Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005977.1 Hibiscus syriacus cultivar Beakdansim tig00014050_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: 108137
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:9408 original size:45 final size:45
Alignment explanation
Indices: 9296--9442 Score: 222
Period size: 45 Copynumber: 3.2 Consensus size: 45
9286 TGTTATCCAC
* * * * *
9296 AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCTTATTCAAA
1 AAAAATAAA-CCTAACCGCATGATATCTAGTTCGCATGCCTGTTC--G
9344 AAAAATAAACCTAACCGCATGATATCTAGTTCGCATGCCTGTTCG
1 AAAAATAAACCTAACCGCATGATATCTAGTTCGCATGCCTGTTCG
9389 AAAAATAAACCTAACCGCATGATATCTAGTTCGCATGCCTGTTCG
1 AAAAATAAACCTAACCGCATGATATCTAGTTCGCATGCCTGTTCG
9434 AAAAATAAA
1 AAAAATAAA
9443 AATAAATTAC
Statistics
Matches: 94, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
45 54 0.57
47 32 0.34
48 8 0.09
ACGTcount: A:0.39, C:0.22, G:0.13, T:0.26
Consensus pattern (45 bp):
AAAAATAAACCTAACCGCATGATATCTAGTTCGCATGCCTGTTCG
Found at i:13411 original size:18 final size:18
Alignment explanation
Indices: 13383--13431 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
13373 TGTTAAACAT
13383 TTTGATTTGGATGTTTATG
1 TTTGATTTGGATGTTT-TG
* *
13402 TTTG-TTTGGATATTTTT
1 TTTGATTTGGATGTTTTG
*
13419 TTTGTTTTGGATG
1 TTTGATTTGGATG
13432 CTTGGACGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 5 0.19
18 17 0.65
19 4 0.15
ACGTcount: A:0.12, C:0.00, G:0.24, T:0.63
Consensus pattern (18 bp):
TTTGATTTGGATGTTTTG
Found at i:19630 original size:2 final size:2
Alignment explanation
Indices: 19623--19667 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
19613 TTCATCTTCC
19623 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
19665 TA T
1 TA T
19668 CATTTTTCCT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:23055 original size:2 final size:2
Alignment explanation
Indices: 23048--23074 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
23038 CTCATAACGG
23048 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
23075 AATTAAAAAC
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:23138 original size:24 final size:24
Alignment explanation
Indices: 23091--23163 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
23081 AAACATAATT
* * * *
23091 CAGGTCAAGTAGCAGATCAGAATC
1 CAGGTCAAGTATCATATAAAAATC
* *
23115 CATGTCATGTATCATATAAAAATC
1 CAGGTCAAGTATCATATAAAAATC
*
23139 CAGGTCAAGTATCATATCAAAATC
1 CAGGTCAAGTATCATATAAAAATC
23163 C
1 C
23164 CATCAAAAAT
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.25
Consensus pattern (24 bp):
CAGGTCAAGTATCATATAAAAATC
Found at i:23907 original size:29 final size:29
Alignment explanation
Indices: 23865--23996 Score: 187
Period size: 29 Copynumber: 4.6 Consensus size: 29
23855 ATCAACCATT
23865 TTACAAAAATAACACCCTTTTAAAAATAA
1 TTACAAAAATAACACCCTTTTAAAAATAA
* * *
23894 TTACGAAAATAACACCATTTTATAAATAA
1 TTACAAAAATAACACCCTTTTAAAAATAA
