Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006468.1 Hibiscus syriacus cultivar Beakdansim tig00015669_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: 92489
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1614 original size:27 final size:27
Alignment explanation
Indices: 1583--1635 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
1573 TAGGAGGCAC
1583 TACATAGTCACATTCAAGCAGACGTGT
1 TACATAGTCACATTCAAGCAGACGTGT
1610 TACATAGTCACATTCAAGCAGACGTG
1 TACATAGTCACATTCAAGCAGACGTG
1636 ATCTCAACGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.25
Consensus pattern (27 bp):
TACATAGTCACATTCAAGCAGACGTGT
Found at i:10719 original size:21 final size:21
Alignment explanation
Indices: 10693--10733 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
10683 TCCAGATTCG
*
10693 CAACGCGAACATCGACTATCT
1 CAACGCGAACATCAACTATCT
*
10714 CAACGCGAACTTCAACTATC
1 CAACGCGAACATCAACTATC
10734 GCAATGCTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.34, G:0.12, T:0.20
Consensus pattern (21 bp):
CAACGCGAACATCAACTATCT
Found at i:10808 original size:42 final size:42
Alignment explanation
Indices: 10742--10909 Score: 209
Period size: 42 Copynumber: 4.0 Consensus size: 42
10732 TCGCAATGCT
* * *
10742 ATTTTTTCCAAATTCGTTGCGATAGTCTAAGTTCACGTTGCG
1 ATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCG
* *
10784 ATTTATTCCAAATTCGTTGTGATAGTCCAAGTT--CGTTGCG
1 ATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCG
* *
10824 A--TAGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCG
1 ATTTATTCCAAATT--CGTTGCGATAGTCGAAGTTCGCGTTGCG
* *
10866 ATTTATTCCAAGTTCGTTACGATAGTCGAAGTTCGCGTTGCG
1 ATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCG
10908 AT
1 AT
10910 AGTCCAAAAT
Statistics
Matches: 111, Mismatches: 9, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
38 9 0.08
40 25 0.23
42 67 0.60
44 10 0.09
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (42 bp):
ATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCG
Found at i:10898 original size:82 final size:83
Alignment explanation
Indices: 10756--10916 Score: 252
Period size: 82 Copynumber: 1.9 Consensus size: 83
10746 TTTCCAAATT
* **
10756 CGTTGCGATAGTCTAAGTTCACGTTGCGATTTATTCCAAATTCGTTGTGATAGTCCAAGTT-CGT
1 CGTTGCGATAGTCGAAGTTCACGTTGCGATTTATTCCAAATTCGTTACGATAGTCCAAGTTCCGT
10820 TGCGATAGTCCAAGTTCG
66 TGCGATAGTCCAAGTTCG
* * *
10838 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTACGATAGTCGAAGTTCGCG
1 CGTTGCGATAGTCGAAGTTCACGTTGCGATTTATTCCAAATTCGTTACGATAGTCCAAGTTC-CG
10903 TTGCGATAGTCCAA
65 TTGCGATAGTCCAA
10917 AATCGCAACG
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
82 55 0.77
84 16 0.23
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.34
Consensus pattern (83 bp):
CGTTGCGATAGTCGAAGTTCACGTTGCGATTTATTCCAAATTCGTTACGATAGTCCAAGTTCCGT
TGCGATAGTCCAAGTTCG
Found at i:10922 original size:21 final size:21
Alignment explanation
Indices: 10756--10916 Score: 163
Period size: 21 Copynumber: 7.8 Consensus size: 21
10746 TTTCCAAATT
* *
10756 CGTTGCGATAGTCTAAGTTCA
1 CGTTGCGATAGTCCAAGTTCG
* *
10777 CGTTGCGATTTATTCCAAATT--
1 CGTTGCGA--TAGTCCAAGTTCG
*
10798 CGTTGTGATAGTCCAAGTT--
1 CGTTGCGATAGTCCAAGTTCG
10817 CGTTGCGATAGTCCAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
*
10838 CGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
*
10859 CGTTGCGATTTATTCCAAGTT--
1 CGTTGCGA--TAGTCCAAGTTCG
* *
10880 CGTTACGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
10901 CGTTGCGATAGTCCAA
1 CGTTGCGATAGTCCAA
10917 AATCGCAACG
Statistics
Matches: 117, Mismatches: 15, Indels: 16
0.79 0.10 0.11
Matches are distributed among these distances:
19 36 0.31
21 64 0.55
23 17 0.15
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.34
Consensus pattern (21 bp):
CGTTGCGATAGTCCAAGTTCG
Found at i:11831 original size:42 final size:42
Alignment explanation
Indices: 11772--11883 Score: 188
Period size: 42 Copynumber: 2.7 Consensus size: 42
11762 ATTTTGGACT
* * *
11772 ATCGCAACGTGAACTTGGACTATCGCAACGAATTTGTAATAA
1 ATCGCAACGCGAACTTGGACTATCGCAACAAATTTGGAATAA
*
11814 ATCGCAATGCGAACTTGGACTATCGCAACAAATTTGGAATAA
1 ATCGCAACGCGAACTTGGACTATCGCAACAAATTTGGAATAA
11856 ATCGCAACGCGAACTTGGACTATCGCAA
1 ATCGCAACGCGAACTTGGACTATCGCAA
11884 TGCGAATATG
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (42 bp):
ATCGCAACGCGAACTTGGACTATCGCAACAAATTTGGAATAA
Found at i:11888 original size:21 final size:20
Alignment explanation
Indices: 11765--11889 Score: 101
Period size: 21 Copynumber: 6.0 Consensus size: 20
11755 CGTTACGATT
*
11765 TTGGACTATCGCAACGTGAAC
1 TTGGACTATCGCAA-GCGAAC
*
11786 TTGGACTATCGCAA-CGAAT
1 TTGGACTATCGCAAGCGAAC
* *
11805 TTGTAATAAATCGCAATGCGAAC
1 TTGGACT--ATCGCAA-GCGAAC
* *
11828 TTGGACTATCGCAA-CAAAT
1 TTGGACTATCGCAAGCGAAC
*
