Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003213.1 Hibiscus syriacus cultivar Beakdansim tig00006766_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: 119455
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:5066 original size:15 final size:16
Alignment explanation
Indices: 5038--5070 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
5028 AAAATCTTTC
5038 TTTCCCGTTCTGGATT
1 TTTCCCGTTCTGGATT
5054 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTGGATT
5069 TT
1 TT
5071 GATCTGCCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.06, C:0.24, G:0.18, T:0.52
Consensus pattern (16 bp):
TTTCCCGTTCTGGATT
Found at i:9624 original size:16 final size:16
Alignment explanation
Indices: 9599--9632 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
9589 ACCCATGGGC
*
9599 AACTTCAATGCTTCCA
1 AACTTAAATGCTTCCA
9615 AACTTAAATGCTTCCA
1 AACTTAAATGCTTCCA
9631 AA
1 AA
9633 AAGTGACCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.38, C:0.26, G:0.06, T:0.29
Consensus pattern (16 bp):
AACTTAAATGCTTCCA
Found at i:18158 original size:164 final size:164
Alignment explanation
Indices: 17845--18176 Score: 506
Period size: 164 Copynumber: 2.0 Consensus size: 164
17835 CAATCCACTC
* *
17845 TTTTGTTCACCTTACCTTGATAAATATCTGGCTTCTTTTTAGTGTTGTAGAGGTTGTGGTTGACT
1 TTTTGTTCACCTTACCTTGATAAATATCTGGCTTCTTTTTAATGTTGTAGAGGTTGTGGTTAACT
* * * * *
17910 GTCTTAGCCATTGATCTCTTGAATGAACTGGAATTTTCTGATATACAGATCTCTTTTTTATGGAT
66 GTCTTAGCCATCGATCACTTGAATGAAATGGAATTTTCTGATAGACAGATCTCTTTTTTATGCAT
** * *
17975 TTTTTTCTTTTTCTTTTCTCCATACAT-ACAAATA
131 AATTTTCTATTTATTTTCTCCATAC-TCACAAATA
18009 TTTTGTTCACCTTACCTTGATAAATATCTGGCTTCTTTTTAATGTTGTAGAGGTTGTGGTTAACT
1 TTTTGTTCACCTTACCTTGATAAATATCTGGCTTCTTTTTAATGTTGTAGAGGTTGTGGTTAACT
**
18074 GTCTTAGCCCATCGATCACTTGAATGAAATGGAATTTTCTGATAGATGGATCTCTTTTTTATGCA
66 GTCTTAG-CCATCGATCACTTGAATGAAATGGAATTTTCTGATAGACAGATCTCTTTTTTATGCA
*
18139 -AATTTTCTATTTATTTTCTCCATGCTCACAAATA
130 TAATTTTCTATTTATTTTCTCCATACTCACAAATA
18173 TTTT
1 TTTT
18177 CACCTTCAGG
Statistics
Matches: 152, Mismatches: 14, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
163 1 0.01
164 101 0.66
165 50 0.33
ACGTcount: A:0.23, C:0.16, G:0.15, T:0.46
Consensus pattern (164 bp):
TTTTGTTCACCTTACCTTGATAAATATCTGGCTTCTTTTTAATGTTGTAGAGGTTGTGGTTAACT
GTCTTAGCCATCGATCACTTGAATGAAATGGAATTTTCTGATAGACAGATCTCTTTTTTATGCAT
AATTTTCTATTTATTTTCTCCATACTCACAAATA
Found at i:33527 original size:20 final size:20
Alignment explanation
Indices: 33499--33550 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
33489 CATTTGGTTT
*
33499 ATAATAATTTTATTTTTCAAA
1 ATAA-AATTTTATTTCTCAAA
* *
33520 ATAAAATTTACATTTCTCTAA
1 ATAAAATTT-TATTTCTCAAA
33541 AT-AAATTTTA
1 ATAAAATTTTA
33551 CATCATTATT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 1 0.04
20 11 0.42
21 14 0.54
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (20 bp):
ATAAAATTTTATTTCTCAAA
Found at i:33534 original size:21 final size:21
Alignment explanation
Indices: 33510--33553 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
33500 TAATAATTTT
*
33510 ATTTTTCAAAATAAAATTTAC
1 ATTTCTCAAAATAAAATTTAC
* *
33531 ATTTCTCTAAATAAATTTTAC
1 ATTTCTCAAAATAAAATTTAC
33552 AT
1 AT
33554 CATTATTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.45
Consensus pattern (21 bp):
ATTTCTCAAAATAAAATTTAC
Found at i:34867 original size:21 final size:20
Alignment explanation
Indices: 34843--34887 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
34833 ACCCTAATTA
*
34843 AAACTCTAAATTATAAACCCT
1 AAACCCTAAATTAT-AACCCT
* *
34864 AAACCCTAACTTATAATCCT
1 AAACCCTAAATTATAACCCT
34884 AAAC
1 AAAC
34888 AATAGTAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.47, C:0.27, G:0.00, T:0.27
Consensus pattern (20 bp):
AAACCCTAAATTATAACCCT
Found at i:37060 original size:19 final size:19
Alignment explanation
Indices: 37036--37098 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
37026 ATTTATCTGG
37036 CGAATGTCCGACATATATT
1 CGAATGTCCGACATATATT
* * *
37055 CGAATGTCAGATC-TACATGA
