Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008815.1 Hibiscus syriacus cultivar Beakdansim tig00111977_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: 95052
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.32
Found at i:5928 original size:64 final size:65
Alignment explanation
Indices: 5804--5939 Score: 179
Period size: 64 Copynumber: 2.1 Consensus size: 65
5794 CACACCCATT
* * **
5804 TCGAATGCATTTTGTGTACCGATGCACAATCCATGCATCGGTGCACTCTTGAATATTTTG-AACA
1 TCGAATGCATTTTATGTACCGATGCACAATCCATGCATCGATGCACTCCAGAATATTTTGAAACA
**
5868 TCGAATGCATTTTATGTACCGATGCAC-ATACCATGCATCGATGCACTCCAGGTTCA-TTTGAAA
1 TCGAATGCATTTTATGTACCGATGCACAAT-CCATGCATCGATGCACTCCAGAAT-ATTTTGAAA
5931 CA
64 CA
5933 TCGAATG
1 TCGAATG
5940 TAATTAGTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
63 2 0.03
64 49 0.78
65 12 0.19
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (65 bp):
TCGAATGCATTTTATGTACCGATGCACAATCCATGCATCGATGCACTCCAGAATATTTTGAAACA
Found at i:11794 original size:23 final size:22
Alignment explanation
Indices: 11728--11803 Score: 91
Period size: 23 Copynumber: 3.4 Consensus size: 22
11718 TAGACAGTGT
11728 ATCGATGCATCCCTTGAATGTGC
1 ATCGATGCAT-CCTTGAATGTGC
* * *
11751 ATCGATACA-CCATGAAGGTGC
1 ATCGATGCATCCTTGAATGTGC
*
11772 ACCGATGCATTCCTTGAATGTGC
1 ATCGATGCA-TCCTTGAATGTGC
11795 ATCGATGCA
1 ATCGATGCA
11804 CACTGCTGTA
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
21 17 0.40
23 26 0.60
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.26
Consensus pattern (22 bp):
ATCGATGCATCCTTGAATGTGC
Found at i:14117 original size:13 final size:13
Alignment explanation
Indices: 14087--14120 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
14077 AGGGGGAGTA
*
14087 ATTTTCAAAATTT
1 ATTTTCAAAATCT
14100 A-TTTCAAAATCT
1 ATTTTCAAAATCT
14112 ATTTTCAAA
1 ATTTTCAAA
14121 GAAAATCCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (13 bp):
ATTTTCAAAATCT
Found at i:17959 original size:17 final size:17
Alignment explanation
Indices: 17925--17958 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
17915 TTGGTAAATT
*
17925 GAGATTAAATAGTAAAA
1 GAGATTAAATAATAAAA
17942 GAGATTAAATGAATAAA
1 GAGATTAAAT-AATAAA
17959 GGCAATTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.59, C:0.00, G:0.18, T:0.24
Consensus pattern (17 bp):
GAGATTAAATAATAAAA
Found at i:23283 original size:467 final size:467
Alignment explanation
Indices: 22402--23281 Score: 1167
Period size: 467 Copynumber: 1.9 Consensus size: 467
22392 ATATCATCCA
* * * * *
22402 GATCTGAGTCATATTATCCAGGTTGAGGATGTCGAGTTGAGACCAGATCTATAGTATGATAAGGA
1 GATCCGAGTCATATTATCAAGGTTAAGGATGTCGAGCTGAAACCAGATCTATAGTATGATAAGGA
* * * *
22467 GCTTATTCAGATTCTGGATCGAGATGAGAAATTTCCTCAAAATAGGCACATCTCGATGGTGAAAG
66 GCTTATTCAAATTCTGGATCGAGATGAGAAAGTTCCTAAAAACAGGCACATCTCGATGGTGAAAG
* * * *
22532 TTTAATGGAATAACTGTGGTCCTGTAGAAGCTACTTGGGAGACAAATGAGTAAATGAAGGATTAG