*
23923 TTACTAAAATAACA-CCTTTT-AAAATAA
1 TTACAAAAATAACACCCTTTTAAAAATAA
23950 TTACAAAAATAACACCCTTTTAGAAAATAA
1 TTACAAAAATAACACCCTTTTA-AAAATAA
* *
23980 TTACTAAAATAGCACCC
1 TTACAAAAATAACACCC
23997 GGTCAACGGT
Statistics
Matches: 91, Mismatches: 9, Indels: 5
0.87 0.09 0.05
Matches are distributed among these distances:
27 19 0.21
28 11 0.12
29 39 0.43
30 22 0.24
ACGTcount: A:0.52, C:0.17, G:0.02, T:0.29
Consensus pattern (29 bp):
TTACAAAAATAACACCCTTTTAAAAATAA
Found at i:23959 original size:56 final size:58
Alignment explanation
Indices: 23865--23995 Score: 194
Period size: 56 Copynumber: 2.3 Consensus size: 58
23855 ATCAACCATT
* * *
23865 TTACAAAAATAACACCCTTTTAAAAATAATTACGAAAATAACACCATTTTA-TAAATAA
1 TTACTAAAATAACA-CCTTTTAAAAATAATTACAAAAATAACACCATTTTAGAAAATAA
*
23923 TTACTAAAATAACACCTTTT-AAAATAATTACAAAAATAACACCCTTTTAGAAAATAA
1 TTACTAAAATAACACCTTTTAAAAATAATTACAAAAATAACACCATTTTAGAAAATAA
*
23980 TTACTAAAATAGCACC
1 TTACTAAAATAACACC
23996 CGGTCAACGG
Statistics
Matches: 67, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
56 27 0.40
57 27 0.40
58 13 0.19
ACGTcount: A:0.52, C:0.17, G:0.02, T:0.29
Consensus pattern (58 bp):
TTACTAAAATAACACCTTTTAAAAATAATTACAAAAATAACACCATTTTAGAAAATAA
Found at i:25149 original size:22 final size:24
Alignment explanation
Indices: 25124--25169 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 24
25114 CTTTATACTC
*
25124 ATTCACATTTA-C-TATAACATAT
1 ATTCACATATATCATATAACATAT
25146 ATTCACATATATCATATAACATAT
1 ATTCACATATATCATATAACATAT
25170 GCAATAACAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 10 0.48
23 1 0.05
24 10 0.48
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.39
Consensus pattern (24 bp):
ATTCACATATATCATATAACATAT
Found at i:37286 original size:2 final size:2
Alignment explanation
Indices: 37277--37308 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
37267 AAAATATAAA
37277 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
37309 ATCGGGGCGG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37309 original size:34 final size:34
Alignment explanation
Indices: 37206--37290 Score: 152
Period size: 34 Copynumber: 2.5 Consensus size: 34
37196 CCCGAACCCG
*
37206 AAAATATTTTATATATAATTAATATAAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
*
37240 AAATTATTATATATATAATTAATATAAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
37274 AAAATATTATATATATA
1 AAAATATTATATATATA
37291 TATATATATA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 48 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (34 bp):
AAAATATTATATATATAATTAATATAAAAAATAT
Found at i:39914 original size:12 final size:12
Alignment explanation
Indices: 39899--39959 Score: 52
Period size: 12 Copynumber: 5.1 Consensus size: 12
39889 TGAATTATTT
39899 TCTGATTTCTGA
1 TCTGATTTCTGA
*
39911 TCTGGA-TTCTGT
1 TCT-GATTTCTGA
*
39923 TCTGATATCTGA
1 TCTGATTTCTGA
* *
39935 TCTGAATTCTGT