1 CGAATGTCCGA-CATATAT-T
*
37075 CGTATGTCCGACATATATT
1 CGAATGTCCGACATATATT
37094 CGAAT
1 CGAAT
37099 CTCATATTTA
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
19 19 0.58
20 14 0.42
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (19 bp):
CGAATGTCCGACATATATT
Found at i:37082 original size:39 final size:39
Alignment explanation
Indices: 36959--37186 Score: 208
Period size: 39 Copynumber: 5.8 Consensus size: 39
36949 TATCTTTAAT
** * * * *
36959 GTATGTCCGACGCATATTCGAATCTCAAATTTGTC-TAAT
1 GTATGTCCGACATATATTCGAATCTCAGATTT-ACATGAC
* * ** * *
36998 GTATATCCGACATACATTTAAATCTCAAATTTATC-TGGC
1 GTATGTCCGACATATATTCGAATCTCAGATTTA-CATGAC
* * *
37037 GAATGTCCGACATATATTCGAATGTCAGATCTACATGAC
1 GTATGTCCGACATATATTCGAATCTCAGATTTACATGAC
*
37076 GTATGTCCGACATATATTCGAATCTCATATTTACATGAC
1 GTATGTCCGACATATATTCGAATCTCAGATTTACATGAC
* * ** *
37115 GTATGTCCGACGTATATTCGAATCTCGGATTTATGTAAC
1 GTATGTCCGACATATATTCGAATCTCAGATTTACATGAC
* * *
37154 GTATGTCCAACGTATATTCGAATCTCGGATTTA
1 GTATGTCCGACATATATTCGAATCTCAGATTTA
37187 TATAATAATA
Statistics
Matches: 157, Mismatches: 30, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
38 1 0.01
39 156 0.99
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.35
Consensus pattern (39 bp):
GTATGTCCGACATATATTCGAATCTCAGATTTACATGAC
Found at i:37186 original size:78 final size:78
Alignment explanation
Indices: 36959--37179 Score: 237
Period size: 78 Copynumber: 2.8 Consensus size: 78
36949 TATCTTTAAT
* * * * * * * **
36959 GTATGTCCGACGCATATTCGAATCTCAAATTTGTCTAATGTATATCCGACATACATTTAAATCTC
1 GTATGTCCGACGTATATTCGAATCTCAGATTTATATAACGTATGTCCGACATATATTCGAATCTC
*
37024 AAATTTATCTGGC
66 AAATTTATCTGAC
* * * * * *
37037 GAATGTCCGACATATATTCGAATGTCAGATCTACATGACGTATGTCCGACATATATTCGAATCTC
1 GTATGTCCGACGTATATTCGAATCTCAGATTTATATAACGTATGTCCGACATATATTCGAATCTC
*
37102 ATATTTA-CATGAC
66 AAATTTATC-TGAC
* * * *
37115 GTATGTCCGACGTATATTCGAATCTCGGATTTATGTAACGTATGTCCAACGTATATTCGAATCTC
1 GTATGTCCGACGTATATTCGAATCTCAGATTTATATAACGTATGTCCGACATATATTCGAATCTC
37180 GGATTTATAT
Statistics
Matches: 115, Mismatches: 27, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
77 1 0.01
78 114 0.99
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.34
Consensus pattern (78 bp):
GTATGTCCGACGTATATTCGAATCTCAGATTTATATAACGTATGTCCGACATATATTCGAATCTC
AAATTTATCTGAC
Found at i:39833 original size:31 final size:31
Alignment explanation
Indices: 39785--39846 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
39775 AAGTGTTCTA
39785 TACGAGCTGTGGCGAGAGGATGAAGCTTTGC
1 TACGAGCTGTGGCGAGAGGATGAAGCTTTGC
* *
39816 TACGTGCTGTGGTGAGAGGATGAAGCTTTGC
1 TACGAGCTGTGGCGAGAGGATGAAGCTTTGC
39847 ATGCGCCATG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.21, C:0.15, G:0.39, T:0.26
Consensus pattern (31 bp):
TACGAGCTGTGGCGAGAGGATGAAGCTTTGC
Found at i:39878 original size:22 final size:22
Alignment explanation
Indices: 39850--39903 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
39840 GCTTTGCATG
39850 CGCCATGCATGTCGGAAGAGGT
1 CGCCATGCATGTCGGAAGAGGT
*
39872 CGCCATGCACGTCGGAAGAGGT
1 CGCCATGCATGTCGGAAGAGGT
39894 CGCC-TGCATG
1 CGCCATGCATG
39904 CAATGGGGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 5 0.17
22 25 0.83
ACGTcount: A:0.20, C:0.28, G:0.35, T:0.17
Consensus pattern (22 bp):
CGCCATGCATGTCGGAAGAGGT
Found at i:39994 original size:29 final size:29
Alignment explanation
Indices: 39947--40034 Score: 104
Period size: 29 Copynumber: 3.0 Consensus size: 29
39937 AAGGCCAAGG
** *
39947 ACAAGGTCGCCCAACGTGCATGGCAACCT
1 ACAAGGTCGCCCGGCGTGCATGGCGACCT
* * *
39976 ACCATGTCGCCTGGCGTGCATGGCGACCT
1 ACAAGGTCGCCCGGCGTGCATGGCGACCT
* *
40005 ACAAGGTCGCCCGGAGGGCATGGCGACCT
1 ACAAGGTCGCCCGGCGTGCATGGCGACCT
40034 A
1 A
40035 TGCTGGGAAG
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.22, C:0.33, G:0.31, T:0.15
Consensus pattern (29 bp):
ACAAGGTCGCCCGGCGTGCATGGCGACCT
Found at i:40587 original size:43 final size:43
Alignment explanation
Indices: 40531--40706 Score: 280
Period size: 43 Copynumber: 4.1 Consensus size: 43