131 TTTAATGGAATAACCGTGGTCCAGTAGAAGCTACTTGGGAGACAAAGGAGTAAATGAAGGATCAG
* **
22597 TTTCTAAATTTGTTCACTTCAGGAAAATTTCAAGGACAATTTTTTTTAGAGGGAGAGTTGTAACA
196 TTTCCAAATTTGTTCACTTCAGGAAAATTTCAAGGACAATTTTTTTTAGAGGGAGAGACGTAACA
* *
22662 CCCCCAATTTAATTGCTTTTAATCTGATTTTATTTTAATTATTTTTAGGGACTATTTTGAAAAAA
261 ACCCCAATTTAATTGCTTTTAATATGATTTTATTTTAATTATTTTTAGGGACTATTTTGAAAAAA
* * * *
22727 AATTGATGATTTTAAGGAAAAATTTGAAGTCTCAAAAAGTTTAGGGACTCGTTCTCTGATTTGAC
326 AATTGATGATTTTAAGGAAAAATTTGAAGTCCCAAAAAGTTCAAGGACTCATTCTCTGATTTGAC
*
22792 CATCATTGGTCTGCAAAGAAAAAAGGTGAGATATTTTAAAACATGCGGCTAAAGGAAATTGAACA
391 CATCATTGGTCAGCAAAGAAAAAAGGTGAGATATTTTAAAACATGCGGCTAAAGGAAATTGAACA
22857 CTTAATCTTTAG
456 CTTAATCTTTAG
* * *
22869 GATCCGAGTCATATTATCAATGTTAAGGATGTCGAGCTGAAACCATATCTATCGTATGATGAA-G
1 GATCCGAGTCATATTATCAAGGTTAAGGATGTCGAGCTGAAACCAGATCTATAGTATGAT-AAGG
* * * * ** *
22933 AGGTTATTCAAATTTTGGATCGAGATGAGAGAGTTCCTAAAAACATGTGCATTTCGATGGTGAAA
65 AGCTTATTCAAATTCTGGATCGAGATGAGAAAGTTCCTAAAAACAGGCACATCTCGATGGTGAAA
* * * * *
22998 GTTTAGTGGAGTAACCGTGGTCCAGTAGAAGCTACTTGGGAGATAGAGGAGTTAATGAAGGATCA
130 GTTTAATGGAATAACCGTGGTCCAGTAGAAGCTACTTGGGAGACAAAGGAGTAAATGAAGGATCA
* * * *
23063 GTTTCCACATTTGTTCACTTCAGGTAAATTTCGAGGACGAA-TTTTTTTAGGGGGAGAGACGTAA
195 GTTTCCAAATTTGTTCACTTCAGGAAAATTTCAAGGAC-AATTTTTTTTAGAGGGAGAGACGTAA
* * * * *
23127 CAACCCCATTTTAATTGCTTTTATTATGTTTTTATTTTAATTATTTTTAGGG-GTCATTTTG-TA
259 CAACCCCAATTTAATTGCTTTTAATATGATTTTATTTTAATTATTTTTAGGGACT-ATTTTGAAA
*** * * * *
23190 AACTTTTGA-GCATTTTAGGGCAAAATTTGATGTCCCTAAAAGTTCAAGGACTCATTCTCTGATT
323 AAAAATTGATG-ATTTTAAGGAAAAATTTGAAGTCCCAAAAAGTTCAAGGACTCATTCTCTGATT
* * * *
23254 TGATCATTATTTGTCAGCAATGAAAAAA
387 TGACCATCATTGGTCAGCAAAGAAAAAA
23282 AGATAAAAAG
Statistics
Matches: 351, Mismatches: 58, Indels: 9
0.84 0.14 0.02
Matches are distributed among these distances:
465 1 0.00
466 76 0.22
467 270 0.77
468 4 0.01
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.34
Consensus pattern (467 bp):
GATCCGAGTCATATTATCAAGGTTAAGGATGTCGAGCTGAAACCAGATCTATAGTATGATAAGGA
GCTTATTCAAATTCTGGATCGAGATGAGAAAGTTCCTAAAAACAGGCACATCTCGATGGTGAAAG
TTTAATGGAATAACCGTGGTCCAGTAGAAGCTACTTGGGAGACAAAGGAGTAAATGAAGGATCAG
TTTCCAAATTTGTTCACTTCAGGAAAATTTCAAGGACAATTTTTTTTAGAGGGAGAGACGTAACA
ACCCCAATTTAATTGCTTTTAATATGATTTTATTTTAATTATTTTTAGGGACTATTTTGAAAAAA
AATTGATGATTTTAAGGAAAAATTTGAAGTCCCAAAAAGTTCAAGGACTCATTCTCTGATTTGAC
CATCATTGGTCAGCAAAGAAAAAAGGTGAGATATTTTAAAACATGCGGCTAAAGGAAATTGAACA
CTTAATCTTTAG
Found at i:27137 original size:20 final size:20
Alignment explanation
Indices: 27112--27159 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
27102 ATAGAAAAAC
* *
27112 TCAACAATTAACGGTTAAAG
1 TCAACAATTAACGATCAAAG
27132 TCAACAGA-TAACGATCAAAG
1 TCAACA-ATTAACGATCAAAG
27152 TCAACAAT
1 TCAACAAT
27160 CAAAGTCAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 1 0.04
