Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004694.1 Hibiscus syriacus cultivar Beakdansim tig00010539_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: 50996
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Found at i:1116 original size:3 final size:3
Alignment explanation
Indices: 1108--1152 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
1098 TATCCTTGGA
1108 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1153 TCGTTGAATC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1909 original size:51 final size:51
Alignment explanation
Indices: 1802--2203 Score: 482
Period size: 51 Copynumber: 8.0 Consensus size: 51
1792 GGCGCAGACT
** * *
1802 CAGCAAGGTGGAAACA-CAGAGTCCCAAACAT-TACTCAACTACCTCAACAG
1 CAGCAAGGTGGAAACATTGGA-TCCCAAACATATACTCAGCTACCACAACAG
* * *
1852 CAGCAAGGTGGAAACTTTGGATCCCAAACATATACTCAGCTACCGCATCAG
1 CAGCAAGGTGGAAACATTGGATCCCAAACATATACTCAGCTACCACAACAG
* * *
1903 CGGCAAGGTGGAAACATTGGATCCCAAACATATACTCATCTACCAGAACAG
1 CAGCAAGGTGGAAACATTGGATCCCAAACATATACTCAGCTACCACAACAG
**
1954 CAGCAAGGTGGAAACATT-GATTCCCAAACATATACTGTGCTACCACAACAG
1 CAGCAAGGTGGAAACATTGGA-TCCCAAACATATACTCAGCTACCACAACAG
* * *
2005 CAGCAAGGTGGAAACATT-GATTCCCAAACATATACTCTGCTAGCACATCAG
1 CAGCAAGGTGGAAACATTGGA-TCCCAAACATATACTCAGCTACCACAACAG
* * * *
2056 CAGCAAGGTGGAAACAATGGAACCCAAACATATGCTCAGTTACCACAACAG
1 CAGCAAGGTGGAAACATTGGATCCCAAACATATACTCAGCTACCACAACAG
* * **
2107 CAGCAAGGTGG-AACATT-GATTCCCAGACATTTACTTTGCTACCAC-A-A-
1 CAGCAAGGTGGAAACATTGGA-TCCCAAACATATACTCAGCTACCACAACAG
*
2154 CAGCAAGGTGGAAA-ATTGGTTCCCAAACATATACTCAGCTACCACAACAG
1 CAGCAAGGTGGAAACATTGGATCCCAAACATATACTCAGCTACCACAACAG
2204 ATCTTAATGT
Statistics
Matches: 302, Mismatches: 40, Indels: 20
0.83 0.11 0.06
Matches are distributed among these distances:
47 35 0.12
48 5 0.02
49 4 0.01
50 50 0.17
51 206 0.68
52 2 0.01
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (51 bp):
CAGCAAGGTGGAAACATTGGATCCCAAACATATACTCAGCTACCACAACAG
Found at i:2082 original size:153 final size:152
Alignment explanation
Indices: 1802--2199 Score: 540
Period size: 153 Copynumber: 2.6 Consensus size: 152
1792 GGCGCAGACT
** * ** *
1802 CAGCAAGGTGGAAACACAGAGTCCCAAACATTACTCAACTACCTCAACAGCAGCAAGGTGGAAAC
1 CAGCAAGGTGGAAACATTGATTCCCAAACATTACTCTGCTACCACAACAGCAGCAAGGTGGAAAC
* * * * *
1867 TTTGGA-TCCCAAACATATACTCAGCTACCGCATCAGCGGCAAGGTGGAAACATTGGATCCCAAA
66 ATT-GATTCCCAAACATATACTCAGCTACCACATCAGCAGCAAGGTGGAAACAATGGAACCCAAA
*
1931 CATATACTCA-TCTACCAGAACAG
130 CATATACTCAGT-TACCACAACAG
*
1954 CAGCAAGGTGGAAACATTGATTCCCAAACATATACTGTGCTACCACAACAGCAGCAAGGTGGAAA
1 CAGCAAGGTGGAAACATTGATTCCCAAACAT-TACTCTGCTACCACAACAGCAGCAAGGTGGAAA
* *
2019 CATTGATTCCCAAACATATACTCTGCTAGCACATCAGCAGCAAGGTGGAAACAATGGAACCCAAA
65 CATTGATTCCCAAACATATACTCAGCTACCACATCAGCAGCAAGGTGGAAACAATGGAACCCAAA
*
2084 CATATGCTCAGTTACCACAACAG
130 CATATACTCAGTTACCACAACAG