40521 TGGTAACAAA
* * *
40531 AAACGCCGTAATAGGTGTTGATATTTAGCGGCGTTTTTCCAAC
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCAC
*
40574 AAACGCCGCAATAGGTGTTGAGATTTAGCGGAGTTTTTCCCAC
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCAC
*
40617 AAACGCCGCAATAGGTGTTGAGATTTAGCAGCGTTTTTCCCAC
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCAC
* * *
40660 AAACACCGCAATATGTCTTGAGATTTAGCGGCGTTTTTCCCAC
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCAC
40703 AAAC
1 AAAC
40707 ACCGTAAAAG
Statistics
Matches: 123, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 123 1.00
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (43 bp):
AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCAC
Found at i:40740 original size:43 final size:43
Alignment explanation
Indices: 40556--40739 Score: 203
Period size: 43 Copynumber: 4.3 Consensus size: 43
40546 TGTTGATATT
* * * * *
40556 TAGCGGCGTTTTTCCAACAAACGCCGCAATAGGTGTTGAGATT
1 TAGCGGCGTTTTTCCCACAAACACCGCAATAAGTCTTGAGATA
* * * * *
40599 TAGCGGAGTTTTTCCCACAAACGCCGCAATAGGTGTTGAGATT
1 TAGCGGCGTTTTTCCCACAAACACCGCAATAAGTCTTGAGATA
* * *
40642 TAGCAGCGTTTTTCCCACAAACACCGCAATATGTCTTGAGATT
1 TAGCGGCGTTTTTCCCACAAACACCGCAATAAGTCTTGAGATA
*
40685 TAGCGGCGTTTTTCCCACAAACACCGTAA-AAGATC-TG-GTATA
1 TAGCGGCGTTTTTCCCACAAACACCGCAATAAG-TCTTGAG-ATA
40727 TAGCGGCGTTTTT
1 TAGCGGCGTTTTT
40740 TAGAACAAAT
Statistics
Matches: 128, Mismatches: 11, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
41 1 0.01
42 19 0.15
43 108 0.84
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.29
Consensus pattern (43 bp):
TAGCGGCGTTTTTCCCACAAACACCGCAATAAGTCTTGAGATA
Found at i:40755 original size:86 final size:86
Alignment explanation
Indices: 40556--40762 Score: 238
Period size: 86 Copynumber: 2.4 Consensus size: 86
40546 TGTTGATATT
*
40556 TAGCGGCGTTTTTCCAACAAACGCCGCAATAGGTGTTGAGATTTAGCGGAGTTTTTCCCACAAAC
1 TAGCGGCGTTTTTCCAACAAACGCCGCAATAGGTCTTGAGATTTAGCGGAGTTTTTCCCACAAAC
* * * * *
40621 GCCGCAATAGGTGTTGAGATT
66 ACCGCAAAAGATGCTGAGATA
* * * * *
40642 TAGCAGCGTTTTTCCCACAAACACCGCAATATGTCTTGAGATTTAGCGGCGTTTTTCCCACAAAC
1 TAGCGGCGTTTTTCCAACAAACGCCGCAATAGGTCTTGAGATTTAGCGGAGTTTTTCCCACAAAC
*
40707 ACCGTAAAAGAT-CTG-GTATA
66 ACCGCAAAAGATGCTGAG-ATA
** * *
40727 TAGCGGCGTTTTTTAGAACAAATGCCGCAAAAGGTC
1 TAGCGGCG-TTTTTCCAACAAACGCCGCAATAGGTC
40763 ATATCTATAG
Statistics
Matches: 99, Mismatches: 20, Indels: 4
0.80 0.16 0.03
Matches are distributed among these distances:
84 1 0.01
85 11 0.11
86 87 0.88
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (86 bp):
TAGCGGCGTTTTTCCAACAAACGCCGCAATAGGTCTTGAGATTTAGCGGAGTTTTTCCCACAAAC
ACCGCAAAAGATGCTGAGATA
Found at i:41343 original size:41 final size:41
Alignment explanation
Indices: 41269--41641 Score: 377
Period size: 41 Copynumber: 9.0 Consensus size: 41
41259 AATGAATACT
* * * * *
41269 GTACGAGTCTATCGCGACGTTTGTACAAAAACGCTACTAAA
1 GTACAAGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAA
* * * **
41310 GTATAAGCCTATAGCGGCGTTTGTATAAAAACGCTACTACT
1 GTACAAGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAA
* * * * * *
41351 GTACGAGTCTATCGTGACGTTTGTACAAAAACGCTACTAAA
1 GTACAAGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAA
* *
41392 GTACAAGCCTATAGCAGCGTTTGTATAAAAACGCCACTAAA
1 GTACAAGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAA
* * *
41433 GTACAAGTCTATTGCGGCATTTTTATAAAAACGCCACTAAA
1 GTACAAGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAA
* * * *
41474 GTACGAGTTTATAGCGGCGTTTGTATAAAAACACCGCTAAA
1 GTACAAGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAA
* * * * *
41515 GTACTACTCTATCGTGGCGTTTTTTATAAAAACGCCACTAAA
1 GTACAAGTCTATAGCGGCG-TTTGTATAAAAACGCCACTAAA
* *
41557 GTACGAGTCTATAGCGGCGTTTGTATAAAAACGTCACTAAA
1 GTACAAGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAA
* * * * * * *
41598 GTACTACTCTGTCGTGGCGTTTTGTATAAAAGCGCCGCTAAA
1 GTACAAGTCTATAGCGGCG-TTTGTATAAAAACGCCACTAAA
41640 GT
1 GT
41642 TACCATTTGT
Statistics
Matches: 271, Mismatches: 59, Indels: 3
0.81 0.18 0.01