11847 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA-GCGAAC
11870 TTGGACTATCGCAATGCGAA
1 TTGGACTATCGCAA-GCGAA
11890 TATGTAAATC
Statistics
Matches: 82, Mismatches: 14, Indels: 16
0.73 0.12 0.14
Matches are distributed among these distances:
19 17 0.21
21 47 0.57
23 18 0.22
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (20 bp):
TTGGACTATCGCAAGCGAAC
Found at i:12317 original size:30 final size:34
Alignment explanation
Indices: 12281--12344 Score: 82
Period size: 35 Copynumber: 2.0 Consensus size: 34
12271 TTAAATTCAC
12281 ATCTTAA-CATTAAA-ATA-TTTA-TTTATTTTT
1 ATCTTAATCATTAAATATATTTTATTTTATTTTT
*
12311 ATCTTAATTTATTAAATATATTTTATTTTATTTT
1 ATCTTAA-TCATTAAATATATTTTATTTTATTTT
12345 GACTTTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
30 7 0.25
32 6 0.21
33 3 0.11
34 4 0.14
35 8 0.29
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (34 bp):
ATCTTAATCATTAAATATATTTTATTTTATTTTT
Found at i:12399 original size:29 final size:29
Alignment explanation
Indices: 12292--12481 Score: 184
Period size: 29 Copynumber: 6.3 Consensus size: 29
12282 TCTTAACATT
* * *
12292 AAAATATTTATTTATTTTTATCTTAATTTA
1 AAAATATAT-TTTATTCTTATTTTAATTTA
* *
12322 TTAAATATATTTTATT-TTATTTTGACTTTAA
1 -AAAATATATTTTATTCTTATTTT-AATTT-A
*
12353 AAAATATATTTTAATCTTATTTTAATTTA
1 AAAATATATTTTATTCTTATTTTAATTTA
* *
12382 AAAATATATCTTATTCTTATATTAACTTTTA
1 AAAATATATTTTATTCTTATTTTAA--TTTA
* *
12413 AAAATATATTTTAATCTTATTTTAACTTA
1 AAAATATATTTTATTCTTATTTTAATTTA
* * *
12442 AAAATATATATTATTATTATATTAACTTTTA
1 AAAATATATTTTATTCTTATTTTAA--TTTA
12473 AAAATATAT
1 AAAATATAT
12482 CTTAAATTAA
Statistics
Matches: 133, Mismatches: 19, Indels: 14
0.80 0.11 0.08
Matches are distributed among these distances:
29 53 0.40
30 27 0.20
31 53 0.40
ACGTcount: A:0.41, C:0.05, G:0.01, T:0.54
Consensus pattern (29 bp):
AAAATATATTTTATTCTTATTTTAATTTA
Found at i:12416 original size:31 final size:31
Alignment explanation
Indices: 12324--12481 Score: 200
Period size: 29 Copynumber: 5.3 Consensus size: 31
12314 TTAATTTATT
* *
12324 AAATATATTTTATT-TTATTTTGACTTTAAA
1 AAATATATTTTATTCTTATTTTAACTTTTAA
*
12354 AAATATATTTTAATCTTATTTTAA--TTTAA
1 AAATATATTTTATTCTTATTTTAACTTTTAA
* *
12383 AAATATATCTTATTCTTATATTAACTTTTAA
1 AAATATATTTTATTCTTATTTTAACTTTTAA
*
12414 AAATATATTTTAATCTTATTTTAAC--TTAA
1 AAATATATTTTATTCTTATTTTAACTTTTAA
* * *
12443 AAATATATATTATTATTATATTAACTTTTAA
1 AAATATATTTTATTCTTATTTTAACTTTTAA
12474 AAATATAT
1 AAATATAT
12482 CTTAAATTAA
Statistics
Matches: 110, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
29 50 0.45
30 13 0.12
31 47 0.43
ACGTcount: A:0.42, C:0.05, G:0.01, T:0.53
Consensus pattern (31 bp):
AAATATATTTTATTCTTATTTTAACTTTTAA
Found at i:12416 original size:60 final size:59
Alignment explanation
Indices: 12309--12486 Score: 248
Period size: 60 Copynumber: 3.0 Consensus size: 59
12299 TTATTTATTT
* * * * * *
12309 TTATCTTAATTTATTAAATATATTTTATTTTATTTTGACTTTAAAAAATATATTTTAATC
1 TTATTTTAATTTA-AAAATATATATTATTTTATATTAACTTTTAAAAATATATTTTAATC
*
12369 TTATTTTAATTTAAAAATATATCTTATTCTTATATTAACTTTTAAAAATATATTTTAATC
1 TTATTTTAATTTAAAAATATATATTATT-TTATATTAACTTTTAAAAATATATTTTAATC
* *
12429 TTATTTTAACTTAAAAATATATATTATTATTATATTAACTTTTAAAAATATATCTTAA
1 TTATTTTAATTTAAAAATATATATTATT-TTATATTAACTTTTAAAAATATATTTTAA
12487 ATTAAAATAA
Statistics
Matches: 107, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
59 13 0.12
60 94 0.88
ACGTcount: A:0.40, C:0.06, G:0.01, T:0.53
Consensus pattern (59 bp):
TTATTTTAATTTAAAAATATATATTATTTTATATTAACTTTTAAAAATATATTTTAATC
Found at i:12504 original size:60 final size:60
Alignment explanation
Indices: 12324--12509 Score: 162
Period size: 60 Copynumber: 3.1 Consensus size: 60
12314 TTAATTTATT
* * * * * * ** * **
12324 AAATATATTTTATT-TTATTTTGACTTTAAAAAATATATTTTAATCTTATTTTAATTTAA
1 AAATATATATTATTATTATATTAACTTTTAAAAATATATTTAAATCTAAAATAAAAGTAA
* * * * ** * **
12383 AAATATATCTTATTCTTATATTAACTTTTAAAAATATATTTTAATCTTATTTTAACTTAA
1 AAATATATATTATTATTATATTAACTTTTAAAAATATATTTAAATCTAAAATAAAAGTAA
12443 AAATATATATTATTATTATATTAACTTTTAAAAATATATCTTAAAT-TAAAATAAAAGT-A
1 AAATATATATTATTATTATATTAACTTTTAAAAATATAT-TTAAATCTAAAATAAAAGTAA
12502 AAATATAT
1 AAATATAT
12510 TTGTAAAAGT
Statistics
Matches: 111, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
59 22 0.20
60 84 0.76
61 5 0.05
ACGTcount: A:0.45, C:0.05, G:0.01, T:0.49
Consensus pattern (60 bp):
AAATATATATTATTATTATATTAACTTTTAAAAATATATTTAAATCTAAAATAAAAGTAA
Found at i:12516 original size:29 final size:28
Alignment explanation
Indices: 12473--12584 Score: 102
Period size: 29 Copynumber: 3.9 Consensus size: 28
12463 TTAACTTTTA
*
12473 AAAATATA-TCTTAAATTAAAATAAAAGT
1 AAAATATATTTTTAAATTAAAATAAAA-T
* **
12501 AAAATATATTTGTAAAAGTTAGTATAAGAAT
1 AAAATATATTT-TTAAA-TTAAAATAA-AAT
