Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006356.1 Hibiscus syriacus cultivar Beakdansim tig00015236_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: 63665
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.33
Found at i:11337 original size:22 final size:20
Alignment explanation
Indices: 11308--11355 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
11298 TCTGAATTAA
*
11308 TTATTGTTCTTATTTGTAGTT
1 TTATTGTTCATATTT-TAGTT
*
11329 TTATCTGTTGATATTTTAGTT
1 TTAT-TGTTCATATTTTAGTT
11350 TTATTG
1 TTATTG
11356 AAACCCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 2 0.08
21 13 0.54
22 9 0.38
ACGTcount: A:0.17, C:0.04, G:0.15, T:0.65
Consensus pattern (20 bp):
TTATTGTTCATATTTTAGTT
Found at i:13538 original size:18 final size:17
Alignment explanation
Indices: 13488--13540 Score: 61
Period size: 18 Copynumber: 3.0 Consensus size: 17
13478 TTATTGGGTT
*
13488 TTTTTATTTTCTTTCAA
1 TTTTTATTTTCTTTTAA
* *
13505 CTTTTATTTTTATTTTAA
1 TTTTTA-TTTTCTTTTAA
13523 GTTTTTATTTTCTTTTAA
1 -TTTTTATTTTCTTTTAA
13541 AAATGCTAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
17 5 0.17
18 19 0.66
19 5 0.17
ACGTcount: A:0.19, C:0.08, G:0.02, T:0.72
Consensus pattern (17 bp):
TTTTTATTTTCTTTTAA
Found at i:14934 original size:21 final size:21
Alignment explanation
Indices: 14910--14979 Score: 56
Period size: 21 Copynumber: 3.2 Consensus size: 21
14900 CGTTTCTTAA
14910 TTTGTTAAAATATATATTCTC
1 TTTGTTAAAATATATATTCTC
* *
14931 TTTG-TAAGAATCACA-AGCTTGC-A
1 TTTGTTAA-AAT-ATATA--TT-CTC
14954 TTTGTTAAAATATATATTCTC
1 TTTGTTAAAATATATATTCTC
14975 TTTGT
1 TTTGT
14980 AAGCTTCACA
Statistics
Matches: 37, Mismatches: 4, Indels: 16
0.65 0.07 0.28
Matches are distributed among these distances:
20 4 0.11
21 15 0.41
22 4 0.11
23 10 0.27
24 4 0.11
ACGTcount: A:0.31, C:0.11, G:0.10, T:0.47
Consensus pattern (21 bp):
TTTGTTAAAATATATATTCTC
Found at i:14972 original size:44 final size:44
Alignment explanation
Indices: 14909--15022 Score: 201
Period size: 44 Copynumber: 2.6 Consensus size: 44
14899 TCGTTTCTTA
14909 ATTTGTTAAAATATATATTCTCTTTGTAAGAATCACAAGCTTGC
1 ATTTGTTAAAATATATATTCTCTTTGTAAGAATCACAAGCTTGC
** *
14953 ATTTGTTAAAATATATATTCTCTTTGTAAGCTTCACAAGCTTGT
1 ATTTGTTAAAATATATATTCTCTTTGTAAGAATCACAAGCTTGC
14997 ATTTGTTAAAATATATATTCTCTTTG
1 ATTTGTTAAAATATATATTCTCTTTG
15023 CTTTTGTTAT
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 67 1.00
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.46
Consensus pattern (44 bp):
ATTTGTTAAAATATATATTCTCTTTGTAAGAATCACAAGCTTGC
Found at i:15775 original size:39 final size:39
Alignment explanation
Indices: 15707--15802 Score: 131
Period size: 39 Copynumber: 2.5 Consensus size: 39
15697 CACATAAGGA
* *
15707 CCTACTGTAAGGTCTTAGCCTGATGACAAAGCAGAGGTG
1 CCTACGGTAAGGTCTTAGCCCGATGACAAAGCAGAGGTG
*
15746 CCTTCGGTAAGGTCTTAGCCCGA-GCACAAAGCAGAGGTG
1 CCTACGGTAAGGTCTTAGCCCGATG-ACAAAGCAGAGGTG
* *
15785 CCTACGATAAGGCCTTAG
1 CCTACGGTAAGGTCTTAG