1 TCTGATTTCTGA
* *
39947 TTTGATTTTTGA
1 TCTGATTTCTGA
39959 T
1 T
39960 ATCTCCGTTT
Statistics
Matches: 37, Mismatches: 10, Indels: 4
0.73 0.20 0.08
Matches are distributed among these distances:
11 2 0.05
12 33 0.89
13 2 0.05
ACGTcount: A:0.16, C:0.13, G:0.18, T:0.52
Consensus pattern (12 bp):
TCTGATTTCTGA
Found at i:39925 original size:24 final size:24
Alignment explanation
Indices: 39888--39959 Score: 90
Period size: 24 Copynumber: 3.0 Consensus size: 24
39878 GATACATTAC
* *
39888 CTGAATTATTTTCTGATTTCTGAT
1 CTGAATTCTGTTCTGATTTCTGAT
* *
39912 CTGGATTCTGTTCTGATATCTGAT
1 CTGAATTCTGTTCTGATTTCTGAT
* *
39936 CTGAATTCTGTTTTGATTTTTGAT
1 CTGAATTCTGTTCTGATTTCTGAT
39960 ATCTCCGTTT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.18, C:0.12, G:0.17, T:0.53
Consensus pattern (24 bp):
CTGAATTCTGTTCTGATTTCTGAT
Found at i:41899 original size:2 final size:2
Alignment explanation
Indices: 41892--41921 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
41882 CTTTTTAAAC
41892 TA TA TA TA TA TA TA TA TA TA TA TA TGA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
41922 TTGAATCCAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:42435 original size:23 final size:23
Alignment explanation
Indices: 42399--42460 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
42389 ATATTTTTAT
* *
42399 AATATCAAGAATTAAATTTAATTAA
1 AATATGAAG-ATTAAA-TTAATAAA
42424 AA-ATGAAGATTAAATTAATAAA
1 AATATGAAGATTAAATTAATAAA
*
42446 AATATGAATATTAAA
1 AATATGAAGATTAAA
42461 AATTAAATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 9 0.27
23 17 0.52
24 5 0.15
25 2 0.06
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.32
Consensus pattern (23 bp):
AATATGAAGATTAAATTAATAAA
Found at i:49732 original size:21 final size:21
Alignment explanation
Indices: 49706--49747 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
49696 ATTCCATATT
49706 ATTAACACACCAATAGTAATA
1 ATTAACACACCAATAGTAATA
*
49727 ATTAACACACCAATTGTAATA
1 ATTAACACACCAATAGTAATA
49748 TTATTATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.50, C:0.19, G:0.05, T:0.26
Consensus pattern (21 bp):
ATTAACACACCAATAGTAATA
Found at i:50523 original size:23 final size:23
Alignment explanation
Indices: 50507--50562 Score: 112
Period size: 23 Copynumber: 2.4 Consensus size: 23
50497 AAAAAGATAA
50507 AAAAACGTACAGTAAAAACAGAG
1 AAAAACGTACAGTAAAAACAGAG
50530 AAAAACGTACAGTAAAAACAGAG
1 AAAAACGTACAGTAAAAACAGAG
50553 AAAAACGTAC
1 AAAAACGTAC
50563 CACATAAACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.61, C:0.14, G:0.16, T:0.09
Consensus pattern (23 bp):
AAAAACGTACAGTAAAAACAGAG
Found at i:50523 original size:25 final size:24
Alignment explanation
Indices: 50495--50562 Score: 86
Period size: 23 Copynumber: 2.9 Consensus size: 24
50485 CGCTATAGAG
*
50495 AAAAAAAGATAAAAAAACGTACAGT
1 AAAAACAGA-AAAAAAACGTACAGT
*
50520 AAAAACAG-AGAAAAACGTACAGT
1 AAAAACAGAAAAAAAACGTACAGT