* *
12532 AAGATATATTTTTAAGA-TAAAATAAGATT
1 AAAATATATTTTTAA-ATTAAAATAA-AAT
12561 AAAATATATTTTTAAATTAAAATA
1 AAAATATATTTTTAAATTAAAATA
12585 TATTTAATAA
Statistics
Matches: 68, Mismatches: 10, Indels: 11
0.76 0.11 0.12
Matches are distributed among these distances:
28 9 0.13
29 31 0.46
30 7 0.10
31 19 0.28
32 2 0.03
ACGTcount: A:0.55, C:0.01, G:0.07, T:0.37
Consensus pattern (28 bp):
AAAATATATTTTTAAATTAAAATAAAAT
Found at i:12597 original size:19 final size:19
Alignment explanation
Indices: 12552--12599 Score: 71
Period size: 18 Copynumber: 2.5 Consensus size: 19
12542 TTTAAGATAA
12552 AATAAGATTAAAATATATTT
1 AATAA-ATTAAAATATATTT
*
12572 -TTAAATTAAAATATATTT
1 AATAAATTAAAATATATTT
12590 AATAAATTAA
1 AATAAATTAA
12600 GATAAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 14 0.56
19 11 0.44
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
AATAAATTAAAATATATTT
Found at i:13456 original size:335 final size:336
Alignment explanation
Indices: 12840--13511 Score: 872
Period size: 335 Copynumber: 2.0 Consensus size: 336
12830 CTACATATGT
* * *
12840 CACCTTATGATTAGTGGAAAGTATATTGAATTAAAAATAAAATAAAATAAAATTAATTATCTAAT
1 CACCCTATGATTAGTGGAAAGTATATTGAATTAAAAATAAAATAAAATAAAATTAATCATCCAAT
* ** * * * * *
12905 TGGTTGATGATGCATGGCTTCATCTTATTGGGTGATTTTATTTTAATTAATTAAAATTAAAAAAT
66 TGGATGATGACACATGGCTTCATCTAATTGAGTAAATTTATTTTAAGTAATTAAAATTAAAAAAT
* * **
12970 AATTAATATAATATGTAATTTTAGTAGCTAGATGTGTAATTATACAAAATGTTTTAACTGCCATG
131 AATTAATATAATATGTAATATCAGTAGCTAGATGTGTAATTATACAAAATGTTTTAACTGCCACA
* * *
13035 TCACCATGTATATTAAATATTAATGGTTAGTGGTTTGATTGAATACAATTAAATAGTTAAGTGAT
196 TCACCATGTATATTAAATATTAACGGCTAGTGGTTTGATTGAATACAATTAAATAGATAAGTGAT
* * * * * * * * *
13100 TTGATTGACAAAATTGAAAGATTAATGGTAAAAGTAAAATGATTAAATAGTTGAGTGGTTAATGG
261 CTAATTGACAAAATTGAAAGATCAATGATAAAAGTAAAAAGACTAAATAATCGAGTGGTCAATGG
13165 TATAGTTTACC
326 TATAGTTTACC
* * * *
13176 CACCCTATGATTGGTGGAAAGTATATTGAATTAAAAATAAATTAAAATATAATTAATCCTCCAAT
1 CACCCTATGATTAGTGGAAAGTATATTGAATTAAAAATAAAATAAAATAAAATTAATCATCCAAT
* * * **
13241 TGGATGATGACACATGGTTTCAT-TCAATT-ATTAAATTTATTTTAAGTAATTAAAATTAGGACC
66 TGGATGATGACACATGGCTTCATCT-AATTGAGTAAATTTATTTTAAGTAATTAAAATTA-AAAA
*
13304 A-AATTAATATAATATGTAAGTATCAGT-GACTAGATGTGTAATTATACCAAATGTTTTAACTGC
129 ATAATTAATATAATATGTAA-TATCAGTAG-CTAGATGTGTAATTATACAAAATGTTTTAACTGC
* *
13367 CACATCA-CATGT-TCATTAAATGTTAACGGCTAGTTGTTTGATTGAATACAATTAAATAGATAA
192 CACATCACCATGTAT-ATTAAATATTAACGGCTAGTGGTTTGATTGAATACAATTAAATAGATAA
* *
13430 GT-AGTCTAATTGACAAAATTGAAAGATCGATGATAAAAGTAAAAAGGCTAAATAATCGAGTGGT
256 GTGA-TCTAATTGACAAAATTGAAAGATCAATGATAAAAGTAAAAAGACTAAATAATCGAGTGGT
13494 CAATGGTATAGTTTACC
320 CAATGGTATAGTTTACC
13511 C
1 C
13512 TAAAGTTTAA
Statistics
Matches: 289, Mismatches: 41, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
334 2 0.01
335 162 0.56
336 125 0.43
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.36
Consensus pattern (336 bp):
CACCCTATGATTAGTGGAAAGTATATTGAATTAAAAATAAAATAAAATAAAATTAATCATCCAAT
TGGATGATGACACATGGCTTCATCTAATTGAGTAAATTTATTTTAAGTAATTAAAATTAAAAAAT
AATTAATATAATATGTAATATCAGTAGCTAGATGTGTAATTATACAAAATGTTTTAACTGCCACA
TCACCATGTATATTAAATATTAACGGCTAGTGGTTTGATTGAATACAATTAAATAGATAAGTGAT
CTAATTGACAAAATTGAAAGATCAATGATAAAAGTAAAAAGACTAAATAATCGAGTGGTCAATGG
TATAGTTTACC
Found at i:14226 original size:20 final size:20
Alignment explanation
Indices: 14201--14315 Score: 115
Period size: 20 Copynumber: 5.7 Consensus size: 20
14191 AATTGGTAAA
*
14201 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
14221 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
14242 ATCGCAACGCGATACTGCCT
1 ATCGCAACGCGATACTGACT
*
14262 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* **
14282 TTCGCAACGCGATTTTGACT
1 ATCGCAACGCGATACTGACT
* *
14302 TTCGCAACGAGATA
1 ATCGCAACGCGATA
14316 ATATAGAATC
Statistics
Matches: 80, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.03
20 62 0.77
21 15 0.19
22 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:14338 original size:41 final size:41
Alignment explanation
Indices: 14198--14335 Score: 145
Period size: 41 Copynumber: 3.4 Consensus size: 41
14188 GTGAATTGGT
* *
14198 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* *
14239 AAAATCGCAACGCGATACTGCCTTTCGCAACGCGATACTGAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAAT-AC
** ** * *
14281 --TTTCGCAACGCGATTTTGACTTTCGCAACGAGATAATAT
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* *
14320 AGAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
14336 TTTCAAAGTT
Statistics
Matches: 79, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
39 1 0.01
40 30 0.38
41 46 0.58
42 2 0.03
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
Found at i:15105 original size:24 final size:24
