Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006405.1 Hibiscus syriacus cultivar Beakdansim tig00015442_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: 103399
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:3127 original size:3 final size:3
Alignment explanation
Indices: 3119--3186 Score: 136
Period size: 3 Copynumber: 22.7 Consensus size: 3
3109 GTTCCCTTTC
3119 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
3167 TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TC
3187 CCCATTGTTT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:5231 original size:21 final size:20
Alignment explanation
Indices: 5193--5229 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5183 ATGCGTTTTC
5193 TTTTTTAGTTTAGTATATTT
1 TTTTTTAGTTTAGTATATTT
*
5213 TTTTTTAGATTA-TATAT
1 TTTTTTAGTTTAGTATAT
5230 ATATATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (20 bp):
TTTTTTAGTTTAGTATATTT
Found at i:5298 original size:22 final size:22
Alignment explanation
Indices: 5225--5346 Score: 90
Period size: 23 Copynumber: 5.3 Consensus size: 22
5215 TTTTAGATTA
*
5225 TATATATATA-TATATTTT-TT
1 TATATATATATTATTTTTTATT
* * *
5245 TAT-TATCAGTTTTATTAATTTATA
1 TATATAT-A-TATTATT-TTTTATT
5269 TATATATATATATACTATTTTTTATT
1 TATATATATAT-TA-T-TTT-TTATT
5295 TATATATATATTA-TTTTTACTT
1 TATATATATATTATTTTTTA-TT
*
5317 TATATTTATTATTATTTTTTATT
1 TATATATA-TATTATTTTTTATT
5340 TATATAT
1 TATATAT
5347 TTTTTCTTTA
Statistics
Matches: 80, Mismatches: 9, Indels: 23
0.71 0.08 0.21
Matches are distributed among these distances:
19 3 0.04
20 4 0.05
21 4 0.05
22 15 0.19
23 18 0.22
24 13 0.16
25 7 0.09
26 16 0.20
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (22 bp):
TATATATATATTATTTTTTATT
Found at i:5307 original size:46 final size:44
Alignment explanation
Indices: 5223--5346 Score: 130
Period size: 45 Copynumber: 2.8 Consensus size: 44
5213 TTTTTTAGAT
*
5223 TATATATATATATATAT-TTTTTTA-TTATCAGT-TTTATTAATTTA
1 TATATATATATATATATATTTTTTATTTAT-A-TATATATT-ATTTA
*
5267 TATATATATATATATACTATTTTTTATTTATATATATATTATTTT
1 TATATATATATATATA-TATTTTTTATTTATATATATATTATTTA
* *
5312 TACTTTATATTTAT-TATTATTTTTTATTTATATAT
1 TA-TATATATATATATA-TATTTTTTATTTATATAT
5347 TTTTTCTTTA
Statistics
Matches: 70, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
44 16 0.23
45 28 0.40
46 22 0.31
47 4 0.06
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (44 bp):
TATATATATATATATATATTTTTTATTTATATATATATTATTTA
Found at i:5325 original size:17 final size:17
Alignment explanation
Indices: 5299--5383 Score: 59
Period size: 17 Copynumber: 5.0 Consensus size: 17
5289 TTTATTTATA
*
5299 TATATATTATTTTTACTT
1 TATAT-TTATTATTACTT
*
5317 TATATTTATTATTATTT
1 TATATTTATTATTACTT
* **
5334 TTTATTTATATATTTTTT
1 TATATTTAT-TATTACTT
* *
5352 CTTTATTT-TTATT-TTT
1 -TATATTTATTATTACTT
5368 TATATTTATT-TTACTT
1 TATATTTATTATTACTT
5384 ACTATTTTAT
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
15 8 0.14
16 7 0.12
17 22 0.39
18 13 0.23
19 7 0.12
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.73
Consensus pattern (17 bp):
TATATTTATTATTACTT
Found at i:5337 original size:13 final size:15