20 22 0.92
21 1 0.04
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.21
Consensus pattern (20 bp):
TCAACAATTAACGATCAAAG
Found at i:27163 original size:13 final size:13
Alignment explanation
Indices: 27145--27188 Score: 79
Period size: 13 Copynumber: 3.4 Consensus size: 13
27135 ACAGATAACG
27145 ATCAAAGTCAACA
1 ATCAAAGTCAACA
27158 ATCAAAGTCAACA
1 ATCAAAGTCAACA
*
27171 ATAAAAGTCAACA
1 ATCAAAGTCAACA
27184 ATCAA
1 ATCAA
27189 TAATATAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.57, C:0.20, G:0.07, T:0.16
Consensus pattern (13 bp):
ATCAAAGTCAACA
Found at i:33292 original size:21 final size:21
Alignment explanation
Indices: 33254--33293 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
33244 ACCACACAAA
** *
33254 GAAGGGATTGATCTTTTTTGG
1 GAAGGGATCAATCATTTTTGG
33275 GAAGGGATCAATCATTTTT
1 GAAGGGATCAATCATTTTT
33294 CTAGAAAAAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.07, G:0.28, T:0.40
Consensus pattern (21 bp):
GAAGGGATCAATCATTTTTGG
Found at i:40959 original size:19 final size:19
Alignment explanation
Indices: 40935--40975 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
40925 GCAGCTTGAG
*
40935 ACCGGTCTGATCGGTCCGA
1 ACCGGTCTGATCGATCCGA
*
40954 ACCGGTTTGATCGATCCGA
1 ACCGGTCTGATCGATCCGA
40973 ACC
1 ACC
40976 AGTTTGACCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.20, C:0.32, G:0.27, T:0.22
Consensus pattern (19 bp):
ACCGGTCTGATCGATCCGA
Found at i:40980 original size:19 final size:19
Alignment explanation
Indices: 40942--40988 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
40932 GAGACCGGTC
* *
40942 TGATCGGTCCGAACCGGTT
1 TGATCGATCCGAACCAGTT
40961 TGATCGATCCGAACCAGTT
1 TGATCGATCCGAACCAGTT
*
40980 TGACCGATC
1 TGATCGATC
40989 TAACCCGACC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.21, C:0.28, G:0.26, T:0.26
Consensus pattern (19 bp):
TGATCGATCCGAACCAGTT
Found at i:41018 original size:18 final size:18
Alignment explanation
Indices: 40995--41038 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
40985 GATCTAACCC
*
40995 GACCCGACCCTACCCGTT
1 GACCCGACCCAACCCGTT
41013 GACCCGACCCAACCCGTT
1 GACCCGACCCAACCCGTT
41031 GACCCGAC
1 GACCCGAC
41039 TTGTGAAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.20, C:0.50, G:0.18, T:0.11
Consensus pattern (18 bp):
GACCCGACCCAACCCGTT
Found at i:42363 original size:13 final size:13
Alignment explanation
Indices: 42345--42387 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
42335 GATCCGACCC
42345 GACCCGACCCGTT
1 GACCCGACCCGTT
**
42358 GACCCGACGTGTT
1 GACCCGACCCGTT
42371 GACCCGACCCGTT
1 GACCCGACCCGTT
42384 GACC
1 GACC
42388 TGACTTGTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.16, C:0.42, G:0.26, T:0.16
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:46381 original size:43 final size:43
Alignment explanation
Indices: 46318--46399 Score: 119