Alignment explanation
Indices: 15048--15107 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
15038 TAGTCAGTAT
*
15048 TCGAAATTTGATCTTGGTCAATAC
1 TCGAAATTTGATATTGGTCAATAC
* * *
15072 CCGGACTTTGATATTGGTCAATAC
1 TCGAAATTTGATATTGGTCAATAC
*
15096 TCGAATTTTGAT
1 TCGAAATTTGAT
15108 GATGTTTCAG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (24 bp):
TCGAAATTTGATATTGGTCAATAC
Found at i:15299 original size:12 final size:12
Alignment explanation
Indices: 15282--15306 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
15272 ATATAATCCT
15282 GAAGAAGAAAAA
1 GAAGAAGAAAAA
15294 GAAGAAGAAAAA
1 GAAGAAGAAAAA
15306 G
1 G
15307 TCTCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:17622 original size:19 final size:19
Alignment explanation
Indices: 17600--17691 Score: 87
Period size: 19 Copynumber: 5.4 Consensus size: 19
17590 GGAAATTACT
17600 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
17619 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
17633 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
17652 ATCGCAACGCG-AAT----
1 ATCGCAATGCGAAATGAAA
*
17666 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
17685 ATCGCAA
1 ATCGCAA
17692 CGAGGGAATC
Statistics
Matches: 57, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 19 0.33
15 4 0.07
16 2 0.04
17 2 0.04
18 4 0.07
19 26 0.46
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:17642 original size:33 final size:33
Alignment explanation
Indices: 17600--17726 Score: 193
Period size: 33 Copynumber: 3.8 Consensus size: 33
17590 GGAAATTACT
17600 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
17633 ATCGCAATGCGAAATGAAAATCGCAACGCGA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
17665 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
17699 ATCGCAATGTGAAATGAAAATTGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
17727 CGAATTTAAT
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
32 1 0.01
33 83 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.18, G:0.24, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:17707 original size:66 final size:66
Alignment explanation
Indices: 17601--17733 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
17591 GAAATTACTA
17601 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
17666 T
66 T
* * *
17667 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGTGAAATGAAAATTGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
17732 T
66 T
17733 T
1 T
17734 AATTTCGCGT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:17757 original size:19 final size:19
Alignment explanation
Indices: 17735--17787 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
17725 CGCGAATTTA
17735 ATTTCGCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
17754 ATTTCGCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
*
17773 ATTTCGCATTGCGAT
1 ATTTCGCGTTGCGAT
17788 AGTACTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.45
Consensus pattern (19 bp):
ATTTCGCGTTGCGATTTTC
Found at i:17913 original size:14 final size:14
Alignment explanation
Indices: 17894--17929 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
17884 CATCAATTAA
*
17894 ACAAATCAACTTTT
1 ACAAATCAACCTTT
17908 ACAAATC-ACCTTT
1 ACAAATCAACCTTT
17921 ACAAATCAA
1 ACAAATCAA
17930 TTAAACAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.28
Consensus pattern (14 bp):
ACAAATCAACCTTT
Found at i:19342 original size:21 final size:21
Alignment explanation
Indices: 19276--19342 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
19266 GTGAATCGGG
*
19276 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
19296 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
19318 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
19339 CTCT
1 CTCT
19343 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:19361 original size:42 final size:41
Alignment explanation
Indices: 19276--19384 Score: 103
Period size: 42 Copynumber: 2.6 Consensus size: 41
19266 GTGAATCGGG
* *
19276 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCAACGATGACAGGGGC
* * *
19318 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCAACG-ATGACAGGGGC
* * * *
19360 CTCTTTAACGATAGGAGTGGACTCT
1 CTCTTGAACGGTGGGAGGGGACTCT
19385 TGAGAGATGA
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
41 4 0.07
42 48 0.86
43 4 0.07
ACGTcount: A:0.22, C:0.19, G:0.35, T:0.24
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCAACGATGACAGGGGC
Found at i:19791 original size:91 final size:90
Alignment explanation
Indices: 19616--19800 Score: 291
Period size: 91 Copynumber: 2.0 Consensus size: 90
19606 ATTTCAAACT
* *
19616 TTCAACCAAAAGATAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
19681 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