* *
2107 CAGCAAGGTGG-AACATTGATTCCCAGACATTTACTTTGCTACCAC-A-A-CAGCAAGGTGGAAA
1 CAGCAAGGTGGAAACATTGATTCCCAAACA-TTACTCTGCTACCACAACAGCAGCAAGGTGGAAA
*
2168 -ATTGGTTCCCAAACATATACTCAGCTACCACA
65 CATTGATTCCCAAACATATACTCAGCTACCACA
2200 ACAGATCTTA
Statistics
Matches: 221, Mismatches: 21, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
148 29 0.13
149 14 0.06
150 1 0.00
151 1 0.00
152 60 0.27
153 115 0.52
154 1 0.00
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (152 bp):
CAGCAAGGTGGAAACATTGATTCCCAAACATTACTCTGCTACCACAACAGCAGCAAGGTGGAAAC
ATTGATTCCCAAACATATACTCAGCTACCACATCAGCAGCAAGGTGGAAACAATGGAACCCAAAC
ATATACTCAGTTACCACAACAG
Found at i:6492 original size:2 final size:2
Alignment explanation
Indices: 6485--6511 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6475 ACAGAAAACA
6485 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
6512 AGAAAAAAAA
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:15037 original size:60 final size:61
Alignment explanation
Indices: 14906--15039 Score: 137
Period size: 60 Copynumber: 2.2 Consensus size: 61
14896 TATGATATTT
* * * * * ** * *
14906 ATTTTAAATTGAT-TGTTAAACTTTTGAATATTTCAATTTTATCTCTAGATTATAACTCTC
1 ATTTTAAATTAATCTGTTAAACTTTTGAACATTCCAATTCTATCTCTAAACGATAACCCAC
* * * *
14966 ATTATAGATTAATCT-TTAAACTTTTGAACATTCCAATTCTGTCTCTAAACGATGACCCAC
1 ATTTTAAATTAATCTGTTAAACTTTTGAACATTCCAATTCTATCTCTAAACGATAACCCAC
15026 ATTTTAAATTAATC
1 ATTTTAAATTAATC
15040 CCTAAAATTT
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
60 57 0.98
61 1 0.02
ACGTcount: A:0.34, C:0.16, G:0.07, T:0.44
Consensus pattern (61 bp):
ATTTTAAATTAATCTGTTAAACTTTTGAACATTCCAATTCTATCTCTAAACGATAACCCAC
Found at i:26179 original size:20 final size:20
Alignment explanation
Indices: 26154--26191 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
26144 ACCTGGAAAT
26154 TAAAAAACAAAATT-TTCATG
1 TAAAAAA-AAAATTATTCATG
26174 TAAAAAAAAAATTATTCA
1 TAAAAAAAAAATTATTCA
26192 CTCACACACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.61, C:0.08, G:0.03, T:0.29
Consensus pattern (20 bp):
TAAAAAAAAAATTATTCATG
Found at i:26208 original size:2 final size:2
Alignment explanation
Indices: 26203--26245 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
26193 TCACACACAC
26203 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
26245 A
1 A
26246 GGGTTATTCC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:26987 original size:2 final size:2
Alignment explanation
Indices: 26980--27034 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
26970 AGTAAAATAT
26980 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
27022 GA GA GA GA GA GA G
1 GA GA GA GA GA GA G
27035 TAAAATTCAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:27467 original size:30 final size:30
Alignment explanation
Indices: 27431--27487 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
