Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001069.1 Hibiscus syriacus cultivar Beakdansim tig00002117_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: 119318
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:2695 original size:114 final size:114
Alignment explanation
Indices: 2491--2828 Score: 568
Period size: 114 Copynumber: 3.0 Consensus size: 114
2481 GATCATGCAG
* * * * * *
2491 TTCATCTTTCAATTCTAATGATTGGTTCTGTGGTTCCTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCTAATGATTAGTTTTGCGGTTCATACCAAACCAGATCAGATAACTCAAAGA
* * *
2556 ACATTTCCAGAAGATGCTATTGGGTCTCCTTATTTATACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
* *
2605 TTCTTCTTTCAAATCTAATGATTAGTTTTGCGATTCATACCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCTAATGATTAGTTTTGCGGTTCATACCAAACCAGATCAGATAACTCAAAGA
2670 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
*
2719 TTCATCTTTCAAATCTAATGATTAGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCTAATGATTAGTTTTGCGGTTCATACCAAACCAGATCAGATAACTCAAAGA
2784 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAG
66 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAG
2829 AACATGGCAC
Statistics
Matches: 210, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
114 210 1.00
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (114 bp):
TTCATCTTTCAAATCTAATGATTAGTTTTGCGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
Found at i:7228 original size:20 final size:20
Alignment explanation
Indices: 7200--7240 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
7190 GCAAAGATGC
* *
7200 AAATGCAAACATGAAAATGT
1 AAATACAAACATAAAAATGT
7220 AAATACAAACATAAAAATGT
1 AAATACAAACATAAAAATGT
7240 A
1 A
7241 CAAATGCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.61, C:0.10, G:0.10, T:0.20
Consensus pattern (20 bp):
AAATACAAACATAAAAATGT
Found at i:8816 original size:11 final size:11
Alignment explanation
Indices: 8800--8825 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
8790 ATGAATTTTA
8800 ATTTATAATTG
1 ATTTATAATTG
8811 ATTTATAATTG
1 ATTTATAATTG
8822 ATTT
1 ATTT
8826 TAAAAGCCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.58
Consensus pattern (11 bp):
ATTTATAATTG
Found at i:9361 original size:21 final size:23
Alignment explanation
Indices: 9323--9372 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 23
9313 TCTTCGATAT
9323 TAAAA-AATAAATAAATAA-TTA
1 TAAAATAATAAATAAATAATTTA
* *
9344 -AAAATAATTAATATATAATTTA
1 TAAAATAATAAATAAATAATTTA
9366 TAAAATA
1 TAAAATA
9373 GGATATTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 4 0.17
21 11 0.46
22 3 0.12
23 6 0.25
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (23 bp):
TAAAATAATAAATAAATAATTTA
Found at i:9551 original size:3 final size:3
Alignment explanation
Indices: 9543--9576 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
9533 TGGCTAAATT
9543 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
9577 AAAAAGTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:10949 original size:3 final size:3
Alignment explanation
Indices: 10943--10984 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
10933 ATTTTTTTAG
* *
10943 TAA TAA TAA TAA TAA TTA TTA TAA TAA TAAA TAA -AA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