15803 TAGTCATAGA
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
38 1 0.02
39 49 0.98
ACGTcount: A:0.27, C:0.24, G:0.28, T:0.21
Consensus pattern (39 bp):
CCTACGGTAAGGTCTTAGCCCGATGACAAAGCAGAGGTG
Found at i:19900 original size:45 final size:43
Alignment explanation
Indices: 19830--19960 Score: 156
Period size: 45 Copynumber: 2.9 Consensus size: 43
19820 CTAGTGATAC
19830 ACACTTTAGATTAATATTTTGTTTAAACTTAAACATAAAATTTAA
1 ACACTTTA-ATTAAT-TTTTGTTTAAACTTAAACATAAAATTTAA
* * *
19875 ACGCTTTATATTAATTTTCTATTTAAA-TTCACACATAAAATTTAA
1 ACACTTTA-ATTAATTTT-TGTTTAAACTT-AAACATAAAATTTAA
* *
19920 ACACTTTAACTTAGTTTTTGTTTAAACTTAAACATGAAATT
1 ACACTTTAA-TTAATTTTTGTTTAAACTTAAACATAAAATT
19961 AATATTTTGT
Statistics
Matches: 73, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
44 23 0.32
45 50 0.68
ACGTcount: A:0.40, C:0.11, G:0.05, T:0.44
Consensus pattern (43 bp):
ACACTTTAATTAATTTTTGTTTAAACTTAAACATAAAATTTAA
Found at i:20382 original size:2 final size:2
Alignment explanation
Indices: 20375--20433 Score: 109
Period size: 2 Copynumber: 29.0 Consensus size: 2
20365 CTACCTAGGA
20375 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
20417 AT AT AT AT AT AT CAT AT
1 AT AT AT AT AT AT -AT AT
20434 CTTGGTACAA
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 54 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20752 original size:14 final size:14
Alignment explanation
Indices: 20730--20779 Score: 64
Period size: 14 Copynumber: 3.6 Consensus size: 14
20720 ATCTGTTTGA
* *
20730 TTATATTCGTTCAT
1 TTATGTTCGTTCGT
20744 TTATGTTCGTTCGT
1 TTATGTTCGTTCGT
* *
20758 TTATGTTCTTTTGT
1 TTATGTTCGTTCGT
20772 TTATGTTC
1 TTATGTTC
20780 TCCAGACCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.12, C:0.12, G:0.14, T:0.62
Consensus pattern (14 bp):
TTATGTTCGTTCGT
Found at i:20975 original size:14 final size:14
Alignment explanation
Indices: 20956--21012 Score: 69
Period size: 14 Copynumber: 3.9 Consensus size: 14
20946 ACTAAATAAT
20956 TTTATGTTCGTTTG
1 TTTATGTTCGTTTG
20970 TTTATGTTCGTTTG
1 TTTATGTTCGTTTG
* *
20984 TTTGTGTTCATTTTTG
1 TTTATGTTC--GTTTG
*
21000 TTTGTGTTCGTTT
1 TTTATGTTCGTTT
21013 ATCATTTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
14 25 0.66
16 13 0.34
ACGTcount: A:0.05, C:0.07, G:0.21, T:0.67
Consensus pattern (14 bp):
TTTATGTTCGTTTG
Found at i:23846 original size:82 final size:81
Alignment explanation
Indices: 23694--23940 Score: 287
Period size: 82 Copynumber: 3.0 Consensus size: 81
23684 AATTTTGCTC
* * * * * *
23694 TCAATTGGGTAAACTGAGTAGAGGTCGAGACATGTTTTTATGGAGGCTTGCGATTCGAACCATTC
1 TCAATCGGGTGAACTGAGTAGAGGTCAAGACATGTTTTT-TGGAGGCTTACAATTCAAACCATTC
* *
23759 GTGATCACCATTAGTCG
65 ATGATCACCATTAGCCG
* * * *
23776 TCAATCGGGTGAATTGAGTAGAGGTCAAGTCGTGTTTTTGTGGAGGCTTACAATTCAAACCGTTC
1 TCAATCGGGTGAACTGAGTAGAGGTCAAGACATGTTTTT-TGGAGGCTTACAATTCAAACCATTC
*
23841 ATGATCTCCATTAGCCG
65 ATGATCACCATTAGCCG
* * ** *
23858 TCAATCGGGTGAACTGAGTAGAGGCCAAGACATGTTTTCTTGGAGGCTTACGATTTGAACTATTC