27421 TTTATATTAG
27431 GAGTAAATTTAAACATATAAAATTTTAGGA
1 GAGTAAATTTAAACATATAAAATTTTAGGA
* *
27461 GAGTAAATTTGAACTTATAAAATTTTA
1 GAGTAAATTTAAACATATAAAATTTTA
27488 CTATTGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.47, C:0.04, G:0.12, T:0.37
Consensus pattern (30 bp):
GAGTAAATTTAAACATATAAAATTTTAGGA
Found at i:27810 original size:12 final size:13
Alignment explanation
Indices: 27779--27810 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
27769 TGACGTAATC
27779 TCATAATTTAGTT
1 TCATAATTTAGTT
27792 TCA-AATTTAGTT
1 TCATAATTTAGTT
27804 T-ATAATT
1 TCATAATT
27811 CCATCCTCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 1 0.06
12 14 0.78
13 3 0.17
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.53
Consensus pattern (13 bp):
TCATAATTTAGTT
Found at i:28613 original size:22 final size:22
Alignment explanation
Indices: 28582--28641 Score: 86
Period size: 22 Copynumber: 2.8 Consensus size: 22
28572 CGAATTTCGT
*
28582 TTTCGCAACTCGAATTCGCCAA
1 TTTCGCAACTCGAATTAGCCAA
* *
28604 TTTCGAAACTTGAATTAGCCAA
1 TTTCGCAACTCGAATTAGCCAA
28626 TTTCGCAACTC-AATTA
1 TTTCGCAACTCGAATTA
28642 CCGATATAGG
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
21 5 0.15
22 28 0.85
ACGTcount: A:0.32, C:0.25, G:0.12, T:0.32
Consensus pattern (22 bp):
TTTCGCAACTCGAATTAGCCAA
Found at i:28983 original size:70 final size:70
Alignment explanation
Indices: 28900--29038 Score: 278
Period size: 70 Copynumber: 2.0 Consensus size: 70
28890 CAAACAAATG
28900 AACCGTCAAAACGATTGTTTCTTTAAGAAGCGAGATTTTACATTTCGCAATACGAATTTGTCAAA
1 AACCGTCAAAACGATTGTTTCTTTAAGAAGCGAGATTTTACATTTCGCAATACGAATTTGTCAAA
28965 TTCGT
66 TTCGT
28970 AACCGTCAAAACGATTGTTTCTTTAAGAAGCGAGATTTTACATTTCGCAATACGAATTTGTCAAA
1 AACCGTCAAAACGATTGTTTCTTTAAGAAGCGAGATTTTACATTTCGCAATACGAATTTGTCAAA
29035 TTCG
66 TTCG
29039 AAACTCAATT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 69 1.00
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (70 bp):
AACCGTCAAAACGATTGTTTCTTTAAGAAGCGAGATTTTACATTTCGCAATACGAATTTGTCAAA
TTCGT
Found at i:29296 original size:20 final size:19
Alignment explanation
Indices: 29249--29300 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
29239 AATTCTACTT
*
29249 CTGTTTTGCGAATTCCAAA
1 CTGTGTTGCGAATTCCAAA
* *
29268 CTCGAGTTGCGAATTCGGAAA
1 CT-GTGTTGCGAATTC-CAAA
29289 CTGTGTTGCGAA
1 CTGTGTTGCGAA
29301 ATTGGATTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 2 0.07
20 20 0.74
21 5 0.19
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (19 bp):
CTGTGTTGCGAATTCCAAA
Found at i:30335 original size:24 final size:24
Alignment explanation
Indices: 30308--30354 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
30298 TTATTTAAAA
30308 AAAAATAAATTATTAATAATATTT
1 AAAAATAAATTATTAATAATATTT
30332 AAAAATAAATTATTAATAATATT
1 AAAAATAAATTATTAATAATATT