Matches are distributed among these distances:
41 216 0.80
42 55 0.20
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (41 bp):
GTACAAGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAA
Found at i:41570 original size:83 final size:83
Alignment explanation
Indices: 41288--41641 Score: 433
Period size: 82 Copynumber: 4.3 Consensus size: 83
41278 TATCGCGACG
* * * * **
41288 TTTGTACAAAAACGCTACTAAAGTATAAGCCTATAGCGGCGTTTGTATAAAAACGCTACTACTGT
1 TTTGTATAAAAACGCCACTAAAGTACAAGCCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGT
* * *
41353 ACGAGTCTATCGTGACG-
66 ACTACTCTATCGTGGCGT
* * *
41370 TTTGTACAAAAACGCTACTAAAGTACAAGCCTATAGCAGCGTTTGTATAAAAACGCCACTAAAGT
1 TTTGTATAAAAACGCCACTAAAGTACAAGCCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGT
* * * * *
41435 ACAAGTCTATTGCGGCAT
66 ACTACTCTATCGTGGCGT
* ** * *
41453 TTT-TATAAAAACGCCACTAAAGTACGAGTTTATAGCGGCGTTTGTATAAAAACACCGCTAAAGT
1 TTTGTATAAAAACGCCACTAAAGTACAAGCCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGT
41517 ACTACTCTATCGTGGCGT
66 ACTACTCTATCGTGGCGT
* * * *
41535 TTTTTATAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGTCACTAAAGT
1 TTTGTATAAAAACGCCACTAAAGTACAAGCCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGT
*
41600 ACTACTCTGTCGTGGCGT
66 ACTACTCTATCGTGGCGT
* *
41618 TTTGTATAAAAGCGCCGCTAAAGT
1 TTTGTATAAAAACGCCACTAAAGT
41642 TACCATTTGT
Statistics
Matches: 239, Mismatches: 31, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
82 141 0.59
83 98 0.41
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (83 bp):
TTTGTATAAAAACGCCACTAAAGTACAAGCCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGT
ACTACTCTATCGTGGCGT
Found at i:42303 original size:23 final size:23
Alignment explanation
Indices: 42277--42329 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
42267 AAACATACCA
42277 AAAGACATAAAAAAACGTGTTAT
1 AAAGACATAAAAAAACGTGTTAT
*
42300 AAAGACATATAAAAACGTGTTAT
1 AAAGACATAAAAAAACGTGTTAT
*
42323 ACAGACA
1 AAAGACA
42330 GACTTATTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.55, C:0.11, G:0.13, T:0.21
Consensus pattern (23 bp):
AAAGACATAAAAAAACGTGTTAT
Found at i:42369 original size:20 final size:21
Alignment explanation
Indices: 42344--42385 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
42334 TATTGAAAAG
42344 AAAATAAAGAT-ACAAT-ATAA
1 AAAATAAA-ATGACAATAATAA
42364 AAAATAAAATGACAATAATAA
1 AAAATAAAATGACAATAATAA
42385 A
1 A
42386 TACTTACAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 2 0.10
20 13 0.65
21 5 0.25
ACGTcount: A:0.71, C:0.05, G:0.05, T:0.19
Consensus pattern (21 bp):
AAAATAAAATGACAATAATAA
Found at i:43531 original size:2 final size:2
Alignment explanation
Indices: 43524--43586 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
43514 TTTTTAAAAC
43524 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
43566 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
43587 CCCCCATCCG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:43694 original size:35 final size:35
Alignment explanation
Indices: 43649--43748 Score: 166
Period size: 35 Copynumber: 2.9 Consensus size: 35
43639 CGTCAAGTCC
43649 AGTAA-GCCCTGAGCACACAGCCGAGGAGCCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAGCCGGTA
43683 AGTAAGGCCCTGAGCACACAGCCGAGGAGCCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAGCCGGTA
* * *
43718 CGTAAGGCCCTGAGCACACAGCTGATGAGCC
1 AGTAAGGCCCTGAGCACACAGCCGAGGAGCC
43749 TTCATGTATA
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
34 5 0.08
35 57 0.92
ACGTcount: A:0.28, C:0.30, G:0.32, T:0.10
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAGCCGGTA
Found at i:43843 original size:24 final size:24
Alignment explanation
Indices: 43816--43963 Score: 102
Period size: 24 Copynumber: 6.2 Consensus size: 24
43806 TATATCAAAA
43816 ATCAAAACATAAAT-CAGGTCAAGT
1 ATCAAAACA-AAATCCAGGTCAAGT
* *
43840 ATCATATCAAAATCCAGGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* * * *
43864 ATCATATCAGAATCCAAGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* * * *