10985 AATCGGGATA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.86
4 3 0.09
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:19564 original size:21 final size:21
Alignment explanation
Indices: 19538--19584 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
19528 CGAGTCGAGT
19538 TCAACAGTACTCAAACTCAAC
1 TCAACAGTACTCAAACTCAAC
*
19559 TCAACAGTACTCGAACTCAAC
1 TCAACAGTACTCAAACTCAAC
19580 TCAAC
1 TCAAC
19585 TCGTTTACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.40, C:0.34, G:0.06, T:0.19
Consensus pattern (21 bp):
TCAACAGTACTCAAACTCAAC
Found at i:20415 original size:19 final size:18
Alignment explanation
Indices: 20391--20426 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
20381 TAATTTAATA
20391 TTTTTATAATTTTAAAATG
1 TTTTTAT-ATTTTAAAATG
*
20410 TTTTTATTTTTTAAAAT
1 TTTTTATATTTTAAAAT
20427 TGTATAGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (18 bp):
TTTTTATATTTTAAAATG
Found at i:20974 original size:20 final size:22
Alignment explanation
Indices: 20949--20990 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
20939 TGAGGTTACA
20949 ATAATAAAAAT-AAT-TCTTTT
1 ATAATAAAAATCAATATCTTTT
*
20969 ATAATAAATATCAATATCTTTT
1 ATAATAAAAATCAATATCTTTT
20991 TTAACAGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
21 3 0.16
22 6 0.32
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (22 bp):
ATAATAAAAATCAATATCTTTT
Found at i:21083 original size:17 final size:19
Alignment explanation
Indices: 21049--21090 Score: 61
Period size: 17 Copynumber: 2.3 Consensus size: 19
21039 TTGAAACTAT
21049 TCAATAGTTTTAATTATTA
1 TCAATAGTTTTAATTATTA
21068 TCAATA-TTTTAA-TATTA
1 TCAATAGTTTTAATTATTA
*
21085 TAAATA
1 TCAATA
21091 AAATAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 10 0.45
18 6 0.27
19 6 0.27
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (19 bp):
TCAATAGTTTTAATTATTA
Found at i:22077 original size:130 final size:126
Alignment explanation
Indices: 21859--22100 Score: 403
Period size: 130 Copynumber: 1.9 Consensus size: 126
21849 GCGGCGACGA
21859 CGAATTAAGGTTAGGATTTAGGATTTTGGGGCTATTTTATAACATAAAAAAAGTTAGGGTTTTTT
1 CGAATTAAGGTTAGGATTTAGGATTTTGGGGCTATTTTATAACATAAAAAAAGTTAGGGTTTTTT
21924 TTTATAAATATAGTAATATTTTAAATATTTTTAAAAAAAATTAAATTTCAAGAGGGCGACAAGGG
66 TTTATAAATATAGTAATATTTTAAATA--TTT-AAAAAAA-TAAATTTCAAGAGGGCGACAAGGG
* * * * *
21989 CGAATTAAGGTTATGATTTCGGATTTTGGGGCTGTTTTATAATATAATAAAAGTTAGGGTTTTTT
1 CGAATTAAGGTTAGGATTTAGGATTTTGGGGCTATTTTATAACATAAAAAAAGTTAGGGTTTTTT
22054 TTTATAAATATAGTAATATTTTAAATATTTAAAAAAATAAATTTCAA
66 TTTATAAATATAGTAATATTTTAAATATTTAAAAAAATAAATTTCAA
22101 AATTACCAGG
Statistics
Matches: 107, Mismatches: 5, Indels: 4
0.92 0.04 0.03
Matches are distributed among these distances:
126 10 0.09
127 7 0.07
128 3 0.03
130 87 0.81
ACGTcount: A:0.39, C:0.04, G:0.17, T:0.40
Consensus pattern (126 bp):
CGAATTAAGGTTAGGATTTAGGATTTTGGGGCTATTTTATAACATAAAAAAAGTTAGGGTTTTTT
TTTATAAATATAGTAATATTTTAAATATTTAAAAAAATAAATTTCAAGAGGGCGACAAGGG
Found at i:28862 original size:15 final size:15
Alignment explanation
Indices: 28839--28868 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28829 ATTCCTAAAG
*
28839 CAAATATAAAAATAA
1 CAAAAATAAAAATAA
28854 CAAAAATAAAAATAA