*
50543 AAAAACAG-AGAAAAACGTAC
1 AAAAACAGAAAAAAAACGTAC
50563 CACATAAACA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
23 34 0.83
25 7 0.17
ACGTcount: A:0.65, C:0.12, G:0.15, T:0.09
Consensus pattern (24 bp):
AAAAACAGAAAAAAAACGTACAGT
Found at i:50547 original size:14 final size:13
Alignment explanation
Indices: 50507--50548 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
50497 AAAAAGATAA
50507 AAAAACGTACAGT
1 AAAAACGTACAGT
*
50520 AAAAAC--AGAG-
1 AAAAACGTACAGT
50530 AAAAACGTACAGT
1 AAAAACGTACAGT
50543 AAAAAC
1 AAAAAC
50549 AGAGAAAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
10 6 0.25
11 3 0.12
12 3 0.12
13 12 0.50
ACGTcount: A:0.62, C:0.14, G:0.14, T:0.10
Consensus pattern (13 bp):
AAAAACGTACAGT
Found at i:59030 original size:2 final size:2
Alignment explanation
Indices: 59023--59050 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
59013 TCAACTTATC
59023 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
59051 TCAAACCATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:62556 original size:2 final size:2
Alignment explanation
Indices: 62549--62624 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
62539 TTGTGGTTCG
62549 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
62591 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
62625 CAATAAAAAG
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:76840 original size:35 final size:35
Alignment explanation
Indices: 76775--76842 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
76765 GCATTAATGA
* *
76775 GGTATCGATACCTGAAGAACATTATAGATACCAAG
1 GGTACCGATACCTGAAGAACAATATAGATACCAAG
* * *
76810 GGTACCGATACCTTAAGGACAATATCGATACCA
1 GGTACCGATACCTGAAGAACAATATAGATACCA
76843 TCTTTTGAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (35 bp):
GGTACCGATACCTGAAGAACAATATAGATACCAAG
Found at i:77513 original size:20 final size:20
Alignment explanation
Indices: 77485--77524 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
77475 AGTAGAGGGT
*
77485 TACATAGGTCCTTCGGGACA
1 TACACAGGTCCTTCGGGACA
77505 TACACAGGTCCTTCGGGACA
1 TACACAGGTCCTTCGGGACA
77525 AATTCACATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.25, C:0.28, G:0.25, T:0.23
Consensus pattern (20 bp):
TACACAGGTCCTTCGGGACA
Found at i:78647 original size:45 final size:45
Alignment explanation
Indices: 78548--78650 Score: 143
Period size: 45 Copynumber: 2.3 Consensus size: 45
78538 GAATAACGTA
* * *
78548 GCCGTGACAACTAGAGTTAATGACGTTGCCGTGGCAAGTGAAGTT
1 GCCGTGGCAAGTAGAGTTAATGACGTTGACGTGGCAAGTGAAGTT
** *
78593 GCCAAGGCAAGTAGAGTTAATGATGTTGACGTGGCAAGTGAAGTT
1 GCCGTGGCAAGTAGAGTTAATGACGTTGACGTGGCAAGTGAAGTT
*
78638 GTCGTGGCAAGTA
1 GCCGTGGCAAGTA
78651 TAGGATCACA
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.28, C:0.15, G:0.33, T:0.24
Consensus pattern (45 bp):
GCCGTGGCAAGTAGAGTTAATGACGTTGACGTGGCAAGTGAAGTT
Found at i:81973 original size:18 final size:18
