Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001946.1 Hibiscus syriacus cultivar Beakdansim tig00003940_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: 77466
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:19182 original size:59 final size:61
Alignment explanation
Indices: 19113--19283 Score: 174
Period size: 60 Copynumber: 2.9 Consensus size: 61
19103 TTTATAGTCT
* * **
19113 TCAAATTATGATCCTCAGTT-GAAATTAGTCCTTAAACTT-T-AAATATTTTAAATTCAACC-
1 TCAAACTATGATCCTCA-TTCTAAATTAGTCCTTAAACTTATGAAA-ATTCCAAATTCAACCA
** *
19172 TCAAACTATGATTTTCATTCTAAATTAGTCCTTAAACTTATGAAAATTCCAAATTCATCCA
1 TCAAACTATGATCCTCATTCTAAATTAGTCCTTAAACTTATGAAAATTCCAAATTCAACCA
* * * *
19233 T-AAACTATGACCCTCATTCTAAATTAGTCTCCT-AACTTTTGAACATTCCAA
1 TCAAACTATGATCCTCATTCTAAATTAGTC-CTTAAACTTATGAAAATTCCAA
19284 TAACTTCCCC
Statistics
Matches: 94, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
58 2 0.02
59 32 0.34
60 54 0.57
61 6 0.06
ACGTcount: A:0.36, C:0.20, G:0.06, T:0.37
Consensus pattern (61 bp):
TCAAACTATGATCCTCATTCTAAATTAGTCCTTAAACTTATGAAAATTCCAAATTCAACCA
Found at i:19419 original size:59 final size:60
Alignment explanation
Indices: 19322--19476 Score: 165
Period size: 59 Copynumber: 2.6 Consensus size: 60
19312 TGGAGATAAC
* * * *
19322 ATTAAAATATTAAAAAGTTTGGGGA-TCAATATAGAATGAGGGCCACAGTTT-GAGGATG-A
1 ATTAAAATATTCAAAAGTTTAGGGACT-AATTTAGAATGAGAGCCACAGTTTAG-GGATGAA
* ** * * *
19381 ATTCATAAT-TTTTAAATTTTAGGGACTAATTTAGAATGAGAGTCATAGTTTAGGGATGAA
1 ATT-AAAATATTCAAAAGTTTAGGGACTAATTTAGAATGAGAGCCACAGTTTAGGGATGAA
19441 ATTAAAATATTCAAAAGTTTAGGGACTAATTTAGAA
1 ATTAAAATATTCAAAAGTTTAGGGACTAATTTAGAA
19477 CAAGGTTCGT
Statistics
Matches: 78, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
59 44 0.56
60 34 0.44
ACGTcount: A:0.41, C:0.06, G:0.21, T:0.33
Consensus pattern (60 bp):
ATTAAAATATTCAAAAGTTTAGGGACTAATTTAGAATGAGAGCCACAGTTTAGGGATGAA
Found at i:19498 original size:60 final size:59
Alignment explanation
Indices: 19368--19498 Score: 142
Period size: 60 Copynumber: 2.2 Consensus size: 59
19358 TGAGGGCCAC
* ** * **
19368 AGTTTGAGGATGAATTCATAATTTTTAAATTTTAGGGACTAATTTAGAATGAGAGTCAT
1 AGTTTGAGGATGAATTCAAAATTTCAAAAGTTTAGGGACTAATTTAGAACAAGAGTCAT
*
19427 AGTTT-AGGGATGAAATT-AAAATATTCAAAAGTTTAGGGACTAATTTAGAACAAG-GTTCGT
1 AGTTTGA-GGATG-AATTCAAAAT-TTCAAAAGTTTAGGGACTAATTTAGAACAAGAG-TCAT
19487 AGTTTGAGGATG
1 AGTTTGAGGATG
19499 CATAGTGCAA
Statistics
Matches: 60, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
58 1 0.02
59 15 0.25
60 43 0.72
61 1 0.02
ACGTcount: A:0.37, C:0.05, G:0.23, T:0.35
Consensus pattern (59 bp):
AGTTTGAGGATGAATTCAAAATTTCAAAAGTTTAGGGACTAATTTAGAACAAGAGTCAT
Found at i:37657 original size:49 final size:49
Alignment explanation
Indices: 37597--37694 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
37587 CAAAACTTAC
37597 TTCAGTAAGAATAATTCTGAATCAGGTTACATTGGTAATAGAGGAGAGT
1 TTCAGTAAGAATAATTCTGAATCAGGTTACATTGGTAATAGAGGAGAGT
37646 TTCAGTAAGAATAATTCTGAATCAGGTTACATTGGTAATAGAGGAGAGT
1 TTCAGTAAGAATAATTCTGAATCAGGTTACATTGGTAATAGAGGAGAGT
37695 AAGAAATATA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.37, C:0.08, G:0.24, T:0.31