Period size: 43 Copynumber: 1.9 Consensus size: 43
46308 AGTAGGTTTA
* *
46318 GGATTAATCCTTTGAATTAAGAGATCGATCTTTTTTTAGGAAG
1 GGATTAATCCTTTCAATTAAGAGATCGATCCTTTTTTAGGAAG
** *
46361 GGATTAATCCTTTCCCTTAAGGGATCGATCCTTTTTTAG
1 GGATTAATCCTTTCAATTAAGAGATCGATCCTTTTTTAG
46400 AAAATTGCAG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.40
Consensus pattern (43 bp):
GGATTAATCCTTTCAATTAAGAGATCGATCCTTTTTTAGGAAG
Found at i:50698 original size:20 final size:20
Alignment explanation
Indices: 50654--50700 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
50644 CAGAAAATGT
* *
50654 CAACGGTCAAAGTCAACAAT
1 CAACAGTCAAAGTCAACAAC
* *
50674 AAACAGTCAAAGTTAACAAC
1 CAACAGTCAAAGTCAACAAC
50694 CAACAGT
1 CAACAGT
50701 TAACGATCAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.49, C:0.23, G:0.13, T:0.15
Consensus pattern (20 bp):
CAACAGTCAAAGTCAACAAC
Found at i:51655 original size:32 final size:30
Alignment explanation
Indices: 51594--51656 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 30
51584 ATTTAAAAAA
51594 TTAAAAATGATGTCTAATTTTTTGGTATTTC
1 TTAAAAATGATGTCTAATTTTTT-GTATTTC
*
51625 TTAAAGAATGAGTGTGTAATATTTTT-TATTTC
1 TTAAA-AATGA-TGTCTAAT-TTTTTGTATTTC
51657 CCTCCTTTCC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
31 5 0.18
32 11 0.39
33 7 0.25
34 5 0.18
ACGTcount: A:0.30, C:0.05, G:0.14, T:0.51
Consensus pattern (30 bp):
TTAAAAATGATGTCTAATTTTTTGTATTTC
Found at i:54231 original size:23 final size:23
Alignment explanation
Indices: 54205--54260 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
54195 TTGGTCAACG
*
54205 TTAAATAAATATATTCATGAGTA
1 TTAAATAAATATATTCATGAATA
* *
54228 TTAAATAAATATGTTCGTGAATA
1 TTAAATAAATATATTCATGAATA
*
54251 CTAAATAAAT
1 TTAAATAAAT
54261 CAAACACGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.48, C:0.05, G:0.09, T:0.38
Consensus pattern (23 bp):
TTAAATAAATATATTCATGAATA
Found at i:71772 original size:6 final size:6
Alignment explanation
Indices: 71754--71785 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
71744 TCAAAAATAA
71754 ATAAAT AATAAAT ATAAAT ATAAAT ATAAAT A
1 ATAAAT -ATAAAT ATAAAT ATAAAT ATAAAT A
71786 AATAACTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
ATAAAT
Found at i:75626 original size:22 final size:22
Alignment explanation
Indices: 75585--75651 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
75575 CTCGTATAAA
75585 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
75608 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
75630 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
75652 GATGTCCATA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 31 0.72
23 12 0.28
ACGTcount: A:0.25, C:0.28, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:77370 original size:21 final size:21
Alignment explanation
Indices: 77346--77390 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
77336 TCTTGTTCGT
* *