43888 ATCAGATCAGAATCCATGTC-AGAT
1 ATCAAAACAAAATCCAGGTCAAG-T
* * * *
43912 ATCAGATCAGAATCCATGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* * * *
43936 ATCATATCAGAATCCATGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
43960 ATCA
1 ATCA
43964 TATCAGAATT
Statistics
Matches: 114, Mismatches: 7, Indels: 6
0.90 0.06 0.05
Matches are distributed among these distances:
23 6 0.05
24 106 0.93
25 2 0.02
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.25
Consensus pattern (24 bp):
ATCAAAACAAAATCCAGGTCAAGT
Found at i:43964 original size:24 final size:24
Alignment explanation
Indices: 43833--43972 Score: 219
Period size: 24 Copynumber: 5.8 Consensus size: 24
43823 CATAAATCAG
* *
43833 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCATATCAGAATCCAT
*
43857 GTCAAGTATCATATCAGAATCCAA
1 GTCAAGTATCATATCAGAATCCAT
*
43881 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCATATCAGAATCCAT
*
43905 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCATATCAGAATCCAT
43929 GTCAAGTATCATATCAGAATCCAT
1 GTCAAGTATCATATCAGAATCCAT
43953 GTCAAGTATCATATCAGAAT
1 GTCAAGTATCATATCAGAAT
43973 TCAAATCGAA
Statistics
Matches: 109, Mismatches: 5, Indels: 4
0.92 0.04 0.03
Matches are distributed among these distances:
23 2 0.02
24 105 0.96
25 2 0.02
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.26
Consensus pattern (24 bp):
GTCAAGTATCATATCAGAATCCAT
Found at i:43988 original size:72 final size:72
Alignment explanation
Indices: 43840--43995 Score: 208
Period size: 72 Copynumber: 2.2 Consensus size: 72
43830 CAGGTCAAGT
* *
43840 ATCATATCAAAATCCAGGTCAAGTATCATATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAT
1 ATCAGATCAAAATCCAGGTCAAGTATCATATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAA
* *
43905 GTCAGAT
66 ATCAGAA
* * * * *
43912 ATCAGATCAGAATCCATGTCAAGTATCATATCAGAATCCATGTCAAGTATCATATCAGAATTCAA
1 ATCAGATCAAAATCCAGGTCAAGTATCATATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAA
43977 ATC-GAAA
66 ATCAG-AA
43984 ATCAGAT-AAAAT
1 ATCAGATCAAAAT
43996 ATTCATGTGA
Statistics
Matches: 73, Mismatches: 10, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
71 5 0.07
72 68 0.93
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.26
Consensus pattern (72 bp):
ATCAGATCAAAATCCAGGTCAAGTATCATATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAA
ATCAGAA
Found at i:45800 original size:36 final size:36
Alignment explanation
Indices: 45753--45825 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
45743 GATAAATTAT
45753 AATCTACATATCCATGGCTGATTCTTTTATCACTTA
1 AATCTACATATCCATGGCTGATTCTTTTATCACTTA
*
45789 AATCTATATATCCATGGCTGATTCTTTTATCACTTA
1 AATCTACATATCCATGGCTGATTCTTTTATCACTTA
45825 A
1 A
45826 TTCCAGAACT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.29, C:0.21, G:0.08, T:0.42
Consensus pattern (36 bp):
AATCTACATATCCATGGCTGATTCTTTTATCACTTA
Found at i:53122 original size:30 final size:30
Alignment explanation
Indices: 53088--53146 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
53078 CGGACTGGTA
*
53088 ATGAATCAGCTGAAAA-TCGGTAAAACCGGG
1 ATGAATCAGCTGAAAACT-GGCAAAACCGGG
*
53118 ATGAATCGGCTGAAAACTGGCAAAACCGG
1 ATGAATCAGCTGAAAACTGGCAAAACCGG
53147 TTTGAACCGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 25 0.96
31 1 0.04
ACGTcount: A:0.39, C:0.19, G:0.27, T:0.15
Consensus pattern (30 bp):
ATGAATCAGCTGAAAACTGGCAAAACCGGG
Found at i:59245 original size:18 final size:18
Alignment explanation
Indices: 59206--59248 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
59196 GAAAGCAGAG
*
59206 AGAGAGAGAGAGAGGGAG
1 AGAGAGAGAGAGAGGGAC
* *
59224 AGAGAGAGAGAGATGGCC
1 AGAGAGAGAGAGAGGGAC
59242 AGAGAGA
1 AGAGAGA
59249 AGGAGAGTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.05, G:0.49, T:0.02
Consensus pattern (18 bp):
AGAGAGAGAGAGAGGGAC
Found at i:59248 original size:2 final size:2
Alignment explanation
Indices: 59202--59236 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
59192 GAAAGAAAGC
*