19709 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
*
19773 GTATTGGCAGCAACCGAATAAATTTAC
64 GAATTGGCAGCAACCGAATAAATTTAC
19800 T
1 T
19801 AAGCAATCTA
Statistics
Matches: 87, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
91 42 0.48
93 18 0.21
95 27 0.31
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:21520 original size:20 final size:19
Alignment explanation
Indices: 21489--21629 Score: 104
Period size: 19 Copynumber: 7.8 Consensus size: 19
21479 TCTTTTGGTT
21489 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
21508 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
21529 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
21548 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
** *
21562 GAAATGACTATCGCGACGA
1 GAAATGAAAATCGCAACGA
*
21581 G--A-G--AATCGCAACGT
1 GAAATGAAAATCGCAACGA
*
21595 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
21614 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
21630 TATTCTCTCG
Statistics
Matches: 96, Mismatches: 14, Indels: 24
0.72 0.10 0.18
Matches are distributed among these distances:
14 19 0.20
16 4 0.04
17 4 0.04
19 38 0.40
20 29 0.30
21 2 0.02
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:21571 original size:33 final size:33
Alignment explanation
Indices: 21514--21612 Score: 153
Period size: 33 Copynumber: 3.0 Consensus size: 33
21504 ACGAGATAAT
21514 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
*
21548 GAGAATCGCAACGCGAAATGACTATCGCGACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
* **
21581 GAGAATCGCAACGTGAAATGAAAATCGCAACG
1 GAGAATCGCAACGCGAAATGACTATCGCAACG
21613 CGAAATGAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
33 46 0.77
34 14 0.23
ACGTcount: A:0.39, C:0.22, G:0.26, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:22292 original size:41 final size:42
Alignment explanation
Indices: 22191--22324 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 42
22181 CGCTATGTAA
* * **
22191 ATCGCGTTGCGAAAGTCAGAATCGCTTTGCGA--AAGTCAGT
1 ATCGCGTTGCGAAAGTCAGTATCGCATTGCGATTTTGTCAGT
* * * *
22231 ATCACGTTGCGAAAGGCAGTATCGCGTTGCGATTTTGT-ATT
1 ATCGCGTTGCGAAAGTCAGTATCGCATTGCGATTTTGTCAGT
* ** *
22272 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGAAAGTCAGTATCGCATTGCGATTTTGTCAGT
22314 -TCGCGTTGCGA
1 ATCGCGTTGCGA
22325 TTTACTTATT
Statistics
Matches: 77, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
40 28 0.36
41 45 0.58
42 4 0.05
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.31
Consensus pattern (42 bp):
ATCGCGTTGCGAAAGTCAGTATCGCATTGCGATTTTGTCAGT
Found at i:22304 original size:20 final size:20
Alignment explanation
Indices: 22191--22303 Score: 120
Period size: 20 Copynumber: 5.6 Consensus size: 20
22181 CGCTATGTAA
*
22191 ATCGCGTTGCGAAAGTCAGA
1 ATCGCGTTGCGAAAGTCAGT
*
22211 ATCGCTTTGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTCAGT
* *
22231 ATCACGTTGCGAAAGGCAGT
1 ATCGCGTTGCGAAAGTCAGT
** *
22251 ATCGCGTTGCGATTTTGT-ATT
1 ATCGCGTTGCGA--AAGTCAGT
*
22272 ATCGCGTTGCGATAGTCAGT
1 ATCGCGTTGCGAAAGTCAGT
*
22292 ATCGCATTGCGA
1 ATCGCGTTGCGA
22304 TTTTCCCAAT
Statistics
Matches: 77, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
19 3 0.04
20 59 0.77
21 14 0.18
22 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.29
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTCAGT
Found at i:22415 original size:21 final size:21
Alignment explanation
Indices: 22375--22415 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
22365 ACTGTAGACC
**
22375 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
22396 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
22416 GCGAATTTGC
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:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:27110 original size:35 final size:36
Alignment explanation
Indices: 27064--27134 Score: 126
Period size: 35 Copynumber: 2.0 Consensus size: 36
27054 TTTTTTTTTC
27064 ATTCATCTTTTTGCCAATTACCTTTATCAAC-GTTT
1 ATTCATCTTTTTGCCAATTACCTTTATCAACAGTTT
*
27099 ATTCATCTTTTTGCCGATTACCTTTATCAACAGTTT
1 ATTCATCTTTTTGCCAATTACCTTTATCAACAGTTT
27135 CCTAGTGCTT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 30 0.88
36 4 0.12
ACGTcount: A:0.23, C:0.23, G:0.07, T:0.48
Consensus pattern (36 bp):
ATTCATCTTTTTGCCAATTACCTTTATCAACAGTTT
Found at i:37243 original size:6 final size:6
Alignment explanation
Indices: 37232--37274 Score: 86
Period size: 6 Copynumber: 7.2 Consensus size: 6
37222 TTTCCTTCAC
37232 TTCCGA TTCCGA TTCCGA TTCCGA TTCCGA TTCCGA TTCCGA T
1 TTCCGA TTCCGA TTCCGA TTCCGA TTCCGA TTCCGA TTCCGA T
37275 ATTTAGTACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.16, C:0.33, G:0.16, T:0.35
Consensus pattern (6 bp):
TTCCGA
Found at i:37895 original size:2 final size:2