77346 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
77367 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
77388 TTG
1 TTG
77391 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:80574 original size:22 final size:22
Alignment explanation
Indices: 80533--80599 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
80523 CTCGTATAAA
80533 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
80556 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
80578 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
80600 GATGTCCATA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 31 0.72
23 12 0.28
ACGTcount: A:0.25, C:0.28, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:82321 original size:21 final size:21
Alignment explanation
Indices: 82297--82341 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
82287 TCTTGTTCGT
* *
82297 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
82318 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
82339 TTG
1 TTG
82342 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:87108 original size:3 final size:3
Alignment explanation
Indices: 87100--87162 Score: 85
Period size: 3 Copynumber: 21.3 Consensus size: 3
87090 AATATGTAAA
*
87100 AAT AAT AAT TAT AAT AAT AA- ATAT AAT AAT AAT -AT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT
*
87144 AAT ATT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT A
87163 TGACGATAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
2 3 0.06
3 49 0.92
4 1 0.02
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:87162 original size:29 final size:28
Alignment explanation
Indices: 87089--87163 Score: 95
Period size: 29 Copynumber: 2.8 Consensus size: 28
87079 CAATTACTTG
*
87089 TAATATGTAAAAATAATAAT-TATAATAA
1 TAATAT-TAATAATAATAATATATAATAA
87117 TAA-A-T-ATAATAATAATATAATAATAA
1 TAATATTAATAATAATAATAT-ATAATAA
87143 TAATATTAATAATAATAATAT
1 TAATATTAATAATAATAATAT
87164 GACGATAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
24 10 0.24
25 2 0.05
26 10 0.24
27 2 0.05
28 4 0.10
29 13 0.32
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (28 bp):
TAATATTAATAATAATAATATATAATAA
Found at i:90703 original size:36 final size:36
Alignment explanation
Indices: 90648--90729 Score: 130
Period size: 36 Copynumber: 2.3 Consensus size: 36
90638 GTGGCTTCGC
*
90648 GCCATCCCATTGTTGGCGTACTCCCTATAGCCATTG
1 GCCATCCCATTGTTGGCGTACTCCCCATAGCCATTG
90684 GCCA-CCCAATTGTTGGCGTACTCCCCATAGCCATTG
1 GCCATCCC-ATTGTTGGCGTACTCCCCATAGCCATTG
*
90720 GCAATCCCAT
1 GCCATCCCAT
90730 GGTTCTCGTA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
35 3 0.07
36 36 0.86
37 3 0.07
ACGTcount: A:0.20, C:0.35, G:0.18, T:0.27
Consensus pattern (36 bp):
GCCATCCCATTGTTGGCGTACTCCCCATAGCCATTG
Found at i:92935 original size:20 final size:21
Alignment explanation
Indices: 92910--92957 Score: 71
Period size: 22 Copynumber: 2.3 Consensus size: 21