1 TCAATCGGGTGAACTGAGTAGAGGTCAAGACATGTTTT-TTGGAGGCTTACAATTCAAACCATTC
* *
23923 TTGATAACCATTAGCCG
65 ATGATCACCATTAGCCG
23940 T
1 T
23941 TGTTGTTTTT
Statistics
Matches: 138, Mismatches: 26, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
82 137 0.99
83 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.31
Consensus pattern (81 bp):
TCAATCGGGTGAACTGAGTAGAGGTCAAGACATGTTTTTTGGAGGCTTACAATTCAAACCATTCA
TGATCACCATTAGCCG
Found at i:30797 original size:82 final size:82
Alignment explanation
Indices: 30660--30820 Score: 232
Period size: 82 Copynumber: 2.0 Consensus size: 82
30650 AAATTTGCTC
* * * *
30660 TCAATCGGGTGAACTGAGTTGAGGCCGAGGCATGTTTTCGTGGAGGCTTACGATTTAAACCATTT
1 TCAATCAGGTGAACTGAGTAGAGGCCGAGACATGTTTTCGTGGAGGCTTACGATTTAAACCATTC
30725 GTGATCACCATTAGCCG
66 GTGATCACCATTAGCCG
* * ** * *
30742 TCAATCAGGTGAACTGAGTAGAGGCCGAGACGTGTTTTCGTTGAGGCTTTTGATTTGAACCGTTC
1 TCAATCAGGTGAACTGAGTAGAGGCCGAGACATGTTTTCGTGGAGGCTTACGATTTAAACCATTC
30807 GTGATCACCATTAG
66 GTGATCACCATTAG
30821 TTGTTGTTGT
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
82 69 1.00
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (82 bp):
TCAATCAGGTGAACTGAGTAGAGGCCGAGACATGTTTTCGTGGAGGCTTACGATTTAAACCATTC
GTGATCACCATTAGCCG
Found at i:31098 original size:2 final size:2
Alignment explanation
Indices: 31091--31135 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
31081 TAAATATGTC
31091 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
31133 AT A
1 AT A
31136 ATCAATTCAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:31755 original size:2 final size:2
Alignment explanation
Indices: 31748--31799 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
31738 TTGTTTCATA
31748 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
31790 AT AT AT AT AT
1 AT AT AT AT AT
31800 CATTCATACT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34403 original size:3 final size:3
Alignment explanation
Indices: 34397--34489 Score: 186
Period size: 3 Copynumber: 31.0 Consensus size: 3
34387 CTACTACAAC
34397 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
34445 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
34490 ATATAACATA
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 90 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:36219 original size:2 final size:2
Alignment explanation
Indices: 36212--36246 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
36202 TAATATGTAC
*
36212 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
36247 GTTTAGCATG
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:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:39152 original size:15 final size:16
Alignment explanation
Indices: 39134--39163 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39124 TTAAAAGTTT
39134 AGGGA-CTAAATTTAA
1 AGGGACCTAAATTTAA
39149 AGGGACCTAAATTTA
1 AGGGACCTAAATTTA
39164 TATATTAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.43, C:0.10, G:0.20, T:0.27