Alignment explanation
Indices: 37888--37913 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
37878 TGTACACAGA
37888 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
37914 TAAGAGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47260 original size:32 final size:32
Alignment explanation
Indices: 47219--47292 Score: 130
Period size: 32 Copynumber: 2.3 Consensus size: 32
47209 CACCATCCTT
*
47219 ATTCTAATTTGGTATTTTCCAATCCCATCCCA
1 ATTCCAATTTGGTATTTTCCAATCCCATCCCA
*
47251 ATTCCAATTTGGTATTTTTCAATCCCATCCCA
1 ATTCCAATTTGGTATTTTCCAATCCCATCCCA
47283 ATTCCAATTT
1 ATTCCAATTT
47293 AGTACCAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.26, C:0.27, G:0.05, T:0.42
Consensus pattern (32 bp):
ATTCCAATTTGGTATTTTCCAATCCCATCCCA
Found at i:48342 original size:23 final size:24
Alignment explanation
Indices: 48314--48373 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 24
48304 CAGTGCATAA
* *
48314 GCACTAAT-CTGGAGTGCACGAAT
1 GCACTAATACTAGAGTGCACAAAT
*
48337 GCACTAATACTAGAGTGTACAAAT
1 GCACTAATACTAGAGTGCACAAAT
*
48361 ACACTAA-ACTAGA
1 GCACTAATACTAGA
48374 TTGATCTATA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 14 0.44
24 18 0.56
ACGTcount: A:0.40, C:0.20, G:0.18, T:0.22
Consensus pattern (24 bp):
GCACTAATACTAGAGTGCACAAAT
Found at i:58051 original size:2 final size:2
Alignment explanation
Indices: 58044--58070 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
58034 CCGCCCCGAT
58044 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
58071 TTTTATATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:60476 original size:29 final size:30
Alignment explanation
Indices: 60406--60465 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
60396 CAATTTAAGG
60406 CAAAATGGTTTTTAGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTAGACTTGAATTGAATTTA
*
60437 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTAGACTTGAATTGAATTTA
60466 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTAGACTTGAATTGAATTTA
Found at i:60570 original size:22 final size:22
Alignment explanation
Indices: 60545--60599 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
60535 TATGGTACCG
60545 ATACTCCCCTGCAGGGGTATGC
1 ATACTCCCCTGCAGGGGTATGC
60567 ATACTCCCCTGCAGGGGTATGC
1 ATACTCCCCTGCAGGGGTATGC
*
60589 ATACCCCCCTG
1 ATACTCCCCTG
60600 AAGGCTCAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.18, C:0.36, G:0.24, T:0.22
Consensus pattern (22 bp):
ATACTCCCCTGCAGGGGTATGC
Found at i:61059 original size:34 final size:32
Alignment explanation
Indices: 61014--61083 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
61004 TTTTGTAAAG
*
61014 GGGAAAGGTTCTAGCTAATCCCGTATAAAAGCTA
1 GGGAAAGGTTCTAGCTAATCCCGGA-AAAA-CTA
* * *
61048 GGGAAATGTTCTAGTTTATCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTAATCCCGGAAAAACTA
61080 GGGA
1 GGGA
61084 GTTTGTAAGG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 7 0.22
33 4 0.12
34 21 0.66
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTAATCCCGGAAAAACTA
Found at i:71451 original size:37 final size:37
Alignment explanation
Indices: 71410--71484 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
71400 ACTCTCTTTA
71410 GGTTTTTGAAAAATACAAATTCTAGTGTGCTATTTTG
1 GGTTTTTGAAAAATACAAATTCTAGTGTGCTATTTTG
71447 GGTTTTTGAAAAATACAAATTCTAGTGTGCTATTTTG
1 GGTTTTTGAAAAATACAAATTCTAGTGTGCTATTTTG
71484 G
1 G
71485 TATTGATACT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.29, C:0.08, G:0.20, T:0.43
Consensus pattern (37 bp):
GGTTTTTGAAAAATACAAATTCTAGTGTGCTATTTTG
Found at i:78517 original size:566 final size:566
Alignment explanation
Indices: 77445--78580 Score: 2164
Period size: 566 Copynumber: 2.0 Consensus size: 566
77435 TTGTGAGAAA
77445 AAAATGGGTTAAAAATGTAGAGTTGACAAATACTACTAAGATGAACTAAGTATCATTGTTGAAAG
1 AAAATGGGTTAAAAATGTAGAGTTGACAAATACTACTAAGATGAACTAAGTATCATTGTTGAAAG
*
77510 TCACCAATAAAGCTGGAAATATTTTGTATAAATGGCATACAATAATTTCTTCGTTTAATCATTGT
66 TCACCAATAAAGCTGGAAATATTTTGTATAAATGGCATACAATAATTTCTTCATTTAATCATTGT
*
77575 GATTAAAGATTTTCCAACAAATGATCAAATATAATGAAATCCCAAACAACGCATTCACCTCTCAG
131 GATTAAAGATTTTCCAACAAATGATCAAATATAATGAAATCCCAAACAACACATTCACCTCTCAG
* *
77640 TCTCTTTCGCTCACATGCACTCTCGTTTTGTTTTTGTTCTTCAGTTTTCCGGCATGTAAAATTGT
196 TCTCTTTCGCTCACATGAACTCTCGTTTTGTTTTTGTTATTCAGTTTTCCGGCATGTAAAATTGT
*
77705 AAACCCAAGCAGTGTTCTGTTTTTTAGCTTTTTATTTACAAAGAAAAAATGGAGGAAAAATTGCT
261 AAACCCAAGCAGTGTTATGTTTTTTAGCTTTTTATTTACAAAGAAAAAATGGAGGAAAAATTGCT
77770 TGAACGCAACACCGATTGTGTTTATTTCTTAGCCTCTCCCTTCACTTGCAAGAAGATATTTATTT
326 TGAACGCAACACCGATTGTGTTTATTTCTTAGCCTCTCCCTTCACTTGCAAGAAGATATTTATTT
*
77835 TCTCTTTTGGGCTATTCGGAAGTAAGCTTTTCCTTTTTCGCACTTTCCCATTTTCATCTCGCATT
391 TCTCTTTTGGGCTATTCAGAAGTAAGCTTTTCCTTTTTCGCACTTTCCCATTTTCATCTCGCATT
* *
