAAAAA
4650623 AAAAAGAAAAAAAA
1 AAAAAGAAAAAAAA
4650637 AA
1 AA
4650639 TATGCGTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.90, C:0.00, G:0.07, T:0.03
Consensus pattern (14 bp):
AAAAAGAAAAAAAA
Found at i:4650822 original size:18 final size:19
Alignment explanation
Indices: 4650799--4650847 Score: 66
Period size: 18 Copynumber: 2.6 Consensus size: 19
4650789 ACATATACGT
4650799 ATATAATAATAAA-AAATA
1 ATATAATAATAAATAAATA
4650817 ATATAATAGCATAAATAAATA
1 ATATAATA--ATAAATAAATA
4650838 A-ATAATAATA
1 ATATAATAATA
4650848 GTAAAAAGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 11 0.39
20 11 0.39
21 6 0.21
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (19 bp):
ATATAATAATAAATAAATA
Done.