1 CAAAAATAAAAATAA
28869 AAATCCAGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.77, C:0.07, G:0.00, T:0.17
Consensus pattern (15 bp):
CAAAAATAAAAATAA
Found at i:29488 original size:23 final size:22
Alignment explanation
Indices: 29464--29518 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
29454 ACATATATAT
29464 TTTTAATTTTTTAATAATTTAA
1 TTTTAATTTTTTAATAATTTAA
* *
29486 -TTTAATTTTTTAATATTTTTA
1 TTTTAATTTTTTAATAATTTAA
*
29507 TATTCAATTTTT
1 T-TTTAATTTTT
29519 CTATATTTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 19 0.68
23 9 0.32
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTTAATTTTTTAATAATTTAA
Found at i:29536 original size:24 final size:23
Alignment explanation
Indices: 29468--29540 Score: 80
Period size: 23 Copynumber: 3.2 Consensus size: 23
29458 ATATATTTTT
* *
29468 AATTTTTTAATAATT-TA-ATTT
1 AATTTTTTAATATTTGTATATTC
*
29489 AATTTTTTAATATTTTTATATTC
1 AATTTTTTAATATTTGTATATTC
29512 AATTTTTCT-ATATTTGTATAGTTC
1 AATTTTT-TAATATTTGTATA-TTC
29536 AATTT
1 AATTT
29541 AAAATTTCAA
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
21 14 0.31
22 2 0.04
23 20 0.44
24 9 0.20
ACGTcount: A:0.32, C:0.04, G:0.03, T:0.62
Consensus pattern (23 bp):
AATTTTTTAATATTTGTATATTC
Found at i:36336 original size:18 final size:18
Alignment explanation
Indices: 36301--36336 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
36291 CAAATACCTG
*
36301 ATAAAAATAAATTAAAAA
1 ATAAAAATAAAATAAAAA
36319 ATAAAAATAAAAATAAAA
1 ATAAAAAT-AAAATAAAA
36337 GGAACGAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (18 bp):
ATAAAAATAAAATAAAAA
Found at i:39170 original size:12 final size:12
Alignment explanation
Indices: 39153--39179 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
39143 GTTTAGCCTT
39153 AATCTCAATAAA
1 AATCTCAATAAA
39165 AATCTCAATAAA
1 AATCTCAATAAA
39177 AAT
1 AAT
39180 AAAATATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.59, C:0.15, G:0.00, T:0.26
Consensus pattern (12 bp):
AATCTCAATAAA
Found at i:48988 original size:10 final size:10
Alignment explanation
Indices: 48973--49008 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
48963 TAGGGATTTT
48973 ATTAATTTAA
1 ATTAATTTAA
*
48983 ATTAATTAAA
1 ATTAATTTAA
48993 TATTAATTTAA
1 -ATTAATTTAA
49004 ATTAA
1 ATTAA
49009 ATATTTGGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
ATTAATTTAA
Found at i:55451 original size:2 final size:2
Alignment explanation
Indices: 55397--55436 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
55387 TAATCAAAAT
55397 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
55437 AACTTTAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:57348 original size:30 final size:30
Alignment explanation
Indices: 57308--57415 Score: 76
Period size: 30 Copynumber: 3.5 Consensus size: 30
57298 GAGAATGGTC
*
57308 TCCCTTCAACATCGCCAATGACCAATAACA
1 TCCCTCCAACATCGCCAATGACCAATAACA
* **
57338 TCCCTCCAACA-CTGCCAAATAACCGAGAATGGTC-
1 TCCCTCCAACATC-GCC-AATGACC---AAT-AACA
* * *
57372 TCCCTACAGCATCGCCATTGACCAATAACA
1 TCCCTCCAACATCGCCAATGACCAATAACA
*
57402 TCCCTCCAATATCG
1 TCCCTCCAACATCG
57416 TCAAATATGG
Statistics
Matches: 57, Mismatches: 13, Indels: 16
0.66 0.15 0.19
Matches are distributed among these distances:
29 2 0.04
30 27 0.47
31 6 0.11
33 5 0.09
34 15 0.26
35 2 0.04
ACGTcount: A:0.32, C:0.37, G:0.10, T:0.20
Consensus pattern (30 bp):
TCCCTCCAACATCGCCAATGACCAATAACA
Found at i:57394 original size:64 final size:64
Alignment explanation
Indices: 57289--57410 Score: 208
Period size: 64 Copynumber: 1.9 Consensus size: 64
57279 TACACATTGT
* *
57289 CAAATAATCGAGAATGGTCTCCCTTCAACATCGCCAATGACCAATAACATCCCTCCAACACTGC
1 CAAATAACCGAGAATGGTCTCCCTACAACATCGCCAATGACCAATAACATCCCTCCAACACTGC
* *
57353 CAAATAACCGAGAATGGTCTCCCTACAGCATCGCCATTGACCAATAACATCCCTCCAA
1 CAAATAACCGAGAATGGTCTCCCTACAACATCGCCAATGACCAATAACATCCCTCCAA
57411 TATCGTCAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
64 54 1.00
ACGTcount: A:0.34, C:0.34, G:0.11, T:0.20
Consensus pattern (64 bp):
CAAATAACCGAGAATGGTCTCCCTACAACATCGCCAATGACCAATAACATCCCTCCAACACTGC
Found at i:75068 original size:3 final size:3
Alignment explanation
Indices: 75057--75102 Score: 67
Period size: 3 Copynumber: 15.7 Consensus size: 3
75047 TTATTAGTAT
* *
75057 TAA TGA TAA TAA T-A TAT TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
75103 TATTTTAATC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:75074 original size:23 final size:23
Alignment explanation
Indices: 75048--75102 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
75038 AATTATAAAT
* * *
75048 TATTAGTATTAATGATAATAATA
1 TATTAATAATAATAATAATAATA
75071 TATTAATAATAATAATAATAATA
1 TATTAATAATAATAATAATAATA
75094 -A-TAATAATA
1 TATTAATAATA
75103 TATTTTAATC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 8 0.28
22 1 0.03
23 20 0.69
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (23 bp):
TATTAATAATAATAATAATAATA
Found at i:75075 original size:26 final size:26
Alignment explanation
Indices: 75037--75097 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
75027 ACAAAATATG
* * * * *
75037 TAATTATAAATTATTAGTATTAATGA
1 TAATAATAAATTAATAATAATAATAA
*
75063 TAATAATATATTAATAATAATAATAA
1 TAATAATAAATTAATAATAATAATAA
75089 TAATAATAA
1 TAATAATAA
75098 TAATATATTT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (26 bp):
TAATAATAAATTAATAATAATAATAA
Found at i:76595 original size:30 final size:30
Alignment explanation
Indices: 76549--76620 Score: 126
Period size: 30 Copynumber: 2.3 Consensus size: 30
76539 TCCCCCTTAC
76549 TTTAACACTTCTTCAATTTATTATGTAAAACA
1 TTTAACAC--CTTCAATTTATTATGTAAAACA
76581 TTTAACACCTTCAATTTATTATGTAAAACA
1 TTTAACACCTTCAATTTATTATGTAAAACA
76611 TTTAACACCT
1 TTTAACACCT
76621 ATTCTTCTCC
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
30 32 0.80
32 8 0.20
ACGTcount: A:0.38, C:0.18, G:0.03, T:0.42
Consensus pattern (30 bp):
TTTAACACCTTCAATTTATTATGTAAAACA
Found at i:76883 original size:17 final size:17
Alignment explanation
Indices: 76861--76903 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
76851 TCATAAATTT
*
76861 AAAATCCAACAATCCAC
1 AAAATCAAACAATCCAC
76878 AAAATCAAACAATCCA-
1 AAAATCAAACAATCCAC
76894 AAATATCAAA
1 AAA-ATCAAA
76904 AATGTTGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.60, C:0.26, G:0.00, T:0.14
Consensus pattern (17 bp):
AAAATCAAACAATCCAC
Found at i:78846 original size:21 final size:21
Alignment explanation
Indices: 78820--78859 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