Consensus pattern (16 bp):
AGGGACCTAAATTTAA
Found at i:40854 original size:3 final size:3
Alignment explanation
Indices: 40846--40925 Score: 151
Period size: 3 Copynumber: 26.7 Consensus size: 3
40836 TCTTTTTTCT
*
40846 TTA TTA TTA TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
40894 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
40926 TGGATAAAAA
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 75 1.00
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:41247 original size:40 final size:40
Alignment explanation
Indices: 41180--41317 Score: 197
Period size: 40 Copynumber: 3.4 Consensus size: 40
41170 AAACATTGAC
* *
41180 CCAACTCCTT-TGTGATGGTTGACCCAAGGTGATGCTGAT
1 CCAACTCCTTATGTGATGGATGAGCCAAGGTGATGCTGAT
41219 CCAACTCCTTATGTGATGGATGAGCCAAGGTGATGCTGAT
1 CCAACTCCTTATGTGATGGATGAGCCAAGGTGATGCTGAT
** * *
41259 CCAACTCCTTATGTGATGGACAAGCGAAATGATGATGCTGAT
1 CCAACTCCTTATGTGATGGATGAGC-CAA-GGTGATGCTGAT
41301 CCAACTCCTTATGTGAT
1 CCAACTCCTTATGTGAT
41318 TGAAGAGAAA
Statistics
Matches: 90, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
39 10 0.11
40 50 0.56
41 2 0.02
42 28 0.31
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (40 bp):
CCAACTCCTTATGTGATGGATGAGCCAAGGTGATGCTGAT
Found at i:41346 original size:42 final size:42
Alignment explanation
Indices: 41209--41339 Score: 115
Period size: 42 Copynumber: 3.2 Consensus size: 42
41199 TGACCCAAGG
* ** ** **
41209 TGATGCTGATCCAACTCCTTATGTGATGGATGAG-CCAA-GG
1 TGATACTGATCCAACTCCTTATGTGATGGACAAGAAAAATAA
* ** *
41249 TGATGCTGATCCAACTCCTTATGTGATGGACAAGCGAAATGA
1 TGATACTGATCCAACTCCTTATGTGATGGACAAGAAAAATAA
* *
41291 TGATGCTGATCCAACTCCTTATGTGATTGA-AGAGAAAAATAA
1 TGATACTGATCCAACTCCTTATGTGATGGACA-AGAAAAATAA
41333 TGATACT
1 TGATACT
41340 AGTCCAAATC
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
40 32 0.41
41 3 0.04
42 43 0.55
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (42 bp):
TGATACTGATCCAACTCCTTATGTGATGGACAAGAAAAATAA
Found at i:45062 original size:24 final size:24
Alignment explanation
Indices: 45045--45159 Score: 153
Period size: 24 Copynumber: 4.8 Consensus size: 24
45035 TTGATTTGAT
45045 TTCTGATCTGATACTTGACATGGA
1 TTCTGATCTGATACTTGACATGGA
45069 TTCTGATCTGATA-TCTGACATGGA
1 TTCTGATCTGATACT-TGACATGGA
*
45093 TTCTGATCTGATACTTGACTTGGA
1 TTCTGATCTGATACTTGACATGGA
* * *
45117 TTCTGATCTGTTACTTGACCT-TA
1 TTCTGATCTGATACTTGACATGGA
*
45140 TTTCTGATATGATACTTGAC
1 -TTCTGATCTGATACTTGAC
45160 CTGATTTATG
Statistics
Matches: 82, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
23 2 0.02
24 79 0.96
25 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.42
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACATGGA
Found at i:45080 original size:48 final size:49
Alignment explanation
Indices: 45028--45159 Score: 155
Period size: 48 Copynumber: 2.8 Consensus size: 49
45018 AATATTTTAC
*
45028 CTGATTTTTGA-TTTGATTTCTGATCTGATACTTGACATGGATTCTGAT