Alignment explanation
Indices: 5193--5357 Score: 74
Period size: 15 Copynumber: 10.8 Consensus size: 15
5183 ATGCGTTTTC
5193 TTTTTTAGTTTAGTATA
1 TTTTTTA-TTTA-TATA
*
5210 TTTTTT-TTTAGAT-
1 TTTTTTATTTATATA
* * *
5223 TATATATATATATATA
1 T-TTTTTATTTATATA
5239 TTTTTT-TATTATCAGT-
1 TTTTTTAT-TTAT-A-TA
*
5255 TTTATTAATTTATATA
1 TTT-TTTATTTATATA
* * *
5271 -TATATATATATACTA
1 TTTTTTATTTATA-TA
5286 TTTTTTATTTATATA
1 TTTTTTATTTATATA
* *
5301 TATATTATTT-T-TA
1 TTTTTTATTTATATA
* *
5314 CTTTATATTTATTATTA
1 TTTTTTATTTA-TA-TA
5331 TTTTTTATTTATATA
1 TTTTTTATTTATATA
*
5346 TTTTTTCTTTAT
1 TTTTTTATTTAT
5358 TTTTATTTTT
Statistics
Matches: 108, Mismatches: 25, Indels: 32
0.65 0.15 0.19
Matches are distributed among these distances:
13 9 0.08
14 14 0.13
15 43 0.40
16 17 0.16
17 24 0.22
18 1 0.01
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.66
Consensus pattern (15 bp):
TTTTTTATTTATATA
Found at i:5364 original size:6 final size:6
Alignment explanation
Indices: 5305--5379 Score: 55
Period size: 6 Copynumber: 12.2 Consensus size: 6
5295 TATATATATA
* * * *
5305 TTATTT TTA-CT TTATAT TTATTA TTATTTT TTATTT ATATATTT TT-TCT
1 TTATTT TTATTT TTATTT TTATTT TTA-TTT TTATTT -T-TATTT TTATTT
*
5354 TTATTT TTATTTT TTATAT TTATTT T
1 TTATTT TTA-TTT TTATTT TTATTT T
5380 ACTTACTATT
Statistics
Matches: 54, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
5 8 0.15
6 28 0.52
7 13 0.24
8 5 0.09
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (6 bp):
TTATTT
Found at i:5370 original size:45 final size:45
Alignment explanation
Indices: 5284--5379 Score: 110
Period size: 45 Copynumber: 2.1 Consensus size: 45
5274 ATATATATAC
5284 TATTTTTTATTTATATATATATTATTTTTACTTTATATTTAT-TAT
1 TATTTTTTATTTATATATATATTATTTTTACTTTATATTTATAT-T
* *
5329 TATTTTTTATTTATATAT-T-TT-TTCTTTATTTTTATTTTTTATATT
1 TATTTTTTATTTATATATATATTATT-TTTA-CTTTA-TATTTATATT
5374 TATTTT
1 TATTTT
5380 ACTTACTATT
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
42 2 0.04
43 6 0.13
44 5 0.11
45 31 0.69
46 1 0.02
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (45 bp):
TATTTTTTATTTATATATATATTATTTTTACTTTATATTTATATT
Found at i:5375 original size:13 final size:13
Alignment explanation
Indices: 5315--5379 Score: 57
Period size: 13 Copynumber: 5.1 Consensus size: 13
5305 TTATTTTTAC
5315 TTTATATTTATTAT
1 TTTATATTTATT-T
5329 TATT-T-TTTA-TT
1 T-TTATATTTATTT
*
5340 TATATATTT-TTT
1 TTTATATTTATTT
*
5352 CTTTATTTTTATTT
1 -TTTATATTTATTT
5366 TTTATATTTATTT
1 TTTATATTTATTT
5379 T
1 T
5380 ACTTACTATT
Statistics
Matches: 41, Mismatches: 4, Indels: 13
0.71 0.07 0.22
Matches are distributed among these distances:
10 1 0.02
11 3 0.07
12 6 0.15
13 24 0.59
14 5 0.12
15 2 0.05
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTATATTTATTT
Found at i:5376 original size:38 final size:38
Alignment explanation
Indices: 5284--5378 Score: 113
Period size: 38 Copynumber: 2.4 Consensus size: 38
5274 ATATATATAC
*
5284 TATTTTTTATTTATATATATATTATTTTTACTTTATATT
1 TATTTTTTATTT-TATTTATATTATTTTTACTTTATATT
* *
5323 TATTATTATT-TTTTATTTATA-TATTTTTTCTTTATTTT
1 TATT-TT-TTATTTTATTTATATTATTTTTACTTTATATT
5361 TATTTTTTATATTTATTT