78810 CAGAACCCCA
*
78820 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
78841 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
78860 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:82744 original size:22 final size:21
Alignment explanation
Indices: 82702--82741 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
82692 AGTTTGTTTT
*
82702 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
82723 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
82742 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:85190 original size:43 final size:43
Alignment explanation
Indices: 85129--85216 Score: 167
Period size: 43 Copynumber: 2.0 Consensus size: 43
85119 TGTTGGGCCA
85129 GTATCAACTTCATGCAAGAAAAGTGAAGTCTTGTCACGTAATG
1 GTATCAACTTCATGCAAGAAAAGTGAAGTCTTGTCACGTAATG
*
85172 GTATCAACTTCATGCAAGAAAAGTGCAGTCTTGTCACGTAATG
1 GTATCAACTTCATGCAAGAAAAGTGAAGTCTTGTCACGTAATG
85215 GT
1 GT
85217 GGGACTCCTT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (43 bp):
GTATCAACTTCATGCAAGAAAAGTGAAGTCTTGTCACGTAATG
Found at i:92436 original size:20 final size:20
Alignment explanation
Indices: 92407--92445 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
92397 ATTCCACCAC
*
92407 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
92427 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
92446 TATGAGCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:93763 original size:2 final size:2
Alignment explanation
Indices: 93751--93782 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
93741 AAAACAACTA
93751 AT AT GAT 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 A
93783 ATGTAAAACT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:93978 original size:21 final size:21
Alignment explanation
Indices: 93954--94001 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
93944 AGGTTTGGAA
*
93954 TTTAGGGTATAGGATTTAGGG
1 TTTAGAGTATAGGATTTAGGG
* *
93975 TTTAGAGTTTAGGATTTATGG
1 TTTAGAGTATAGGATTTAGGG
93996 TTTAGA
1 TTTAGA
94002 TTTAGAGTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.31, T:0.44
Consensus pattern (21 bp):
TTTAGAGTATAGGATTTAGGG
Found at i:93985 original size:14 final size:14
Alignment explanation
Indices: 93934--94021 Score: 65
Period size: 14 Copynumber: 6.4 Consensus size: 14
93924 GGTTTAAGAA
*
93934 TTAGAGTTTAAGGT
1 TTAGAGTTTAGGGT
* *
93948 TTGGAATTTAGGGT
1 TTAGAGTTTAGGGT
*
93962 ATAG-GATTTAGGGT
1 TTAGAG-TTTAGGGT
*
93976 TTAGAGTTTAGGAT
1 TTAGAGTTTAGGGT
*
93990 TTATG-GTTTA-GAT
1 TTA-GAGTTTAGGGT
* *
94003 TTAGAGTGTAGAGT
1 TTAGAGTTTAGGGT
94017 TTAGA
1 TTAGA
94022 ATTTGAGTTT
Statistics
Matches: 58, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
12 1 0.02
13 10 0.17
14 45 0.78
15 2 0.03
ACGTcount: A:0.27, C:0.00, G:0.31, T:0.42
Consensus pattern (14 bp):
TTAGAGTTTAGGGT
Found at i:94029 original size:20 final size:19
Alignment explanation
Indices: 93995--94048 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
93985 AGGATTTATG
93995 GTTTAGATTTAGAGTGTAGA
1 GTTTAGATTT-GAGTGTAGA
* * *
94015 GTTTAGAATTTGAGTTTGGG
1 GTTTAG-ATTTGAGTGTAGA
94035 GTTTAGCATTTGAG
1 GTTTAG-ATTTGAG
94049 GGTTGAGATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 25 0.86
21 4 0.14