Consensus pattern (49 bp):
TTCAGTAAGAATAATTCTGAATCAGGTTACATTGGTAATAGAGGAGAGT
Found at i:47662 original size:2 final size:2
Alignment explanation
Indices: 47657--47692 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
47647 GGTTCATACG
47657 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
47693 GCAAAAATCG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48351 original size:30 final size:28
Alignment explanation
Indices: 48272--48351 Score: 81
Period size: 30 Copynumber: 2.8 Consensus size: 28
48262 TATTTCATAC
*
48272 TCAGAAATCAGATACAAAA-ATACAATAA
1 TCAGATATCAGATA-AAAATATACAATAA
* * *
48300 TCAGATATCATATCAGAAATATACAGTAAA
1 TCAGATATCAGAT-AAAAATATACAAT-AA
48330 TCAGATATCAGATAAACAATAT
1 TCAGATATCAGATAAA-AATAT
48352 TTAGAAAATC
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
28 14 0.33
29 9 0.21
30 19 0.45
ACGTcount: A:0.54, C:0.14, G:0.09, T:0.24
Consensus pattern (28 bp):
TCAGATATCAGATAAAAATATACAATAA
Found at i:48685 original size:16 final size:16
Alignment explanation
Indices: 48620--48678 Score: 109
Period size: 16 Copynumber: 3.7 Consensus size: 16
48610 CATTTAATAA
48620 ATAAACGAACACGAAC
1 ATAAACGAACACGAAC
48636 ATAAACGAACACGAAC
1 ATAAACGAACACGAAC
*
48652 ATAAATGAACACGAAC
1 ATAAACGAACACGAAC
48668 ATAAACGAACA
1 ATAAACGAACA
48679 TAAACATTGG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.58, C:0.22, G:0.12, T:0.08
Consensus pattern (16 bp):
ATAAACGAACACGAAC
Found at i:48685 original size:32 final size:32
Alignment explanation
Indices: 48620--48685 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
48610 CATTTAATAA
*
48620 ATAAACGAACACGAACATAAACGAACACGAAC
1 ATAAACGAACACGAACATAAACGAACACAAAC
* *
48652 ATAAATGAACACGAACATAAACGAACATAAAC
1 ATAAACGAACACGAACATAAACGAACACAAAC
48684 AT
1 AT
48686 TGGAGACCCT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.58, C:0.21, G:0.11, T:0.11
Consensus pattern (32 bp):
ATAAACGAACACGAACATAAACGAACACAAAC
Found at i:49624 original size:10 final size:10
Alignment explanation
Indices: 49609--49667 Score: 64
Period size: 10 Copynumber: 5.5 Consensus size: 10
49599 ATAAATGAAT
49609 GAACATAAAC
1 GAACATAAAC
*
49619 GAACATAACC
1 GAACATAAAC
49629 GAACATAACTGAAC
1 GAACAT-A---AAC
49643 GAACATAAAC
1 GAACATAAAC
*
49653 GAACATAACC
1 GAACATAAAC
49663 GAACA
1 GAACA
49668 AACATAACCG
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
10 32 0.76
11 1 0.02
13 1 0.02
14 8 0.19
ACGTcount: A:0.54, C:0.24, G:0.12, T:0.10
Consensus pattern (10 bp):
GAACATAAAC
Found at i:49643 original size:24 final size:24
Alignment explanation
Indices: 49616--49680 Score: 103
Period size: 24 Copynumber: 2.7 Consensus size: 24
49606 AATGAACATA
*
49616 AACGAACATAACCGAACATAACTG
1 AACGAACATAACCGAACATAACCG
*
49640 AACGAACATAAACGAACATAACCG
1 AACGAACATAACCGAACATAACCG
*
49664 AACAAACATAACCGAAC
1 AACGAACATAACCGAAC
49681 GTTCACGAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.54, C:0.26, G:0.11, T:0.09
Consensus pattern (24 bp):
AACGAACATAACCGAACATAACCG
Found at i:49647 original size:14 final size:14
Alignment explanation
Indices: 49628--49681 Score: 62
Period size: 14 Copynumber: 4.1 Consensus size: 14