1 TATTTTTTAT-TTTATTT
5379 TACTTACTAT
Statistics
Matches: 49, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
36 2 0.04
37 3 0.06
38 26 0.53
39 11 0.22
40 5 0.10
41 2 0.04
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (38 bp):
TATTTTTTATTTTATTTATATTATTTTTACTTTATATT
Found at i:11426 original size:29 final size:30
Alignment explanation
Indices: 11392--11448 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
11382 CACGTTTAAC
11392 ATCTAAC-TATCA-TTTTTGTTTCGTTTTAT
1 ATCTAACGT-TCATTTTTTGTTTCGTTTTAT
*
11421 ATCTAACGTTTATTTTTTGTTTCGTTTT
1 ATCTAACGTTCATTTTTTGTTTCGTTTT
11449 GTTATCTTGC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 9 0.36
30 16 0.64
ACGTcount: A:0.18, C:0.12, G:0.09, T:0.61
Consensus pattern (30 bp):
ATCTAACGTTCATTTTTTGTTTCGTTTTAT
Found at i:11962 original size:31 final size:31
Alignment explanation
Indices: 11920--11996 Score: 127
Period size: 31 Copynumber: 2.5 Consensus size: 31
11910 AACAAATGAA
* *
11920 AGTTTAGGTACTAAAATGAAATAAAACTTAT
1 AGTTTAAGTACTAAAATAAAATAAAACTTAT
11951 AGTTTAAGTACTAAAATAAAATAAAACTTAT
1 AGTTTAAGTACTAAAATAAAATAAAACTTAT
*
11982 AGTTTAAGCACTAAA
1 AGTTTAAGTACTAAA
11997 CGTGTAGTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.51, C:0.08, G:0.10, T:0.31
Consensus pattern (31 bp):
AGTTTAAGTACTAAAATAAAATAAAACTTAT
Found at i:12045 original size:15 final size:17
Alignment explanation
Indices: 12021--12053 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
12011 TTAAATATTC
12021 AATTCTAATAT-ATTTT
1 AATTCTAATATGATTTT
12037 AATTC-AATATGATTTT
1 AATTCTAATATGATTTT
12053 A
1 A
12054 TAAGATTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.52
Consensus pattern (17 bp):
AATTCTAATATGATTTT
Found at i:14609 original size:23 final size:23
Alignment explanation
Indices: 14583--14653 Score: 97
Period size: 23 Copynumber: 3.1 Consensus size: 23
14573 TATTCGATTT
*
14583 ATTTAGCGTTTATGAATATGTTC
1 ATTTAGCATTTATGAATATGTTC
*
14606 ATTTAGCATTTACGAATATGTTC
1 ATTTAGCATTTATGAATATGTTC
* * *
14629 ATTTAACATTTGTGAACATGTTC
1 ATTTAGCATTTATGAATATGTTC
14652 AT
1 AT
14654 CGATATATTT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.45
Consensus pattern (23 bp):
ATTTAGCATTTATGAATATGTTC
Found at i:16774 original size:11 final size:10
Alignment explanation
Indices: 16754--16788 Score: 52
Period size: 11 Copynumber: 3.3 Consensus size: 10
16744 TGTTAAAGCA
16754 CATGCAAAAT
1 CATGCAAAAT
16764 CATGTCAAAAT
1 CATG-CAAAAT
16775 CATGGCAAAAT
1 CAT-GCAAAAT
16786 CAT
1 CAT
16789 CTCTTAGACT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 4 0.17
11 18 0.78
12 1 0.04
ACGTcount: A:0.46, C:0.20, G:0.11, T:0.23
Consensus pattern (10 bp):
CATGCAAAAT
Found at i:17813 original size:2 final size:2
Alignment explanation
Indices: 17801--17878 Score: 115
Period size: 2 Copynumber: 40.0 Consensus size: 2
17791 AGAGATCAGG
*
17801 TA TA CA 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
* *
17843 TA TA TA TA TA TA TA TA TA TG TA TA CA -A T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17879 GCTTATAGAA
Statistics
Matches: 69, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
1 2 0.03
2 67 0.97