59202 AG AG AG AG AG AG AG AG AG GG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
59237 TGGCCAGAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:59924 original size:19 final size:20
Alignment explanation
Indices: 59887--59930 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
59877 AATTTTGAGT
* *
59887 TTTTTTATTATAATTTAAAG
1 TTTTTTATTATAATATAAAA
*
59907 TTTTTTATTTTAA-ATAAAA
1 TTTTTTATTATAATATAAAA
59926 TTTTT
1 TTTTT
59931 AAATTTATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (20 bp):
TTTTTTATTATAATATAAAA
Found at i:62691 original size:14 final size:14
Alignment explanation
Indices: 62672--62700 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
62662 ATGAGACTCG
62672 ATCCCACGACCTCA
1 ATCCCACGACCTCA
62686 ATCCCACGACCTCA
1 ATCCCACGACCTCA
62700 A
1 A
62701 GATTAAGAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.48, G:0.07, T:0.14
Consensus pattern (14 bp):
ATCCCACGACCTCA
Found at i:66677 original size:24 final size:22
Alignment explanation
Indices: 66641--66684 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 22
66631 TATAAAAAAT
66641 TATTTTTTATTAAATATTTTTTGG
1 TATTTTTTATT-AAT-TTTTTTGG
66665 TATTTTTGT-TTAATTTTTTT
1 TATTTTT-TATTAATTTTTTT
66685 AATAATTATG
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 6 0.32
23 3 0.16
24 9 0.47
25 1 0.05
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (22 bp):
TATTTTTTATTAATTTTTTTGG
Found at i:70268 original size:2 final size:2
Alignment explanation
Indices: 70223--70255 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
70213 TGCTCCTTGT
70223 TA TA TA 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 TA TA TA T
70256 GACATGCATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:77765 original size:2 final size:2
Alignment explanation
Indices: 77758--77801 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
77748 CTTAATTTGT
77758 TA 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 TA
77800 TA
1 TA
77802 GCGAAGAGGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:90216 original size:6 final size:6
Alignment explanation
Indices: 90205--90243 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
90195 GAGCAATGCA
90205 GGACAT GGACAT GGACAT GGACAT GGACAT GGACAT GGA
1 GGACAT GGACAT GGACAT GGACAT GGACAT GGACAT GGA
90244 AAATCCAGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.33, C:0.15, G:0.36, T:0.15
Consensus pattern (6 bp):
GGACAT
Found at i:97242 original size:16 final size:15
Alignment explanation
Indices: 97223--97264 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
97213 TGTTAGTATT
97223 TTATTTAATTATTGTA
1 TTATTTAATT-TTGTA
*
97239 TTATTTAATTTTTTA
1 TTATTTAATTTTGTA
*
97254 TTATTTTATTT
1 TTATTTAATTT
97265 AATTATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (15 bp):
TTATTTAATTTTGTA
Found at i:97254 original size:20 final size:21
Alignment explanation
Indices: 97231--97276 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
97221 TTTTATTTAA
*
97231 TTATTGTATTATTTAATT-TT
1 TTATTATATTATTTAATTATT
*
97251 TTATTATTTTATTTAATTATT
1 TTATTATATTATTTAATTATT
97272 TTATT
1 TTATT
97277 TTTTTTCAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (21 bp):
TTATTATATTATTTAATTATT
Found at i:97280 original size:20 final size:20
Alignment explanation
Indices: 97239--97280 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
97229 AATTATTGTA
97239 TTATTTAATTTTTTATTATT
1 TTATTTAATTTTTTATTATT
97259 TTATTTAATTATTTTATT-TT
1 TTATTTAATT-TTTTATTATT
97279 TT
1 TT
97281 TTCAGTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (20 bp):
TTATTTAATTTTTTATTATT
Found at i:97566 original size:20 final size:21
Alignment explanation
Indices: 97529--97580 Score: 79
Period size: 20 Copynumber: 2.5 Consensus size: 21
97519 TTTATAACTG
97529 TAAAAAAATAAAATAATTAAA
1 TAAAAAAATAAAATAATTAAA
*
97550 TAAAATAATAAAA-AATTAAA
1 TAAAAAAATAAAATAATTAAA
*
97570 TAATAAAATAA
1 TAAAAAAATAA
97581 TTAATACAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (21 bp):
TAAAAAAATAAAATAATTAAA
Found at i:97570 original size:15 final size:15