1 CTGATTTTTGACATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
* * * *
45076 CTGATATCTGACATGGA-TTCTGATCTGATACTTGACTTGGATTCTGAT
1 CTGATTTTTGACATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
* * *
45124 CTG-TTACTTGACCTT-ATTTCTGATATGATACTTGAC
1 CTGATT-TTTGACATTGATTTCTGATCTGATACTTGAC
45160 CTGATTTATG
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
47 2 0.03
48 65 0.93
49 3 0.04
ACGTcount: A:0.22, C:0.16, G:0.18, T:0.44
Consensus pattern (49 bp):
CTGATTTTTGACATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
Found at i:45176 original size:24 final size:24
Alignment explanation
Indices: 45096--45169 Score: 69
Period size: 24 Copynumber: 3.1 Consensus size: 24
45086 ACATGGATTC
* * *
45096 TGATCTGATACTTGACTTGGA-TTC
1 TGATATGATACTTGACCT-GATTTA
* * * *
45120 TGATCTGTTACTTGACCTTATTTC
1 TGATATGATACTTGACCTGATTTA
45144 TGATATGATACTTGACCTGATTTA
1 TGATATGATACTTGACCTGATTTA
45168 TG
1 TG
45170 TTTTGATTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
23 1 0.02
24 41 0.98
ACGTcount: A:0.22, C:0.16, G:0.18, T:0.45
Consensus pattern (24 bp):
TGATATGATACTTGACCTGATTTA
Found at i:46372 original size:118 final size:116
Alignment explanation
Indices: 46125--46399 Score: 325
Period size: 118 Copynumber: 2.3 Consensus size: 116
46115 TGTTTGAACA
* * * * * * *
46125 AGTTATTCTCATTATGAACTTCTTCATTGGAAATATTGATCCACCTCCTTCTGTGATGGATCGAG
1 AGTTCTTCTCATTATGAACTT-TCCATTGGAAATGTTGATCCACCTCATTCTGTGATGAATCAAA
* * * * *
46190 CAAAAGTTGAACAAGTTATTCTCATTATGAATTTCTTCTCCCTCATCAGACG
65 CAAAAGCTAAACAAGTTATTCTCATTATGAACTTCTTATCCCTCATAAGACG
** *
46242 AGTTCTTCTCATTATGAACTATTCCATTAAAAATGTTGATCCACCTTATTCTGTGATAGAATCAA
1 AGTTCTTCTCATTATGAACT-TTCCATTGGAAATGTTGATCCACCTCATTCTGTGAT-GAATCAA
* * * * *
46307 ACAAAGGCTAAACATGTTCTTCTTATTATGAACTTCTTATCCCTCATAAGATG
64 ACAAAAGCTAAACAAGTTATTCTCATTATGAACTTCTTATCCCTCATAAGACG
*
46360 AGTTCTTCTCATTATAAACTCTTCCATTGGAAATGTTGAT
1 AGTTCTTCTCATTATGAACT-TTCCATTGGAAATGTTGAT
46400 TGATTTATCC
Statistics
Matches: 132, Mismatches: 24, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
117 48 0.36
118 84 0.64
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (116 bp):
AGTTCTTCTCATTATGAACTTTCCATTGGAAATGTTGATCCACCTCATTCTGTGATGAATCAAAC
AAAAGCTAAACAAGTTATTCTCATTATGAACTTCTTATCCCTCATAAGACG
Found at i:47216 original size:54 final size:54
Alignment explanation
Indices: 47125--47539 Score: 419
Period size: 54 Copynumber: 7.6 Consensus size: 54
47115 TTACAGTTAT
* ** * * *
47125 CATCAAGAAACCCCTAAAACATTGGGCTTAGTTTCTTTAAAAATTCATTTGAATA
1 CATCAAGAAACCCCTGAAA-ATCAGGCTTAGCTTCTTTCAAAATTCATTTGAAAA
* *
47180 CATCAAGAAACCCATGAAAATCAGGCTTAGCTTCTTTCAACATTCATTTGAAAA
1 CATCAAGAAACCCCTGAAAATCAGGCTTAGCTTCTTTCAAAATTCATTTGAAAA
* * * * *
47234 CATCAAAAAACCCTTGAAAAT-ATGCTTAGCTTCTTTGAAAACTCATTT-ATAAA
1 CATCAAGAAACCCCTGAAAATCAGGCTTAGCTTCTTTCAAAATTCATTTGA-AAA
*** * * * *
47287 TCATCAAGAAACTTTTGAAAATCAGACTTAG-TTCCTTTGAAAATTCTTTTTAAAA
1 -CATCAAGAAACCCCTGAAAATCAGGCTTAGCTT-CTTTCAAAATTCATTTGAAAA