49618 CGAACATAAC
*
49628 CGAACATAACTGAA
1 CGAACATAACCGAA
49642 CGAACAT-A---AA
1 CGAACATAACCGAA
49652 CGAACATAACCGAA
1 CGAACATAACCGAA
*
49666 CAAACATAACCGAA
1 CGAACATAACCGAA
49680 CG
1 CG
49682 TTCACGAACG
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
10 9 0.26
11 1 0.03
13 1 0.03
14 23 0.68
ACGTcount: A:0.52, C:0.26, G:0.13, T:0.09
Consensus pattern (14 bp):
CGAACATAACCGAA
Found at i:49680 original size:34 final size:34
Alignment explanation
Indices: 49596--49667 Score: 126
Period size: 34 Copynumber: 2.1 Consensus size: 34
49586 GATTGGGTTA
* *
49596 AACATAAATGAATGAACATAAACGAACATAACCG
1 AACATAACTGAACGAACATAAACGAACATAACCG
49630 AACATAACTGAACGAACATAAACGAACATAACCG
1 AACATAACTGAACGAACATAAACGAACATAACCG
49664 AACA
1 AACA
49668 AACATAACCG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.56, C:0.21, G:0.11, T:0.12
Consensus pattern (34 bp):
AACATAACTGAACGAACATAAACGAACATAACCG
Found at i:55524 original size:21 final size:21
Alignment explanation
Indices: 55499--55552 Score: 90
Period size: 21 Copynumber: 2.5 Consensus size: 21
55489 TAAAATTAAC
55499 AGTAAAGGAACCTTTTCATCA
1 AGTAAAGGAACCTTTTCATCA
55520 AGTAAAGGAACCTTTTCATCA
1 AGTAAAGGAACCTTTTCATCA
*
55541 TGTAAAGAGAAC
1 AGTAAAG-GAAC
55553 AAAATCTCTG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 27 0.87
22 4 0.13
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.26
Consensus pattern (21 bp):
AGTAAAGGAACCTTTTCATCA
Found at i:55647 original size:4 final size:4
Alignment explanation
Indices: 55638--55663 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
55628 CTACTTTTAT
55638 GAAA GAAA GAAA GAAA GAAA GAAA GA
1 GAAA GAAA GAAA GAAA GAAA GAAA GA
55664 CAACATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:58752 original size:22 final size:22
Alignment explanation
Indices: 58724--58767 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
58714 AATATTAGAC
*
58724 GTAGAATATGATGTGATAATCA
1 GTAGAATAGGATGTGATAATCA
*
58746 GTAGAATGGGATGTGATAATCA
1 GTAGAATAGGATGTGATAATCA
58768 ATAAAAATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.39, C:0.05, G:0.27, T:0.30
Consensus pattern (22 bp):
GTAGAATAGGATGTGATAATCA
Found at i:67269 original size:30 final size:30
Alignment explanation
Indices: 67235--67296 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 30
67225 AACCAAGTTT
67235 ACGAGTCA-AGACGAGCAACAAAATATTTTA
1 ACGAGT-AGAGACGAGCAACAAAATATTTTA
* *
67265 ACGAGTATGAGTCGAGCAATAAAATATTTTA
1 ACGAGTA-GAGACGAGCAACAAAATATTTTA
67296 A
1 A
67297 TGAGCACTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 1 0.04
30 6 0.21
31 21 0.75
ACGTcount: A:0.45, C:0.13, G:0.18, T:0.24
Consensus pattern (30 bp):
ACGAGTAGAGACGAGCAACAAAATATTTTA
Found at i:67311 original size:31 final size:31
Alignment explanation
Indices: 67246--67311 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
67236 CGAGTCAAGA
* *
67246 CGAGCAACAAAATATTTTAACGAGTATGAGT
1 CGAGCAACAAAATATTTTAACGAGCATGAAT
* *
67277 CGAGCAATAAAATATTTTAATGAGCACT-AAT
1 CGAGCAACAAAATATTTTAACGAGCA-TGAAT
67308 CGAG
1 CGAG
67312 TTGTAACACC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 29 0.97