77900 GCGTGTTTTATGTTGAAATTTTTATGTTTCTGGAAATGTATGTCAAGGATATGGATATTCGGTGT
456 ACGTGTTTTATGTTGAAATTTTTATGTTTCTGGAAATGTATGTCAAGGATATGGATATTCAGTGT
77965 TAGTTTTGAACCAAAACCATTTAATTTTCTTTCTTTCTTCTTAATC
521 TAGTTTTGAACCAAAACCATTTAATTTTCTTTCTTTCTTCTTAATC
*
78011 AAAATGGGTTAGAAATGTAGAGTTGACAAATACTACTAAGATGAACTAAGTATCATTGTTGAAAG
1 AAAATGGGTTAAAAATGTAGAGTTGACAAATACTACTAAGATGAACTAAGTATCATTGTTGAAAG
*
78076 TCATCAATAAAGCTGGAAATATTTTGTATAAATGGCATACAATAATTTCTTCATTTAATCATTGT
66 TCACCAATAAAGCTGGAAATATTTTGTATAAATGGCATACAATAATTTCTTCATTTAATCATTGT
78141 GATTAAAGATTTTCCAACAAATGATCAAATATAATGAAATCCCAAACAACACATTCACCTCTCAG
131 GATTAAAGATTTTCCAACAAATGATCAAATATAATGAAATCCCAAACAACACATTCACCTCTCAG
78206 TCTCTTTCGCTCACATGAACTCTCGTTTTGTTTTTGTTATTCAGTTTTCCGGCATGTAAAATTGT
196 TCTCTTTCGCTCACATGAACTCTCGTTTTGTTTTTGTTATTCAGTTTTCCGGCATGTAAAATTGT
78271 AAACCCAAGCAGTGTTATGTTTTTTAGCTTTTTATTTACAAAGAAAAAATGGAGGAAAAATTGCT
261 AAACCCAAGCAGTGTTATGTTTTTTAGCTTTTTATTTACAAAGAAAAAATGGAGGAAAAATTGCT
*
78336 TGAACGCAACACCGATTGTGTTTATTTCTTAGCCTCTCCCTTCACTTGCAAGAAGGTATTTATTT
326 TGAACGCAACACCGATTGTGTTTATTTCTTAGCCTCTCCCTTCACTTGCAAGAAGATATTTATTT
78401 TCTCTTTTGGGCTATTCAGAAGTAAGCTTTTCCTTTTTCGCACTTTCCCATTTTCATCTCGCATT
391 TCTCTTTTGGGCTATTCAGAAGTAAGCTTTTCCTTTTTCGCACTTTCCCATTTTCATCTCGCATT
*
78466 ACGTGTTTTATGTTGAAATTTTTATGTTTCTGGAACTGTATGTCAAGGATATGGATATTCAGTGT
456 ACGTGTTTTATGTTGAAATTTTTATGTTTCTGGAAATGTATGTCAAGGATATGGATATTCAGTGT
78531 TAGTTTTGAACCAAAACCATTTAATTTTCTTTCTTTCTTCTTAATC
521 TAGTTTTGAACCAAAACCATTTAATTTTCTTTCTTTCTTCTTAATC
78577 AAAA
1 AAAA
78581 CTTTTAGTAT
Statistics
Matches: 558, Mismatches: 12, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
566 558 1.00
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.39
Consensus pattern (566 bp):
AAAATGGGTTAAAAATGTAGAGTTGACAAATACTACTAAGATGAACTAAGTATCATTGTTGAAAG
TCACCAATAAAGCTGGAAATATTTTGTATAAATGGCATACAATAATTTCTTCATTTAATCATTGT
GATTAAAGATTTTCCAACAAATGATCAAATATAATGAAATCCCAAACAACACATTCACCTCTCAG
TCTCTTTCGCTCACATGAACTCTCGTTTTGTTTTTGTTATTCAGTTTTCCGGCATGTAAAATTGT
AAACCCAAGCAGTGTTATGTTTTTTAGCTTTTTATTTACAAAGAAAAAATGGAGGAAAAATTGCT
TGAACGCAACACCGATTGTGTTTATTTCTTAGCCTCTCCCTTCACTTGCAAGAAGATATTTATTT
TCTCTTTTGGGCTATTCAGAAGTAAGCTTTTCCTTTTTCGCACTTTCCCATTTTCATCTCGCATT
ACGTGTTTTATGTTGAAATTTTTATGTTTCTGGAAATGTATGTCAAGGATATGGATATTCAGTGT
TAGTTTTGAACCAAAACCATTTAATTTTCTTTCTTTCTTCTTAATC
Found at i:79752 original size:35 final size:35
Alignment explanation
Indices: 79678--79745 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
79668 TTCATATTCA
*
79678 AAATTTCAAAACACTTCAATTACATTCTAAACCCC
1 AAATTCCAAAACACTTCAATTACATTCTAAACCCC
* *
79713 AAATTCCAAAATACTTCAATTATATTCTAAACC
1 AAATTCCAAAACACTTCAATTACATTCTAAACC
79746 TTAAATTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (35 bp):
AAATTCCAAAACACTTCAATTACATTCTAAACCCC
Found at i:79803 original size:35 final size:35
Alignment explanation
Indices: 79748--79824 Score: 109
Period size: 35 Copynumber: 2.2 Consensus size: 35
79738 TCTAAACCTT
* *
79748 AAATTAAAGTATTTTAGAATTTAAGGTTTAAAATA
1 AAATTGAATTATTTTAGAATTTAAGGTTTAAAATA
* * *
79783 TAATTGAATTATTTTAGAATTTGAGGTTTAGAATA
1 AAATTGAATTATTTTAGAATTTAAGGTTTAAAATA
79818 AAATTGA
1 AAATTGA
79825 TGATTGTGTT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.44, C:0.00, G:0.14, T:0.42
Consensus pattern (35 bp):
AAATTGAATTATTTTAGAATTTAAGGTTTAAAATA
Found at i:80299 original size:14 final size:14
Alignment explanation
Indices: 80276--80354 Score: 61
Period size: 14 Copynumber: 5.6 Consensus size: 14
80266 AAATATTAAG
*
80276 TTAGAGTTTATGGT
1 TTAGAATTTATGGT
80290 TTAGAATTTATGGT
1 TTAGAATTTATGGT
** *
80304 TTAGAGGTTATGGGG
1 TTAGAATTTAT-GGT
* *
80319 TTATG-TTTTAAGGT
1 TTA-GAATTTATGGT
*
80333 TTATAATTTATGGT
1 TTAGAATTTATGGT
*
80347 TTTGAATT
1 TTAGAATT
80355 AGAACAGCGT
Statistics
Matches: 49, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
14 40 0.82
15 8 0.16
16 1 0.02
ACGTcount: A:0.24, C:0.00, G:0.25, T:0.51
Consensus pattern (14 bp):
TTAGAATTTATGGT
Found at i:80681 original size:36 final size:34
Alignment explanation
Indices: 80641--80756 Score: 100
Period size: 36 Copynumber: 3.4 Consensus size: 34
80631 TACTAGTTTT
80641 TTTTAAGTTTAATGTATAATAATTGTACAAATTATA
1 TTTTAAGTTTAATGTA-AATAATTGT-CAAATTATA
*
80677 TTTTAAGTTTAATATAAATAATAT-T--AATT-T-
1 TTTTAAGTTTAATGTAAATAAT-TGTCAAATTATA
* *
80707 TTATAAGGTTTAATGTAAAAATAAATGTTCAAATTATA
1 TTTTAA-GTTTAATGT--AAATAATTG-TCAAATTATA
80745 TTTTAA-TTTAAT
1 TTTTAAGTTTAAT
80757 TTTAGTGTTT
Statistics
Matches: 65, Mismatches: 5, Indels: 20
0.72 0.06 0.22
Matches are distributed among these distances:
30 5 0.08
31 9 0.14
32 5 0.08
33 6 0.09
34 1 0.02
35 7 0.11
36 26 0.40
37 1 0.02
38 5 0.08
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (34 bp):
TTTTAAGTTTAATGTAAATAATTGTCAAATTATA
Found at i:80708 original size:67 final size:67