Alignment explanation
Indices: 81950--82001 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
81940 ATATAACACA
81950 TATGTCCCGAAGGACCAC
1 TATGTCCCGAAGGACCAC
* * *
81968 TATGTCCCTAATGTCCAC
1 TATGTCCCGAAGGACCAC
*
81986 TATGCCCCGAAGGACC
1 TATGTCCCGAAGGACC
82002 GCGTACACCC
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.25, C:0.35, G:0.19, T:0.21
Consensus pattern (18 bp):
TATGTCCCGAAGGACCAC
Found at i:82871 original size:63 final size:63
Alignment explanation
Indices: 82759--82917 Score: 180
Period size: 63 Copynumber: 2.5 Consensus size: 63
82749 CCCTTAACGT
* * **
82759 GTGCATCGATGCACTACTTGTGCATCGGTACACAATTCACCTTCGATGTTT-TAATATT-AAGGG
1 GTGCATCGATGCACTACTTGTGCATCGATACACAATTCACATTCGATGTTTGT-AT-TTAAAGAA
* * *
82822 GTGCATCGATGCACTACTTGTGCATCGATACACTGA-TGACATTCTATGTTTGTATTTAAAGAA
1 GTGCATCGATGCACTACTTGTGCATCGATACAC-AATTCACATTCGATGTTTGTATTTAAAGAA
* * *
82885 GTGCATCGATACACTCCATGTGCATCGATACAC
1 GTGCATCGATGCACTACTTGTGCATCGATACAC
82918 CTTGAACAAT
Statistics
Matches: 83, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
62 2 0.02
63 79 0.95
64 2 0.02
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.32
Consensus pattern (63 bp):
GTGCATCGATGCACTACTTGTGCATCGATACACAATTCACATTCGATGTTTGTATTTAAAGAA
Found at i:83913 original size:20 final size:19
Alignment explanation
Indices: 83890--83947 Score: 53
Period size: 20 Copynumber: 2.8 Consensus size: 19
83880 GATGCAAAAG
*
83890 TAAGTGCATCGATGCACCGT
1 TAAGTGCATCGATGCA-CGA
*
83910 TAAGGATGCATCGATACACGA
1 TAA-G-TGCATCGATGCACGA
*
83931 TATAGTGAATCGATGCA
1 TA-AGTGCATCGATGCA
83948 TACCTTTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
20 13 0.42
21 6 0.19
22 12 0.39
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.24
Consensus pattern (19 bp):
TAAGTGCATCGATGCACGA
Found at i:84807 original size:23 final size:23
Alignment explanation
Indices: 84774--84841 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
84764 ATTATTATAT
84774 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
84797 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* *
84820 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
84842 AGTTGTGGTG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.21, C:0.28, G:0.26, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:89506 original size:45 final size:44
Alignment explanation
Indices: 89412--89511 Score: 121
Period size: 45 Copynumber: 2.2 Consensus size: 44
89402 GCACATTCAA
* *
89412 AGTGCATCGATGCACCCTTTAAAGAAGAAACATCGAATGCAATT
1 AGTGCATCGATGCACCCTTGAAACAAGAAACATCGAATGCAATT
* * *
89456 AGTGCATCGATGCACTCCCTTGATACAA-AAACATCGAATGTATTT
1 AGTGCATCGATGCA--CCCTTGAAACAAGAAACATCGAATGCAATT
*
89501 TGTGCATCGAT
1 AGTGCATCGAT
89512 ACACGGTATA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
44 14 0.29
45 25 0.52
46 9 0.19
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (44 bp):
AGTGCATCGATGCACCCTTGAAACAAGAAACATCGAATGCAATT