32 1 0.03
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.26
Consensus pattern (31 bp):
CGAGCAACAAAATATTTTAACGAGCATGAAT
Found at i:70621 original size:30 final size:30
Alignment explanation
Indices: 70585--70660 Score: 143
Period size: 30 Copynumber: 2.5 Consensus size: 30
70575 TCGTACCCTG
70585 ACCGAACTAATTCGGTGGCCGACCGAATTA
1 ACCGAACTAATTCGGTGGCCGACCGAATTA
*
70615 ACCGAACTAATTCGGTGGCCGGCCGAATTA
1 ACCGAACTAATTCGGTGGCCGACCGAATTA
70645 ACCGAACTAATTCGGT
1 ACCGAACTAATTCGGT
70661 TCTGTCGGTT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.29, C:0.26, G:0.24, T:0.21
Consensus pattern (30 bp):
ACCGAACTAATTCGGTGGCCGACCGAATTA
Found at i:72025 original size:43 final size:43
Alignment explanation
Indices: 71902--72227 Score: 385
Period size: 43 Copynumber: 7.7 Consensus size: 43
71892 AAAAAAATGT
* * *
71902 CGCTATAGATCAT--ACCTTTTGTGGGGTTTGTTCGAAAAACGC
1 CGCTATAGATC-TCGACCTTTTGCGGCGTTTGTTCCAAAAACGC
* * *
71944 CGCTATAGATCT-GACCTTTTGCGGTGTTTGTTCGAAAAACAC
1 CGCTATAGATCTCGACCTTTTGCGGCGTTTGTTCCAAAAACGC
** * *
71986 TACTATAGATCTCGACTTTTTGTGGCGTTTGTTCCAAAAACGC
1 CGCTATAGATCTCGACCTTTTGCGGCGTTTGTTCCAAAAACGC
* * * *
72029 CACTATAGATCT-GATCTTTTACAGC-TTTGTTCCAAAAACGC
1 CGCTATAGATCTCGACCTTTTGCGGCGTTTGTTCCAAAAACGC
* **
72070 CGCTATAGATCTCGATCTTTTGCGGCGTTTGTTCCAAAAATAC
1 CGCTATAGATCTCGACCTTTTGCGGCGTTTGTTCCAAAAACGC
* * *
72113 CGCTATAGATCTCAACCTTTTGCGGCGTTTGTT-CTAAAGCGC
1 CGCTATAGATCTCGACCTTTTGCGGCGTTTGTTCCAAAAACGC
* * *
72155 CGCTATAGATCTCGACCTTTTGCGACGTTTGTTCTAAAAGCGC
1 CGCTATAGATCTCGACCTTTTGCGGCGTTTGTTCCAAAAACGC
*
72198 CGCTCTAGATCTCGACCTTTTGCGGCGTTT
1 CGCTATAGATCTCGACCTTTTGCGGCGTTT
72228 TTTGTTCTCA
Statistics
Matches: 246, Mismatches: 33, Indels: 9
0.85 0.11 0.03
Matches are distributed among these distances:
41 28 0.11
42 102 0.41
43 116 0.47
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (43 bp):
CGCTATAGATCTCGACCTTTTGCGGCGTTTGTTCCAAAAACGC
Found at i:72027 original size:85 final size:85
Alignment explanation
Indices: 71902--72227 Score: 367
Period size: 85 Copynumber: 3.9 Consensus size: 85
71892 AAAAAAATGT
* * * *
71902 CGCTATAGATCAT--ACCTTTTGTGGGGTTTGTTCGAAAAACGCCGCTATAGATCT-GACCTTTT
1 CGCTATAGATC-TCGACTTTTTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCTTTT
* *
71964 GCGGTGTTTGTTCGAAAAACAC
65 GCGGCGTTTGTTC-AAAAACGC
** * * * *
71986 TACTATAGATCTCGACTTTTTGTGGCGTTTGTTCCAAAAACGCCACTATAGATCT-GATCTTTTA
1 CGCTATAGATCTCGACTTTTTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCTTTTG
*
72050 CAGC-TTTGTTCCAAAAACGC
66 CGGCGTTTGTT-CAAAAACGC
** *
72070 CGCTATAGATCTCGA-TCTTTTGCGGCGTTTGTTCCAAAAATACCGCTATAGATCTCAACCTTTT
1 CGCTATAGATCTCGACT-TTTTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCTTTT
* *
72134 GCGGCGTTTGTTCTAAAGCGC
65 GCGGCGTTTGTTCAAAAACGC
* * * * *
72155 CGCTATAGATCTCGACCTTTTGCGACGTTTGTTCTAAAAGCGCCGCTCTAGATCTCGACCTTTTG
1 CGCTATAGATCTCGACTTTTTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCTTTTG
72220 CGGCGTTT
66 CGGCGTTT
72228 TTTGTTCTCA
Statistics
Matches: 204, Mismatches: 31, Indels: 13
0.82 0.12 0.05
Matches are distributed among these distances:
83 2 0.01
84 69 0.34
85 127 0.62
86 6 0.03