92900 ACTCTTCAGG
*
92910 GAAAAA-TTAAGTCTTTTTAT
1 GAAAAAGTTAAGTCTTTTCAT
92930 GAAAAATGTTAAGTCTTTTCAT
1 GAAAAA-GTTAAGTCTTTTCAT
92952 GAAAAA
1 GAAAAA
92958 AAAATATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 6 0.24
22 19 0.76
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (21 bp):
GAAAAAGTTAAGTCTTTTCAT
Found at i:92944 original size:22 final size:22
Alignment explanation
Indices: 92916--92957 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
92906 CAGGGAAAAA
*
92916 TTAAGTCTTTTTATGAAAAATG
1 TTAAGTCTTTTCATGAAAAATG
92938 TTAAGTCTTTTCATGAAAAA
1 TTAAGTCTTTTCATGAAAAA
92958 AAAATATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.38, C:0.07, G:0.12, T:0.43
Consensus pattern (22 bp):
TTAAGTCTTTTCATGAAAAATG
Found at i:93831 original size:4 final size:4
Alignment explanation
Indices: 93801--93870 Score: 58
Period size: 4 Copynumber: 17.8 Consensus size: 4
93791 AAAAAAATAT
* *
93801 TAAA TAAA TCAAA GAAA AAACA TAAA TAAA T-AA TAAAA TAAA TAAA TAAA
1 TAAA TAAA T-AAA TAAA TAA-A TAAA TAAA TAAA T-AAA TAAA TAAA TAAA
*
93851 -AAA T-AA T-AA TAAA AAAA TAA
1 TAAA TAAA TAAA TAAA TAAA TAA
93871 TATTAAAAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
3 12 0.22
4 34 0.62
5 9 0.16
ACGTcount: A:0.76, C:0.03, G:0.01, T:0.20
Consensus pattern (4 bp):
TAAA
Found at i:93832 original size:33 final size:33
Alignment explanation
Indices: 93789--93870 Score: 87
Period size: 34 Copynumber: 2.5 Consensus size: 33
93779 AATATGTTAG
*
93789 ATAAAAAAAT-ATTAAATAAATCAAAGAAAAAAC
1 ATAAAAAAATAATAAAATAAAT-AAAGAAAAAAC
* * *
93822 ATAAATAAATAATAAAATAAATAAATAAAAAATA
1 ATAAAAAAATAATAAAATAAATAAAGAAAAAA-C
93856 ATAATAAAAA-AATAA
1 ATAA-AAAAATAATAA
93871 TATTAAAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
33 18 0.44
34 19 0.46
35 4 0.10
ACGTcount: A:0.76, C:0.02, G:0.01, T:0.21
Consensus pattern (33 bp):
ATAAAAAAATAATAAAATAAATAAAGAAAAAAC
Found at i:93858 original size:14 final size:14
Alignment explanation
Indices: 93825--94006 Score: 71
Period size: 14 Copynumber: 12.8 Consensus size: 14
93815 AAAAAACATA
93825 AATAAATAATAAAAT
1 AATAAATAA-AAAAT
93840 AAATAAATAAAAAAT
1 -AATAAATAAAAAAT
93855 AAT-AATAAAAAAAT
1 AATAAAT-AAAAAAT
*
93869 AATATTAA-AAAAATGT
1 AATA--AATAAAAA-AT
* *
93885 AA-AACTTAAAAAT
1 AATAAATAAAAAAT
93898 AA-AAA-AATAAAAT
1 AATAAATAA-AAAAT
*
93911 AATATAAGTCAAAGGAA-
1 AATA-AA-T-AAA-AAAT
93928 AA-AAATAAAAAGAT
1 AATAAATAAAAA-AT
93942 AA-AAATAAATAAA-
1 AATAAATAAA-AAAT
93955 AATAAAATAAAAAAT
1 AAT-AAATAAAAAAT
* **
93970 CA-AAGGAAAAAA-
1 AATAAATAAAAAAT
* *
93982 AAAAAATAAAAAAA
1 AATAAATAAAAAAT
*
93996 AATTAATAAAA
1 AATAAATAAAA
94007 TATTAAATAA
Statistics
Matches: 129, Mismatches: 16, Indels: 44
0.68 0.08 0.23
Matches are distributed among these distances:
12 3 0.02
13 38 0.29
14 41 0.32
15 25 0.19
16 13 0.10
17 5 0.04
18 4 0.03