Found at i:90402 original size:23 final size:23
Alignment explanation
Indices: 90366--90434 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
90356 CATTATTATA
90366 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
90389 TGGCACTCCTGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
90412 TGGCACTTCGGTGCAATTATACG
1 TGGCACTACGGTGCAATTCTACG
90435 AGCTGTGGTG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.20, C:0.26, G:0.25, T:0.29
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:98361 original size:60 final size:60
Alignment explanation
Indices: 98244--98390 Score: 165
Period size: 60 Copynumber: 2.5 Consensus size: 60
98234 AAAACTTTGA
* **
98244 ACTAATTTAGAATGAGAGTCATAGTTTGAGGATGAAATTGGAATGCTCAAAAGTTTAAGG
1 ACTAATTTAGAATGAGAGTCATAGTTTGAGGATAAAATTAAAATGCTCAAAAGTTTAAGG
* * ** *
98304 ATTAATTTAGAATGAGAGTCGTAGTTT-AGGGATAAAATTAAAATTTTTAGAAA-TTTAAGG
1 ACTAATTTAGAATGAGAGTCATAGTTTGA-GGATAAAATTAAAATGCTCA-AAAGTTTAAGG
* *
98364 ACTAATTTA-AATAAGGGTCATAGTTTG
1 ACTAATTTAGAATGAGAGTCATAGTTTG
98391 GAGACATATG
Statistics
Matches: 72, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
59 15 0.21
60 54 0.75
61 3 0.04
ACGTcount: A:0.39, C:0.05, G:0.22, T:0.34
Consensus pattern (60 bp):
ACTAATTTAGAATGAGAGTCATAGTTTGAGGATAAAATTAAAATGCTCAAAAGTTTAAGG
Found at i:100957 original size:43 final size:43
Alignment explanation
Indices: 100905--101213 Score: 300
Period size: 43 Copynumber: 7.2 Consensus size: 43
100895 TTTCAACAAA
* **
100905 AAACGCCGCAATAGGTGTTGATGTTTAGCGGCATTTTTTTCAC
1 AAACGCCGCAGTAGGTGTTGATGTTTAGCGGCATTTTTCCCAC
* * *
100948 AAACGCCGCAGTAGGTGTTGATATTTTGCGGCATTTTTCCCGC
1 AAACGCCGCAGTAGGTGTTGATGTTTAGCGGCATTTTTCCCAC
* * * **
100991 TAACGCCGCAGTAGGTGTTGATGTTTTGCGGCGTTTTTCCCGT
1 AAACGCCGCAGTAGGTGTTGATGTTTAGCGGCATTTTTCCCAC
* * * *
101034 TAATGCCGCAGTAGGTGTTGATTTTTAGCGACATTTTTCCCAC
1 AAACGCCGCAGTAGGTGTTGATGTTTAGCGGCATTTTTCCCAC
* * * * *
101077 AAACACCGCAGTAGGTATTGATGTTTAGTGGCGTTTTTTCCAC
1 AAACGCCGCAGTAGGTGTTGATGTTTAGCGGCATTTTTCCCAC
* * * * *
101120 AAATGCCGCAGTAGATGTTGATATTTAACGGCGTTTTAT--CAC
1 AAACGCCGCAGTAGGTGTTGATGTTTAGCGGCATTTT-TCCCAC
* * * ** *
101162 AAACGCTGCAATAGGTGTTGA-GATTTAGCGGCGTTTTTAGCGC
1 AAACGCCGCAGTAGGTGTTGATG-TTTAGCGGCATTTTTCCCAC
101205 AAACGCCGC
1 AAACGCCGC
101214 TAAATATGGT
Statistics
Matches: 221, Mismatches: 41, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
41 1 0.00
42 33 0.15
43 186 0.84
44 1 0.00
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (43 bp):
AAACGCCGCAGTAGGTGTTGATGTTTAGCGGCATTTTTCCCAC
Found at i:101006 original size:86 final size:87
Alignment explanation
Indices: 100905--101199 Score: 341
Period size: 86 Copynumber: 3.4 Consensus size: 87
100895 TTTCAACAAA
* * * *
100905 AAACGCCGCAATAGGTGTTGATGTTTAGCGGCATTTTTTTCACAAACGCCGCAGTAGGTGTTGAT
1 AAACGCCGCAGTAGGTGTTGATGTTTAGCGGCGTTTTTTCCACAAATGCCGCAGTAGGTGTTGAT
* *