ACGTcount: A:0.24, C:0.02, G:0.31, T:0.43
Consensus pattern (19 bp):
GTTTAGATTTGAGTGTAGA
Found at i:94625 original size:15 final size:16
Alignment explanation
Indices: 94595--94629 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
94585 TCAATTAGAA
94595 TTTTATTTATTTTTAG
1 TTTTATTTATTTTTAG
*
94611 TTTTCTTTA-TTTTAG
1 TTTTATTTATTTTTAG
94626 TTTT
1 TTTT
94630 TCCTTATTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.14, C:0.03, G:0.06, T:0.77
Consensus pattern (16 bp):
TTTTATTTATTTTTAG
Found at i:94636 original size:16 final size:15
Alignment explanation
Indices: 94605--94638 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
94595 TTTTATTTAT
*
94605 TTTTAGTTTTCTTTA
1 TTTTAGTTTTCCTTA
94620 TTTTAGTTTTTCCTTA
1 TTTTAG-TTTTCCTTA
94636 TTT
1 TTT
94639 GATTTAGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.12, C:0.09, G:0.06, T:0.74
Consensus pattern (15 bp):
TTTTAGTTTTCCTTA
Found at i:95979 original size:26 final size:26
Alignment explanation
Indices: 95946--96007 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
95936 TTTATAATTT
*
95946 TTAAAATTTAAGATTT-AGAATTGATA
1 TTAAAATTTAAGATTTAAG-ATTGAGA
*
95972 TTAAAATTTAGGATTTAAGATTGAGA
1 TTAAAATTTAAGATTTAAGATTGAGA
*
95998 TTGAAATTTA
1 TTAAAATTTA
96008 TGAATGCATA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
26 30 0.94
27 2 0.06
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.42
Consensus pattern (26 bp):
TTAAAATTTAAGATTTAAGATTGAGA
Found at i:101144 original size:20 final size:20
Alignment explanation
Indices: 101121--101158 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
101111 TACTGAGTGG
*
101121 GTAGTATCGATACTCTAGTT
1 GTAGTATCGATACCCTAGTT
101141 GTAGTATCGATACCCTAG
1 GTAGTATCGATACCCTAG
101159 GGTCAAGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.34
Consensus pattern (20 bp):
GTAGTATCGATACCCTAGTT
Found at i:101886 original size:19 final size:20
Alignment explanation
Indices: 101852--101891 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
101842 ATGAGGAAGT
101852 AGAAAATGGAAAATGAGAGGA
1 AGAAAATGGAAAATGAG-GGA
101873 AGAAAAT-G-AAATGAGGGA
1 AGAAAATGGAAAATGAGGGA
101891 A
1 A
101892 TATAAATGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.21
19 7 0.37
20 1 0.05
21 7 0.37
ACGTcount: A:0.57, C:0.00, G:0.33, T:0.10
Consensus pattern (20 bp):
AGAAAATGGAAAATGAGGGA
Found at i:116182 original size:28 final size:28
Alignment explanation
Indices: 116123--116182 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
116113 TGAAAAACTT
****
116123 TTTTGTCATTGATATTAAAAAACTCTTT
1 TTTTGTCATTGATATTAAAAAACTAAAG
116151 TTTTGTCATTGATATTAAAAAA-TAAAAG
1 TTTTGTCATTGATATTAAAAAACT-AAAG
116179 TTTT
1 TTTT
116183 ATTTGATTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 1 0.04
28 26 0.96
ACGTcount: A:0.37, C:0.07, G:0.08, T:0.48
Consensus pattern (28 bp):
TTTTGTCATTGATATTAAAAAACTAAAG
Found at i:117837 original size:14 final size:14
Alignment explanation
Indices: 117818--117847 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
117808 TAAACATTTT
117818 ATAAATATCTTTGA
1 ATAAATATCTTTGA
*
117832 ATAAATATTTTTGA
1 ATAAATATCTTTGA
117846 AT
1 AT
117848 TAGATCGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (14 bp):
ATAAATATCTTTGA
Done.