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (85 bp):
CGCTATAGATCTCGACTTTTTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCTTTTG
CGGCGTTTGTTCAAAAACGC
Found at i:72983 original size:182 final size:182
Alignment explanation
Indices: 72622--72986 Score: 594
Period size: 183 Copynumber: 2.0 Consensus size: 182
72612 TTAATAAAAG
*
72622 TAATATTTTTAATTCAAAAAATAGTTTCTAATTAATTTAAATAATATATAATTATAAAATAAAAA
1 TAATATTTTTAATTAAAAAAATAGTTTCTAATTAATTTAAATAATATATAATTATAAAATAAAAA
** *
72687 TGTTATATAAAAATTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTA
66 TAATATATAAAAATTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATTGGATCTTAAATTA
*
72752 TTAATTGGGTTTTAAATGGTTTGGGCTGAGCCCATATGTTATATATAATATA
131 TTAATTGGGTTTTAAATGGTTTGGGCTGAACCCATATGTTATATATAATATA
72804 TAATATTTTTTAAATTTAAAAAAATAGTTTAC-AATTAATTTAAATAATATATAATTAT-AAATA
1 TAATA-TTTTT-AA-TTAAAAAAATAGTTT-CTAATTAATTTAAATAATATATAATTATAAAATA
**
72867 AAAA-AATATATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATTGGATCTTAA
62 AAAATAATATATAAAAATTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATTGGATCTTAA
*
72931 ATTATTAATT-GGTTTTAAATTGTTTGGGCTGAACCCATATGTTATATATAATATA
127 ATTATTAATTGGGTTTTAAATGGTTTGGGCTGAACCCATATGTTATATATAATATA
72986 T
1 T
72987 TTAAAATTTA
Statistics
Matches: 171, Mismatches: 8, Indels: 8
0.91 0.04 0.04
Matches are distributed among these distances:
182 49 0.29
183 70 0.41
184 11 0.06
185 40 0.23
186 1 0.01
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.45
Consensus pattern (182 bp):
TAATATTTTTAATTAAAAAAATAGTTTCTAATTAATTTAAATAATATATAATTATAAAATAAAAA
TAATATATAAAAATTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATTGGATCTTAAATTA
TTAATTGGGTTTTAAATGGTTTGGGCTGAACCCATATGTTATATATAATATA
Found at i:73108 original size:21 final size:21
Alignment explanation
Indices: 73068--73108 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
73058 TAACTGTTAA
*
73068 CCGACCGAACTCATTCGGTGT
1 CCGACCGAACTAATTCGGTGT
* *
73089 CCGACCGAATTAATTTGGTG
1 CCGACCGAACTAATTCGGTG
73109 GTTGACTGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (21 bp):
CCGACCGAACTAATTCGGTGT
Found at i:75247 original size:20 final size:18
Alignment explanation
Indices: 75222--75262 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
75212 TAAATTTATA
*
75222 AAATTTTAAGATGTAAAAAT
1 AAATTTTAA-AT-AAAAAAT
75242 AAATTTTAAATAAAAAAT
1 AAATTTTAAATAAAAAAT
75260 AAA
1 AAA
75263 ATAGATGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 9 0.45
19 2 0.10
20 9 0.45
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (18 bp):
AAATTTTAAATAAAAAAT
Found at i:76045 original size:2 final size:2
Alignment explanation
Indices: 76038--76116 Score: 137
Period size: 2 Copynumber: 41.0 Consensus size: 2
76028 CAGATCAGAT
76038 TA TA TA TA TA TA TA T- TA TA TA TA TA T- TA -A TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
76077 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
76117 AATGGTTGTT
Statistics
Matches: 74, Mismatches: 0, Indels: 6
0.93 0.00 0.08
Matches are distributed among these distances:
1 3 0.04
2 71 0.96
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.