100970 ATTTT-GCGGCATTTTTCCCGC
66 ATTTTAGCGACATTTTTCCCAC
* * * ***
100991 TAACGCCGCAGTAGGTGTTGATGTTTTGCGGCGTTTTTCCCGTTAATGCCGCAGTAGGTGTTGAT
1 AAACGCCGCAGTAGGTGTTGATGTTTAGCGGCGTTTTTTCCACAAATGCCGCAGTAGGTGTTGAT
101056 -TTTTAGCGACATTTTTCCCAC
66 ATTTTAGCGACATTTTTCCCAC
* * * *
101077 AAACACCGCAGTAGGTATTGATGTTTAGTGGCGTTTTTTCCACAAATGCCGCAGTAGATGTTGAT
1 AAACGCCGCAGTAGGTGTTGATGTTTAGCGGCGTTTTTTCCACAAATGCCGCAGTAGGTGTTGAT
* * *
101142 A-TTTAACGGCGTTTTAT--CAC
66 ATTTTAGCGACATTTT-TCCCAC
* *
101162 AAACGCTGCAATAGGTGTTGA-GATTTAGCGGCGTTTTT
1 AAACGCCGCAGTAGGTGTTGATG-TTTAGCGGCGTTTTT
101200 AGCGCAAACG
Statistics
Matches: 175, Mismatches: 30, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
84 1 0.01
85 38 0.22
86 135 0.77
87 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (87 bp):
AAACGCCGCAGTAGGTGTTGATGTTTAGCGGCGTTTTTTCCACAAATGCCGCAGTAGGTGTTGAT
ATTTTAGCGACATTTTTCCCAC
Found at i:101623 original size:21 final size:21
Alignment explanation
Indices: 101573--101631 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
101563 TGCTGATATG
* * *
101573 CTGCTTCTCTCTGTGTTGGCG
1 CTGCTTCTCTCTGTGCTGCCA
*
101594 TTG-TCTCTCTCTGTGCTGCCA
1 CTGCT-TCTCTCTGTGCTGCCA
*
101615 CTGCTTCTCTCTCTGCT
1 CTGCTTCTCTCTGTGCT
101632 TCCCTTGCTT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
20 1 0.03
21 28 0.93
22 1 0.03
ACGTcount: A:0.02, C:0.34, G:0.20, T:0.44
Consensus pattern (21 bp):
CTGCTTCTCTCTGTGCTGCCA
Found at i:105691 original size:160 final size:162
Alignment explanation
Indices: 105474--105765 Score: 410
Period size: 160 Copynumber: 1.8 Consensus size: 162
105464 TGCGTTTACT
* * * *
105474 TAAAAACGCCACTAATGTCCAAATATTTCGCGGCGTTTGTGTGCCAAAAAAGCCACTAACGTAAG
1 TAAAAACGCCACTAATGTCCAAATATTTAGCGACGTTTGTGTGCCAAAAAAGCCACTAAAGTAAC
** * *
105539 CCTCTATAGCGGCATTTTCTTAAAAACGCCGCTACAGTTCTATTATATTGCGGCGTTT-TA-AAA
66 CCTCTATAGCGGCATTTTAATAAAAACGCCGCTAAAGTTATATTATATTGCGGCGTTTATACAAA
105602 AATACCACTAAATTAAATATGCCGCGTTTGAA
131 AATACCACTAAATTAAATATGCCGCGTTTGAA
* * ** *
105634 TAAAAACGCCACTAATGTCCAAATGTTTAGCGACGTTT-TTTGTTTAAAAACGCCACTAAAGTAA
1 TAAAAACGCCACTAATGTCCAAATATTTAGCGACGTTTGTGTG-CCAAAAAAGCCACTAAAGTAA
* **
105698 CCCTCTATAGCGGCGTTTTAATATCAACGCCGCTAAAGTTATATTATATTGCGGCGTTTATACAA
65 CCCTCTATAGCGGCATTTTAATAAAAACGCCGCTAAAGTTATATTATATTGCGGCGTTTATACAA
105763 AAA
130 AAA
105766 CGCCTCTAGT
Statistics
Matches: 113, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
159 3 0.03
160 103 0.91
161 2 0.02
162 5 0.04
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.30
Consensus pattern (162 bp):
TAAAAACGCCACTAATGTCCAAATATTTAGCGACGTTTGTGTGCCAAAAAAGCCACTAAAGTAAC
CCTCTATAGCGGCATTTTAATAAAAACGCCGCTAAAGTTATATTATATTGCGGCGTTTATACAAA
AATACCACTAAATTAAATATGCCGCGTTTGAA
Found at i:105953 original size:41 final size:39
Alignment explanation
Indices: 105824--105957 Score: 110
Period size: 40 Copynumber: 3.3 Consensus size: 39
105814 GGATGAATAT
* * *