Alignment explanation
Indices: 97547--97584 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
97537 TAAAATAATT
*
97547 AAATAAAATAATAAA
1 AAATTAAATAATAAA
97562 AAATTAAATAATAAA
1 AAATTAAATAATAAA
97577 ATAATTAA
1 A-AATTAA
97585 TACAAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AAATTAAATAATAAA
Found at i:97591 original size:28 final size:28
Alignment explanation
Indices: 97531--97593 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 28
97521 TATAACTGTA
*
97531 AAAAAATAAAATAATTAAATAAAATAAT
1 AAAAAATAAAATAATAAAATAAAATAAT
* *
97559 AAAAAATTAAATAATAAAAT-AATTAAT
1 AAAAAATAAAATAATAAAATAAAATAAT
*
97586 ACAAAATA
1 AAAAAATA
97594 TGATTAAATT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 12 0.40
28 18 0.60
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (28 bp):
AAAAAATAAAATAATAAAATAAAATAAT
Found at i:101312 original size:37 final size:36
Alignment explanation
Indices: 101240--101313 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 36
101230 GTTGAAAAAT
*
101240 ATTTATATATTTTTTTTAAAAAAATAAATTCATAAA
1 ATTTATATATTTTTTTTAAAAAAATAAAATCATAAA
* *
101276 ATTTATATAATTTTTTTTACAAAATTAAAAAT-ATAAA
1 ATTTATAT-ATTTTTTTTAAAAAAAT-AAAATCATAAA
101313 A
1 A
101314 AAGATTTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
36 8 0.24
37 21 0.64
38 4 0.12
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (36 bp):
ATTTATATATTTTTTTTAAAAAAATAAAATCATAAA
Found at i:101929 original size:15 final size:15
Alignment explanation
Indices: 101905--101945 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
101895 GTATAATTAA
*
101905 ATTAATTTATAAAAT
1 ATTAAATTATAAAAT
101920 ATTAAATTATAAAAT
1 ATTAAATTATAAAAT
101935 ATTAAACTTAT
1 ATTAAA-TTAT
101946 GATTATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 20 0.83
16 4 0.17
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
ATTAAATTATAAAAT
Found at i:106016 original size:21 final size:21
Alignment explanation
Indices: 105969--106017 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
105959 GAACGTTACT
* **
105969 TAAAATGTTATTTTTTCTACA
1 TAAAATGTTAATTTCGCTACA
* *
105990 TGAAATGTTAATTTCGCTACC
1 TAAAATGTTAATTTCGCTACA
106011 TAAAATG
1 TAAAATG
106018 AATATTTCCG
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (21 bp):
TAAAATGTTAATTTCGCTACA
Found at i:106975 original size:23 final size:23
Alignment explanation
Indices: 106924--106987 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
106914 AATATTTAAA
106924 TATTTTAACATATAAAAAATATTT
1 TATTTTAA-ATATAAAAAATATTT
* ***
106948 AATTTTAAATATAAAGTCTATTT
1 TATTTTAAATATAAAAAATATTT
106971 TA-TTTAAATAGTAAAAA
1 TATTTTAAATA-TAAAAA
106988 TAAGAAACTC
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
22 8 0.25
23 17 0.53
24 7 0.22
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (23 bp):
TATTTTAAATATAAAAAATATTT
Found at i:114918 original size:1 final size:1
Alignment explanation
Indices: 114912--114936 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
114902 ATGAGACCAG
114912 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
114937 GTGTTTTCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:116654 original size:179 final size:178
Alignment explanation
Indices: 116437--116964 Score: 814
Period size: 179 Copynumber: 3.0 Consensus size: 178
116427 GGCTGAGCCC
*
116437 ATATGTTATAA-ATATTTTAATT-AAAAAACAATTTACAATTAATTTAAATAATATAATTATAAA
1 ATATG-TATAATATTTTTTAATTAAAAAAACAATTTACAATTAATTTAAATAATATAATTATAAA
* *
116500 AAAAAATTTATATAAATTTTTT-ATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTA
65 AAAAAATTTATATAATTTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTGGATCTT-
116564 AATTATTAATTGAGTTTTAAATGGTTTGGAATGAGCCCATATGTTATATATA
129 AATTATTAATTGAGTTTT-AATGGTTTGG-ATGAGCCCATATGTTATATATA
116616 ATATGTATAATATTTTTTAATTAAAAAAACAA-TTACAATTAATTTAAATATATATAATTATAAA
1 ATATGTATAATATTTTTTAATTAAAAAAACAATTTACAATTAATTTAAATA-ATATAATTATAAA
116680 ATAAAAATTTATATAATTTTTTTAATT-ATT-ATATTGATTTAAGTTT-AAAGTTATTGGATCTT
65 A-AAAAATTTATATAATTTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTGGATCTT
*
116742 AATTATTAATTGGGTTTTAATGGTTTGGGATGAGCCCATA--TTATATATA
129 AATTATTAATTGAGTTTTAATGGTTT-GGATGAGCCCATATGTTATATATA
116791 ATA--TATAATATTTTTTAATTAAAAAAACAATTTACAATTAATTTAAATAAATATAATTATAAA
1 ATATGTATAATATTTTTTAATTAAAAAAACAATTTACAATTAATTTAAAT-AATATAATTAT-AA
116854 ATAAAAAATTTATATAATTTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTA-TGGATCT
64 A-AAAAAATTTATATAATTTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTGGATCT
* *
116918 T-ATTATTAATTGAGTTTTAATGGTTTGG-GGAGCCTATATGTTATATA
128 TAATTATTAATTGAGTTTTAATGGTTTGGATGAGCCCATATGTTATATA
116965 ATATATATTT
Statistics
Matches: 327, Mismatches: 7, Indels: 33
0.89 0.02 0.09
Matches are distributed among these distances:
173 27 0.08
174 35 0.11
175 43 0.13
176 35 0.11
177 43 0.13
178 31 0.09
179 49 0.15
180 38 0.12
181 23 0.07
182 3 0.01
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (178 bp):
ATATGTATAATATTTTTTAATTAAAAAAACAATTTACAATTAATTTAAATAATATAATTATAAAA
AAAAATTTATATAATTTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTGGATCTTAA
TTATTAATTGAGTTTTAATGGTTTGGATGAGCCCATATGTTATATATA
Found at i:116881 original size:175 final size:177
Alignment explanation
Indices: 116291--116971 Score: 881
Period size: 174 Copynumber: 4.0 Consensus size: 177
116281 AAATTAAATG
* * * *
116291 TTTTTTAATTCAAAAAAA-AGTTTATAATTAATTTAAATATA-AT-A-TATAAAAT-AAAATTCA
1 TTTTTTAATT-AAAAAAACAATTTACAATTAATTTAAATAAATATAATTATAAAATAAAAATTTA
* * *
116351 GATAAAATTTTTAATTAATTAATATTGATTT-AGGTT-AAAGTTATGGATCTTAA--ATTAATTG
65 TATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATGGATCTTAATTATTAATTG
* * *
116412 GGTTTTAAATGG-TTGGGCTGAGCCC-----ATATGT--TATA-AATA
130 AGTTTTAAATGGTTTGGGATGAGCCCATATTATATATAATATATAATA
116451 --TTTTAATT-AAAAAACAATTTACAATTAATTTAAAT-AATATAATTATAAAA-AAAAATTTAT
1 TTTTTTAATTAAAAAAACAATTTACAATTAATTTAAATAAATATAATTATAAAATAAAAATTTAT
*
116511 ATAAATTTTTT-ATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTAATT
66 ATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTA-TGGATCTT-AATTATTAATT
*
116575 GAGTTTTAAATGGTTTGGAATGAGCCCATATGTTATATATAATATGTATAATA
129 GAGTTTTAAATGGTTTGGGATGAGCCCATA--TTATATATAATA--TATAATA
*
116628 TTTTTTAATTAAAAAAACAA-TTACAATTAATTTAAATATATATAATTATAAAATAAAAATTTAT
1 TTTTTTAATTAAAAAAACAATTTACAATTAATTTAAATAAATATAATTATAAAATAAAAATTTAT
*
116692 ATAATTTTTTTAATT-ATT-ATATTGATTTAAGTTT-AAAGTTATTGGATCTTAATTATTAATTG
66 ATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTA-TGGATCTTAATTATTAATTG
*
116754 GGTTTT-AATGGTTTGGGATGAGCCCATATTATATATAATATATAATA
130 AGTTTTAAATGGTTTGGGATGAGCCCATATTATATATAATATATAATA
116801 TTTTTTAATTAAAAAAACAATTTACAATTAATTTAAATAAATATAATTATAAAATAAAAAATTTA
1 TTTTTTAATTAAAAAAACAATTTACAATTAATTTAAATAAATATAATTATAAAAT-AAAAATTTA
*
116866 TATAATTTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATGGATCTT-ATTATTAATTG
65 TATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATGGATCTTAATTATTAATTG
*
116930 AGTTTT-AATGGTTTGGG--GAGCCTATATGT-TATATAATATATA
130 AGTTTTAAATGGTTTGGGATGAGCCCATAT-TATATATAATATATA
116972 TTTAAATTTA
Statistics
Matches: 465, Mismatches: 20, Indels: 58
0.86 0.04 0.11
Matches are distributed among these distances:
156 7 0.02
157 20 0.04
158 27 0.06
159 27 0.06
160 7 0.02
161 8 0.02
162 2 0.00
164 19 0.04
165 11 0.02
172 5 0.01
173 27 0.06
174 57 0.12
175 38 0.08
176 32 0.07
177 49 0.11
178 24 0.05
179 41 0.09
180 38 0.08
181 23 0.05
182 3 0.01
ACGTcount: A:0.42, C:0.04, G:0.10, T:0.44
Consensus pattern (177 bp):
TTTTTTAATTAAAAAAACAATTTACAATTAATTTAAATAAATATAATTATAAAATAAAAATTTAT
ATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATGGATCTTAATTATTAATTGA
GTTTTAAATGGTTTGGGATGAGCCCATATTATATATAATATATAATA
Found at i:117062 original size:16 final size:17
Alignment explanation
Indices: 117038--117069 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
117028 CTGTTAACCG
117038 ACCGAACTAATTCGATA
1 ACCGAACTAATTCGATA
117055 ACCG-ACTAATTCGAT
1 ACCGAACTAATTCGAT
117070 TCGATCGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (17 bp):
ACCGAACTAATTCGATA
Done.