Alignment explanation
Indices: 80619--80756 Score: 181
Period size: 67 Copynumber: 2.1 Consensus size: 67
80609 TTGGGTATTG
* * * *
80619 TAATATAAAGAATACTAGTTTTTTTTAA-GTTTAATGT-ATAATAATTGTACAAATTATATTTTA
1 TAATATAAAGAATACTA-ATTTTTATAAGGTTTAATGTAAAAATAAATGTACAAATTATATTTTA
80682 AGTT
65 A-TT
* * *
80686 TAATATAAATAATATTAATTTTTATAAGGTTTAATGTAAAAATAAATGTTCAAATTATATTTTAA
1 TAATATAAAGAATACTAATTTTTATAAGGTTTAATGTAAAAATAAATGTACAAATTATATTTTAA
80751 TT
66 TT
80753 TAAT
1 TAAT
80757 TTTAGTGTTT
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
66 8 0.13
67 30 0.48
68 24 0.39
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.47
Consensus pattern (67 bp):
TAATATAAAGAATACTAATTTTTATAAGGTTTAATGTAAAAATAAATGTACAAATTATATTTTAA
TT
Found at i:81168 original size:22 final size:22
Alignment explanation
Indices: 81143--81195 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 22
81133 CACCAACCCC
*
81143 GTATATGAAC-TCTCACCTTTGT
1 GTATATGAACAAC-CACCTTTGT
81165 G--TATGAACAACCACCTTTGT
1 GTATATGAACAACCACCTTTGT
81185 G--TATGAACAAC
1 GTATATGAACAAC
81196 GAACATATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 27 0.93
21 1 0.03
22 1 0.03
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (22 bp):
GTATATGAACAACCACCTTTGT
Found at i:81171 original size:20 final size:20
Alignment explanation
Indices: 81156--81195 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
81146 TATGAACTCT
81156 CACCTTTGTGTATGAACAAC
1 CACCTTTGTGTATGAACAAC
81176 CACCTTTGTGTATGAACAAC
1 CACCTTTGTGTATGAACAAC
81196 GAACATATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (20 bp):
CACCTTTGTGTATGAACAAC
Found at i:82091 original size:21 final size:21
Alignment explanation
Indices: 82062--82117 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
82052 TATTTAGTAT
82062 GGTATCGATACCCCCATATAG
1 GGTATCGATACCCCCATATAG
*
82083 GGTACCGATACCCCCATATAG
1 GGTATCGATACCCCCATATAG
82104 GGTATCGATACCCC
1 GGTATCGATACCCC
82118 TATGAACATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.27, C:0.32, G:0.20, T:0.21
Consensus pattern (21 bp):
GGTATCGATACCCCCATATAG
Found at i:82215 original size:19 final size:20
Alignment explanation
Indices: 82159--82212 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
82149 ATGCTCGGAT
82159 GGTACCGATACCCCCTATAG
1 GGTACCGATACCCCCTATAG
82179 GGTACCGATACCCCCTATAG
1 GGTACCGATACCCCCTATAG
82199 GGTACCGATACCCC
1 GGTACCGATACCCC
82213 TATGAACATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.24, C:0.37, G:0.20, T:0.19
Consensus pattern (20 bp):
GGTACCGATACCCCCTATAG
Found at i:82216 original size:95 final size:95
Alignment explanation
Indices: 82060--82307 Score: 383
Period size: 95 Copynumber: 2.6 Consensus size: 95
82050 TTTATTTAGT
* *
82060 ATGGTATCGATACCCCCATATAGGGTACCGATACCCCCATATAGGGTATCGATACCCCTATGAAC
1 ATGGTACCGATACCCCC-TATAGGGTACCGATACCCCC-TATAGGGTACCGATACCCCTATGAAC
* *
82125 ATTTTGGTTCCGAGAAATAATAGAATGCTCGG
64 ATTTTGATTCCGAGAAATAACAGAATGCTCGG
82157 ATGGTACCGATACCCCCTATAGGGTACCGATACCCCCTATAGGGTACCGATACCCCTATGAACAT
1 ATGGTACCGATACCCCCTATAGGGTACCGATACCCCCTATAGGGTACCGATACCCCTATGAACAT
82222 TTTGATTCCGAGAAATAACAGAATGCTCGG
66 TTTGATTCCGAGAAATAACAGAATGCTCGG
* *
82252 ATGGTACCGATACCCCCTAGTA-GGTATCAATACCCCCTACTTA-GGTACCGATACCC
1 ATGGTACCGATACCCCCTA-TAGGGTACCGATACCCCCTA--TAGGGTACCGATACCC
82308 TCAGGCATTT
Statistics
Matches: 142, Mismatches: 6, Indels: 7
0.92 0.04 0.05
Matches are distributed among these distances:
95 89 0.63
96 35 0.25
97 18 0.13
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.24
Consensus pattern (95 bp):
ATGGTACCGATACCCCCTATAGGGTACCGATACCCCCTATAGGGTACCGATACCCCTATGAACAT
TTTGATTCCGAGAAATAACAGAATGCTCGG
Found at i:82296 original size:21 final size:20
Alignment explanation
Indices: 82254--82307 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
82244 ATGCTCGGAT
*
82254 GGTACCGATACCCCCTAGTA
1 GGTACCAATACCCCCTAGTA
* *
82274 GGTATCAATACCCCCTACTTA
1 GGTACCAATACCCCCTA-GTA
*
82295 GGTACCGATACCC
1 GGTACCAATACCC
82308 TCAGGCATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.26, C:0.35, G:0.17, T:0.22
Consensus pattern (20 bp):
GGTACCAATACCCCCTAGTA
Found at i:91533 original size:19 final size:19
Alignment explanation
Indices: 91461--91538 Score: 59
Period size: 19 Copynumber: 3.9 Consensus size: 19
91451 ATATTTGGCA
* *
91461 GAGGGAATCGATACCCCCAT
1 GAGGGAATCGAT-TCCCCTT
*
91481 AAGGGAA-CGATTCCCCCTTT
1 GAGGGAATCGATT-CCCC-TT
*
91501 GAATGGGAACCGATTCCCCTT
1 G-A-GGGAATCGATTCCCCTT
*
91522 GAGGGAATCGATACCCC
1 GAGGGAATCGATTCCCC
91539 CACAGGTTCT
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
19 21 0.45
20 8 0.17
21 4 0.09
22 9 0.19
23 5 0.11
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.19
Consensus pattern (19 bp):
GAGGGAATCGATTCCCCTT
Done.