105824 TGCGGCG-TTTTTGAAACAAATGCCGTAAAAGTGTGGTTTA
1 TGCGGCGTTTTTTTATACAAATGCC-AAAAAGTGT-GTTTA
* ** * *
105864 TGGCGGCATTTTTTTATGTAAACGCCGTAAAAAGTGGGTTTA
1 T-GCGGCGTTTTTTTATACAAATGCC--AAAAAGTGTGTTTA
*
105906 TG-GGCGTTTTTTTATACAAATGCCACAAAAGTGTGTCTA
1 TGCGGCGTTTTTTTATACAAATGCCA-AAAAGTGTGTTTA
105945 TAGCGGCGTTTTT
1 T-GCGGCGTTTTT
105958 CGATAAAAAT
Statistics
Matches: 73, Mismatches: 15, Indels: 11
0.74 0.15 0.11
Matches are distributed among these distances:
38 1 0.01
39 12 0.16
40 20 0.27
41 15 0.21
42 18 0.25
43 7 0.10
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.36
Consensus pattern (39 bp):
TGCGGCGTTTTTTTATACAAATGCCAAAAAGTGTGTTTA
Found at i:107534 original size:81 final size:81
Alignment explanation
Indices: 107375--107632 Score: 269
Period size: 81 Copynumber: 3.2 Consensus size: 81
107365 ATTTTTGCAT
* * * **
107375 AAACGCCACTATAAACAATACTATTTGCGGCGTTTGTTTATAAATGCCGCTAAATT--TTCTCTA
1 AAACGCCACTATAAATAA-ACTA-TTACGGCGTTTGTCTATAAATGCCGCTAAATTACCACTCTA
* *
107438 TAGCGGCGTTTGTTAAAC
64 TTGCGGCGTTTGTTAAAA
* * * *
107456 AAATGCCACTATAAATAACACTATCACGGCGTTTGTGTAAAAATGCCGCTAAATTACCACTCTAT
1 AAACGCCACTATAAATAA-ACTATTACGGCGTTTGTCTATAAATGCCGCTAAATTACCACTCTAT
107521 TGCGG-GTTTGTTAAAA
65 TGCGGCGTTTGTTAAAA
* * * *
107537 AAACGCCACTATAAACGT-ATCTATTACGGCATTTTTACTATAAACGCCGCTAAATTACCACTCT
1 AAACGCCACTATAAA--TAAACTATTACGGCGTTTGT-CTATAAATGCCGCTAAATTACCACTCT
107601 ATTGCGGCG-TTGTT-AAA
63 ATTGCGGCGTTTGTTAAAA
*
107618 AAACGCCGCTA-AAAT
1 AAACGCCACTATAAAT
107633 CATTTTGTGG
Statistics
Matches: 151, Mismatches: 20, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
78 1 0.01
80 31 0.21
81 70 0.46
82 47 0.31
83 2 0.01
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (81 bp):
AAACGCCACTATAAATAAACTATTACGGCGTTTGTCTATAAATGCCGCTAAATTACCACTCTATT
GCGGCGTTTGTTAAAA
Found at i:107538 original size:40 final size:41
Alignment explanation
Indices: 107399--107630 Score: 153
Period size: 41 Copynumber: 5.7 Consensus size: 41
107389 ACAATACTAT
* * * **
107399 TTGCGGCGTTTGTTTATAAATGCCGCTAAATT--TTCTCTA
1 TTGCGGCGTTTGTTAAAAAACGCCGCTAAATTACCACTCTA
* * * * *
107438 TAGCGGCGTTTGTTAAACAAATGCCACTATAAATA--ACACTA
1 TTGCGGCGTTTGTTAAA-AAACGCCGCTA-AATTACCACTCTA
** *
107479 TCACGGCGTTTGTGT-AAAAATGCCGCTAAATTACCACTCTA
1 TTGCGGCGTTTGT-TAAAAAACGCCGCTAAATTACCACTCTA
* *
107520 TTGCGG-GTTTGTTAAAAAAACGCCACTATAA--ACGTA-TCTA
1 TTGCGGCGTTTGTT-AAAAAACGCCGCTA-AATTAC-CACTCTA
* * *
107560 TTACGGCATTT-TTACTATAAACGCCGCTAAATTACCACTCTA
1 TTGCGGCGTTTGTTA--AAAAACGCCGCTAAATTACCACTCTA
107602 TTGCGGCG-TTGTTAAAAAACGCCGCTAAA
1 TTGCGGCGTTTGTTAAAAAACGCCGCTAAA
107631 ATCATTTTGT
Statistics
Matches: 151, Mismatches: 25, Indels: 33
0.72 0.12 0.16
Matches are distributed among these distances:
39 20 0.13
40 55 0.36
41 58 0.38
42 18 0.12
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.31
Consensus pattern (41 bp):
TTGCGGCGTTTGTTAAAAAACGCCGCTAAATTACCACTCTA
Done.