* * * *
47342 CATCAAGAAACCCCTG-AAATCAGGCTTAGCTTCTTTGAGAACTCATTTAAAAA
1 CATCAAGAAACCCCTGAAAATCAGGCTTAGCTTCTTTCAAAATTCATTTGAAAA
* *
47395 TCATCAAGAAACTTCC-GAAAAT-AGGACTTAACTTCTTTCAAAATTCATTTGAAAA
1 -CATCAAGAAAC-CCCTGAAAATCAGG-CTTAGCTTCTTTCAAAATTCATTTGAAAA
* ** * *
47450 TCATTAAGAAACTTCTGAAAATCAGACTTAGCTTCTTTCCAAATTCATTTGAAAA
1 -CATCAAGAAACCCCTGAAAATCAGGCTTAGCTTCTTTCAAAATTCATTTGAAAA
* *
47505 TATCAAGAAACCCCTGAAAATCAGGCTTAGTTTCT
1 CATCAAGAAACCCCTGAAAATCAGGCTTAGCTTCT
47540 AAAAAATCAC
Statistics
Matches: 302, Mismatches: 46, Indels: 25
0.81 0.12 0.07
Matches are distributed among these distances:
52 1 0.00
53 55 0.18
54 129 0.43
55 114 0.38
56 3 0.01
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (54 bp):
CATCAAGAAACCCCTGAAAATCAGGCTTAGCTTCTTTCAAAATTCATTTGAAAA
Found at i:53829 original size:13 final size:13
Alignment explanation
Indices: 53808--53849 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
53798 TACAATAACC
*
53808 TAATCTAAATAAA
1 TAATTTAAATAAA
53821 TAATTTAAATAAA
1 TAATTTAAATAAA
*
53834 TAAATTAAAATAAA
1 T-AATTTAAATAAA
53848 TA
1 TA
53850 GACGTAACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 14 0.54
14 12 0.46
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (13 bp):
TAATTTAAATAAA
Found at i:53844 original size:14 final size:14
Alignment explanation
Indices: 53814--53849 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
53804 AACCTAATCT
*
53814 AAATAAAT-AATTT
1 AAATAAATAAATTA
53827 AAATAAATAAATTA
1 AAATAAATAAATTA
53841 AAATAAATA
1 AAATAAATA
53850 GACGTAACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
AAATAAATAAATTA
Found at i:58671 original size:109 final size:114
Alignment explanation
Indices: 58524--58815 Score: 335
Period size: 109 Copynumber: 2.5 Consensus size: 114
58514 GTTAGACGAC
* * *
58524 TGCTATCATATCAGAGTCATAATATGCACACAAAGTGCAATCACATCTGAAAATATACTAGTGT-
1 TGCTATCATATCAGAAT-AGAATATGCACACAAAGTGCAATCACATCTGAATATATACTAGTGTA
* * * *
58588 TCCACTGGTAACACCACAA-TATC-ACATCAGAA-AT-GAA-CACACATAG
65 CCCACCGGT-ACACCACAATTATCAAAATCAGAACATAGAAGCACACACAG
* * *
58634 TGCTATCACATCAGAATAGAATATGCAAACAAAGTGCAATCACATCAAAATGTATATATACTAGT
1 TGCTATCATATCAGAATAGAATATGCACACAAAGTGCAATCACATC----TGAATATATACTAGT
* *
58699 GTACCCACCGGTACACCACAATTTATCAAAATCGGAACATATAAGCACACACAG
62 GTACCCACCGGTACACCACAA-TTATCAAAATCAGAACATAGAAGCACACACAG
* * *
58753 TGCTATCATATCAGAATCGTAATGTGCACACAAAGTGCAATCACATCAGAATATATACTAGTG
1 TGCTATCATATCAGAATAG-AATATGCACACAAAGTGCAATCACATCTGAATATATACTAGTG
58816 CACCTTCAGG
Statistics
Matches: 152, Mismatches: 18, Indels: 18
0.81 0.10 0.10
Matches are distributed among these distances:
109 27 0.18
110 15 0.10
113 24 0.16
114 7 0.05
115 4 0.03
116 21 0.14
117 2 0.01
118 2 0.01
119 25 0.16
120 25 0.16
ACGTcount: A:0.41, C:0.22, G:0.13, T:0.24
Consensus pattern (114 bp):
TGCTATCATATCAGAATAGAATATGCACACAAAGTGCAATCACATCTGAATATATACTAGTGTAC
CCACCGGTACACCACAATTATCAAAATCAGAACATAGAAGCACACACAG
Done.