30355 AATCTTTATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
AAAAATAAATTATTAATAATATTT
Found at i:31354 original size:27 final size:27
Alignment explanation
Indices: 31324--31383 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
31314 AGATATATCG
*
31324 ATAATTAATTAATATAA-ATTATATATT
1 ATAATAAATTAATATAAGATTAT-TATT
*
31351 ATAAAAAATTAATATAAGATTATTATT
1 ATAATAAATTAATATAAGATTATTATT
*
31378 TTAATA
1 ATAATA
31384 TATTTTATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 23 0.82
28 5 0.18
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (27 bp):
ATAATAAATTAATATAAGATTATTATT
Found at i:35877 original size:111 final size:111
Alignment explanation
Indices: 35683--35901 Score: 438
Period size: 111 Copynumber: 2.0 Consensus size: 111
35673 GTACATGTAC
35683 GTACTCTTCGCACAATCAAAGGTTAATACTTCCATAACAACAACTTTAAATATCATTGTCAATGT
1 GTACTCTTCGCACAATCAAAGGTTAATACTTCCATAACAACAACTTTAAATATCATTGTCAATGT
35748 CTAAAGTCTAAATCAGTCCGTTGTTCATATTATTAGAGTACTCCAT
66 CTAAAGTCTAAATCAGTCCGTTGTTCATATTATTAGAGTACTCCAT
35794 GTACTCTTCGCACAATCAAAGGTTAATACTTCCATAACAACAACTTTAAATATCATTGTCAATGT
1 GTACTCTTCGCACAATCAAAGGTTAATACTTCCATAACAACAACTTTAAATATCATTGTCAATGT
35859 CTAAAGTCTAAATCAGTCCGTTGTTCATATTATTAGAGTACTC
66 CTAAAGTCTAAATCAGTCCGTTGTTCATATTATTAGAGTACTC
35902 TTGATGAGTT
Statistics
Matches: 108, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
111 108 1.00
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (111 bp):
GTACTCTTCGCACAATCAAAGGTTAATACTTCCATAACAACAACTTTAAATATCATTGTCAATGT
CTAAAGTCTAAATCAGTCCGTTGTTCATATTATTAGAGTACTCCAT
Found at i:43805 original size:81 final size:80
Alignment explanation
Indices: 43648--43822 Score: 251
Period size: 81 Copynumber: 2.1 Consensus size: 80
43638 GTCGATCAAC
* * * *
43648 CGAACCAGTCTCTTGTACAACTGGCTCGGTAGCTTCCTGCTCTACACCTCTGTGAGAGCTTGTCG
1 CGAACCA-T-TCTTGTACAACCGGCTCAGTAACTTCATGCTCTACACCTCTGTGAGAGCTTGTCG
43713 ATCCGCCATTTCGTGTG
64 ATCCGCCATTTCGTGTG
* * *
43730 CGAACCATTCTTGGTGCAACCGGCTCAGTAACTTCATGCTCTACACCTCTGTGAGAGCTTGTTGC
1 CGAACCATTCTT-GTACAACCGGCTCAGTAACTTCATGCTCTACACCTCTGTGAGAGCTTGTCGA
43795 TCCGCCATTTCGTGTG
65 TCCGCCATTTCGTGTG
*
43811 CAAACCATTCTT
1 CGAACCATTCTT
43823 TGTAACTCGC
Statistics
Matches: 84, Mismatches: 8, Indels: 3
0.88 0.08 0.03
Matches are distributed among these distances:
80 4 0.05
81 73 0.87
82 7 0.08
ACGTcount: A:0.18, C:0.30, G:0.21, T:0.31
Consensus pattern (80 bp):
CGAACCATTCTTGTACAACCGGCTCAGTAACTTCATGCTCTACACCTCTGTGAGAGCTTGTCGAT
CCGCCATTTCGTGTG
Found at i:43997 original size:55 final size:54
Alignment explanation
Indices: 43938--44239 Score: 302
Period size: 54 Copynumber: 5.5 Consensus size: 54
43928 TAGAATTAAC
43938 GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGTAGCCAAAAGT
1 GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGTAGCCAAAA-T
* ***
43993 GATTGAGCACCTCTGTGCTTCAATCGAGAACTGACACCTCTGTGCAGTTAAAAAAAAAT