ACGTcount: A:0.76, C:0.02, G:0.04, T:0.19
Consensus pattern (14 bp):
AATAAATAAAAAAT
Found at i:93863 original size:37 final size:38
Alignment explanation
Indices: 93801--93967 Score: 88
Period size: 37 Copynumber: 4.6 Consensus size: 38
93791 AAAAAAATAT
* *
93801 TAAATAAAT-CAAAGAAAAAACATAAATAAATAATAAAA
1 TAAATAAATAAAAAGATAAAA-ATAAATAAATAATAAAA
* * *
93839 TAAATAAATAAAAA-ATAATAATAAAAAAATAAT--AT
1 TAAATAAATAAAAAGATAAAAATAAATAAATAATAAAA
* * **
93874 TAAAAAAATGTAAAACTTAAAAAT-AA-AAA-AATAAAA
1 TAAATAAAT-AAAAAGATAAAAATAAATAAATAATAAAA
* * * *
93910 TAATATAAGTCAAAGGAAAAAAATAAA-AAGAT-A-AAAA
1 TAA-ATAAATAAAAAGATAAAAATAAATAA-ATAATAAAA
93947 TAAATAAA-AATAAA-ATAAAAA
1 TAAATAAATAA-AAAGATAAAAA
93968 ATCAAAGGAA
Statistics
Matches: 98, Mismatches: 21, Indels: 23
0.69 0.15 0.16
Matches are distributed among these distances:
34 3 0.03
35 19 0.19
36 25 0.26
37 33 0.34
38 15 0.15
39 3 0.03
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.20
Consensus pattern (38 bp):
TAAATAAATAAAAAGATAAAAATAAATAAATAATAAAA
Found at i:93929 original size:28 final size:27
Alignment explanation
Indices: 93898--94036 Score: 93
Period size: 24 Copynumber: 5.4 Consensus size: 27
93888 ACTTAAAAAT
*
93898 AAAAAAATAAAATAATATAAGTCAAAGG
1 AAAAAAATAAAATAATA-AAATCAAAGG
93926 AAAAAAATAAAA-AGATAAAA--ATAA--
1 AAAAAAATAAAATA-ATAAAATCA-AAGG
*
93950 ATAAAAATAAAATAA-AAAATCAAAGG
1 AAAAAAATAAAATAATAAAATCAAAGG
* **
93976 AAAAAAAAAAAATAA-AAAA--AAATT
1 AAAAAAATAAAATAATAAAATCAAAGG
* ** *
94000 AATAAAATATTA-AAT-AAATCAGAGG
1 AAAAAAATAAAATAATAAAATCAAAGG
94025 AAAAAAATAAAA
1 AAAAAAATAAAA
94037 AATGTTTAAA
Statistics
Matches: 85, Mismatches: 16, Indels: 23
0.69 0.13 0.19
Matches are distributed among these distances:
23 9 0.11
24 25 0.29
25 14 0.16
26 19 0.22
27 3 0.04
28 15 0.18
ACGTcount: A:0.76, C:0.02, G:0.06, T:0.16
Consensus pattern (27 bp):
AAAAAAATAAAATAATAAAATCAAAGG
Found at i:93930 original size:50 final size:50
Alignment explanation
Indices: 93840--94037 Score: 167
Period size: 50 Copynumber: 3.9 Consensus size: 50
93830 ATAATAAAAT
** * *
93840 AAATAAATAAAAAATAATAATAAAAAAAT-AATATTAAAAAAATGTAAAACTTAA
1 AAATAAAT-AAAAATAA-AAT-AAAAAATCAA-AGGAAAAAAAT-AAAAACATAA
* *
93894 AAAT-AA-AAAAATAAAATAATATAAGTCAAAGGAAAAAAATAAAAAGATAA
1 AAATAAATAAAAATAAAATAA-A-AAATCAAAGGAAAAAAATAAAAACATAA
93944 AAATAAATAAAAATAAAATAAAAAATCAAAGG-AAAAAA-AAAAA-ATAA
1 AAATAAATAAAAATAAAATAAAAAATCAAAGGAAAAAAATAAAAACATAA
* * * *
93991 AAAAAAATTAATAAA-ATATTAAATAAATCAGAGGAAAAAAATAAAAA
1 AAATAAA-TAA-AAATAAAATAAA-AAATCAAAGGAAAAAAATAAAAA
94038 ATGTTTAAAT
Statistics
Matches: 123, Mismatches: 11, Indels: 23
0.78 0.07 0.15
Matches are distributed among these distances:
47 10 0.08
48 14 0.11
49 20 0.16
50 30 0.24
51 28 0.23
52 15 0.12
53 2 0.02
54 4 0.03
ACGTcount: A:0.75, C:0.02, G:0.05, T:0.18
Consensus pattern (50 bp):
AAATAAATAAAAATAAAATAAAAAATCAAAGGAAAAAAATAAAAACATAA
Done.