1 GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGT---G-T-AGCCAAAAT
* ** * * *
44052 GACTGAGCACCTCTGTGCTTCAGCCGGGAGCTGACACCTCTGTGTAGCTAAGAT
1 GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGTAGCCAAAAT
* *
44106 GATTGAGCACCTCTGTGCTTCAATCGAG-GACTGACACCTCTGTGCAGCCAACTAT
1 GATTGAGCACCTCTGTGCTTCAATCGAGAG-CTGACACCTCTGTGTAGCCAA-AAT
* * * * * * ****
44161 GACTGAGCACCTCTGTGCTTCAATCTAAATTCTGGCACCTCTGTGCA-TTGGAAT
1 GATTGAGCACCTCTGTGCTTCAATCGAGA-GCTGACACCTCTGTGTAGCCAAAAT
*
44215 GATTGAGCACCTCTGTGCTACAATC
1 GATTGAGCACCTCTGTGCTTCAATC
44240 TAAAATCAAG
Statistics
Matches: 206, Mismatches: 32, Indels: 19
0.80 0.12 0.07
Matches are distributed among these distances:
53 1 0.00
54 73 0.35
55 70 0.34
56 16 0.08
58 1 0.00
59 40 0.19
60 5 0.02
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.26
Consensus pattern (54 bp):
GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGTAGCCAAAAT
Found at i:44036 original size:27 final size:28
Alignment explanation
Indices: 43941--44206 Score: 119
Period size: 27 Copynumber: 9.5 Consensus size: 28
43931 AATTAACGAT
*
43941 TGAGCACCTCTGTGCTTCAATCGAGAGC
1 TGAGCACCTCTGTGCTTCAATCGAGAAC
* ** * *
43969 TGA-CACCTCTGTG-TAGCCAAAAGTG-AT
1 TGAGCACCTCTGTGCT--TCAATCGAGAAC
43996 TGAGCACCTCTGTGCTTCAATCGAGAAC
1 TGAGCACCTCTGTGCTTCAATCGAGAAC
* *** *
44024 TGA-CACCTCTGTGCAGTTAAAAAAAAATGAC
1 TGAGCACCTCTGTGC--TTCAATCGAGA--AC
** * *
44055 TGAGCACCTCTGTGCTTCAGCCGGGAGC
1 TGAGCACCTCTGTGCTTCAATCGAGAAC
* *
44083 TGA-CACCTCTGTG-TAGCTAA--GATG-AT
1 TGAGCACCTCTGTGCT-TC-AATCGA-GAAC
*
44109 TGAGCACCTCTGTGCTTCAATCGAGGAC
1 TGAGCACCTCTGTGCTTCAATCGAGAAC
** *
44137 TGA-CACCTCTGTGCAGCCAA-CTATG-AC
1 TGAGCACCTCTGTGC-TTCAATCGA-GAAC
*
44164 TGAGCACCTCTGTGCTTCAATCTA-AATTC
1 TGAGCACCTCTGTGCTTCAATCGAGAA--C
44193 TG-GCACCTCTGTGC
1 TGAGCACCTCTGTGC
44207 ATTGGAATGA
Statistics
Matches: 177, Mismatches: 36, Indels: 50
0.67 0.14 0.19
Matches are distributed among these distances:
26 8 0.05
27 75 0.42
28 64 0.36
29 10 0.06
30 4 0.02
31 5 0.03
32 11 0.06
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (28 bp):
TGAGCACCTCTGTGCTTCAATCGAGAAC
Found at i:44145 original size:113 final size:114
Alignment explanation
Indices: 43941--44152 Score: 363
Period size: 113 Copynumber: 1.9 Consensus size: 114
43931 AATTAACGAT
*
43941 TGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGTAGCCAAAAGTGATTGAGCACCTC
1 TGAGCACCTCTGTGCTTCAACCGAGAGCTGACACCTCTGTGTAGCCAAAAGTGATTGAGCACCTC
44006 TGTGCTTCAATCGAGAACTGACACCTCTGTGCAGTTAAAAAAAAATGAC
66 TGTGCTTCAATCGAGAACTGACACCTCTGTGCAGTTAAAAAAAAATGAC
* * * *
44055 TGAGCACCTCTGTGCTTCAGCCGGGAGCTGACACCTCTGTGTAGCTAAGA-TGATTGAGCACCTC
1 TGAGCACCTCTGTGCTTCAACCGAGAGCTGACACCTCTGTGTAGCCAAAAGTGATTGAGCACCTC
*
44119 TGTGCTTCAATCGAGGACTGACACCTCTGTGCAG
66 TGTGCTTCAATCGAGAACTGACACCTCTGTGCAG
44153 CCAACTATGA
Statistics
Matches: 92, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
113 47 0.51
114 45 0.49
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (114 bp):
TGAGCACCTCTGTGCTTCAACCGAGAGCTGACACCTCTGTGTAGCCAAAAGTGATTGAGCACCTC
TGTGCTTCAATCGAGAACTGACACCTCTGTGCAGTTAAAAAAAAATGAC
Found at i:44239 original size:109 final size:110
Alignment explanation
Indices: 43941--44239 Score: 334
Period size: 109 Copynumber: 2.7 Consensus size: 110
43931 AATTAACGAT
* * * * *
43941 TGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGTAGCCAAAAGTGATTGAGCACCTC
1 TGAGCACCTCTGTGCTTCAACCGAAAGCTGACACCTCTGTGCAGCTAAGA-TGATTGAGCACCTC
44006 TGTGCTTCAATCGAGAACTGACACCTCTGTGCAGTTAAAAAAAAATGAC
65 TGTGCTTCAATCGAGAACTGACACCTCTGTGCAG---AAAAAAAATGAC
* ** *
44055 TGAGCACCTCTGTGCTTCAGCCGGGAGCTGACACCTCTGTGTAGCTAAGATGATTGAGCACCTCT
1 TGAGCACCTCTGTGCTTCAACCGAAAGCTGACACCTCTGTGCAGCTAAGATGATTGAGCACCTCT
* ** **
44120 GTGCTTCAATCGAGGACTGACACCTCTGTGCAG-CCAACTATGAC
66 GTGCTTCAATCGAGAACTGACACCTCTGTGCAGAAAAAAAATGAC
* * * * **
44164 TGAGCACCTCTGTGCTTCAATCTAAATTCTGGCACCTCTGTGCA--TTGGAATGATTGAGCACCT
1 TGAGCACCTCTGTGCTTCAACCGAAA-GCTGACACCTCTGTGCAGCTAAG-ATGATTGAGCACCT
*
44227 CTGTGCTACAATC
64 CTGTGCTTCAATC
44240 TAAAATCAAG
Statistics
Matches: 162, Mismatches: 21, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
108 2 0.01
109 54 0.33
110 14 0.09
113 47 0.29
114 45 0.28
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.26
Consensus pattern (110 bp):
TGAGCACCTCTGTGCTTCAACCGAAAGCTGACACCTCTGTGCAGCTAAGATGATTGAGCACCTCT
GTGCTTCAATCGAGAACTGACACCTCTGTGCAGAAAAAAAATGAC
Found at i:47934 original size:18 final size:18
Alignment explanation
Indices: 47911--47947 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
47901 TTTTTATGTT
*
47911 ATTTTAAATATAATTTTA
1 ATTTTAAATAAAATTTTA
*
47929 ATTTTATATAAAATTTTA
1 ATTTTAAATAAAATTTTA
47947 A
1 A
47948 AATTCCCATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTTTAAATAAAATTTTA
Found at i:50460 original size:16 final size:16
Alignment explanation
Indices: 50429--50500 Score: 110
Period size: 16 Copynumber: 4.6 Consensus size: 16
50419 GTTATTTTAA
*
50429 AATGATT-AAGTGTTG
1 AATGATTCAAATGTTG
50444 AATGATTCAAATGTTG
1 AATGATTCAAATGTTG
*
50460 AGTGATTCAAATGTTG
1 AATGATTCAAATGTTG
*
50476 AACGATTCAAATGTTG
1 AATGATTCAAATGTTG
50492 AATGATTCA
1 AATGATTCA
50501 GAAGTTTTGT
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
15 7 0.14
16 44 0.86
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (16 bp):
AATGATTCAAATGTTG
Found at i:50580 original size:12 final size:13
Alignment explanation
Indices: 50557--50586 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
50547 TGATTCTGAA
50557 TCATTCAGAATGT
1 TCATTCAGAATGT
50570 TCATT-AGAATGT
1 TCATTCAGAATGT
50582 TCATT
1 TCATT
50587 GGGGCTGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.43
Consensus pattern (13 bp):
TCATTCAGAATGT
Done.