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (2 bp):
TA
Found at i:19697 original size:30 final size:29
Alignment explanation
Indices: 19663--19733 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 29
19653 TTTGTCTTTT
19663 ATTATAATTT-TCTAAAAAGTGTTATCCTTA
1 ATTATAATTTAT-T-AAAAGTGTTATCCTTA
*
19693 ATTATAATTTATTGAAAGTGTTATCCTTTA
1 ATTATAATTTATTAAAAGTGTTATCC-TTA
*
19723 A-TGTAATTTAT
1 ATTATAATTTAT
19734 AAATGATATT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
29 21 0.57
30 15 0.41
31 1 0.03
ACGTcount: A:0.35, C:0.07, G:0.08, T:0.49
Consensus pattern (29 bp):
ATTATAATTTATTAAAAGTGTTATCCTTA
Found at i:19716 original size:29 final size:29
Alignment explanation
Indices: 19678--19733 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
19668 AATTTTCTAA
19678 AAAGTGTTATCC-TTAATTATAATTTATTG
1 AAAGTGTTATCCTTTAA-TATAATTTATTG
*
19707 AAAGTGTTATCCTTTAATGTAATTTAT
1 AAAGTGTTATCCTTTAATATAATTTAT
19734 AAATGATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 21 0.84
30 4 0.16
ACGTcount: A:0.34, C:0.07, G:0.11, T:0.48
Consensus pattern (29 bp):
AAAGTGTTATCCTTTAATATAATTTATTG
Found at i:20476 original size:67 final size:67
Alignment explanation
Indices: 20363--20495 Score: 248
Period size: 67 Copynumber: 2.0 Consensus size: 67
20353 AACATTTTAG
20363 TATAAAATGCTTAGGATGCAAAATTAGATATTAAAAAGATAAAAAAATATTTAAATTATATAAAA
1 TATAAAATGCTTAGGATGCAAAATTAGATATTAAAAAGATAAAAAAATATTTAAATTATATAAAA
20428 AT
66 AT
* *
20430 TATAAAATGTTTAGGATGCAAAATTAGATATTAAAAAGATATAAAAATATTTAAATTATATAAAA
1 TATAAAATGCTTAGGATGCAAAATTAGATATTAAAAAGATAAAAAAATATTTAAATTATATAAAA
20495 A
66 A
20496 AAATTTAAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 64 1.00
ACGTcount: A:0.56, C:0.02, G:0.09, T:0.32
Consensus pattern (67 bp):
TATAAAATGCTTAGGATGCAAAATTAGATATTAAAAAGATAAAAAAATATTTAAATTATATAAAA
AT
Found at i:20514 original size:20 final size:20
Alignment explanation
Indices: 20472--20514 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
20462 AAAAAGATAT
* *
20472 AAAAATATTTAAATTATATA
1 AAAAAAATTTAAATTATACA
20492 AAAAAAATTTAAAATT-TACA
1 AAAAAAATTT-AAATTATACA
20512 AAA
1 AAA
20515 GATACAATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAAAATTTAAATTATACA
Found at i:27352 original size:35 final size:35
Alignment explanation
Indices: 27306--27381 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
27296 AAAACAGTCC
* *
27306 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
27341 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
27376 TCAATT
1 TCAATT
27382 AAATTCAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.39, C:0.24, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:27938 original size:130 final size:130
Alignment explanation
Indices: 27782--28026 Score: 409
Period size: 130 Copynumber: 1.9 Consensus size: 130
27772 TTATATAATC
** **
27782 AATTTGGTCCTAAATTAAATGGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTA
1 AATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTA
* *
27847 GCACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCTATT
66 ACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCTATT
27912 AATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTA
1 AATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTA
* * *
27977 ACACATGATCATGATATATGTTATTGGTGACACATGTCACCACCTAATTA
66 ACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTA
28027 GAAGAAAATT
Statistics
Matches: 106, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 106 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (130 bp):
AATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTA
ACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCTATT
Found at i:28057 original size:130 final size:129
Alignment explanation
Indices: 27793--28057 Score: 291
Period size: 130 Copynumber: 2.0 Consensus size: 129
27783 ATTTGGTCCT
** ** *
27793 AAATTAAATGGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* *** * * * **** *
27858 TGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCTATTAATTTGGTCCT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
27923 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* * * *
27988 TGATATATGTTATTGGTGACACATGTCACCACCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
28052 -A
128 CA
28053 AAATT
1 AAATT
28058 TGGGTCTTGG
Statistics
Matches: 111, Mismatches: 21, Indels: 6
0.80 0.15 0.04
Matches are distributed among these distances:
130 99 0.89
132 7 0.06
133 5 0.05
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:28515 original size:17 final size:17
Alignment explanation
Indices: 28489--28521 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
28479 ATTTCTTATT
28489 AAAAATAAAT-ATTCAA
1 AAAAATAAATGATTCAA
28505 AAAATATAAATGATTCA
1 AAAA-ATAAATGATTCA
28522 TACATTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 6 0.40
18 5 0.33
ACGTcount: A:0.64, C:0.06, G:0.03, T:0.27
Consensus pattern (17 bp):
AAAAATAAATGATTCAA
Found at i:31419 original size:22 final size:21
Alignment explanation
Indices: 31394--31435 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
31384 TATAAAAAAT
31394 TATTTTTATTAAATATTTTTAG
1 TATTTTTATTAAAT-TTTTTAG
*
31416 TATTTTTATTTAATTTTTTA
1 TATTTTTATTAAATTTTTTA
31436 AATAATTATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (21 bp):
TATTTTTATTAAATTTTTTAG
Found at i:36635 original size:7 final size:8
Alignment explanation
Indices: 36605--36634 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
36595 GTTTCCCATT
36605 TTTTTTTC
1 TTTTTTTC
36613 TTTTTTTC
1 TTTTTTTC
36621 TTTTTTTC
1 TTTTTTTC
36629 TTTTTT
1 TTTTTT
36635 CGACGGGGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTTTC
Found at i:42315 original size:2 final size:2
Alignment explanation
Indices: 42308--42343 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
42298 ATGGATCTGT
42308 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
42344 GTTAATTACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:42802 original size:24 final size:24
Alignment explanation
Indices: 42748--42808 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
42738 TGGATGATTA
* *
42748 GAAAATTTAAGGTTTTTTTTTAATTT
1 GAAAATTTAA--TGTTTTCTTAATTT
* *
42774 CAAAATTTAATGTTTTCTTATTTT
1 GAAAATTTAATGTTTTCTTAATTT
*
42798 GAAAAATTAAT
1 GAAAATTTAAT
42809 ATTAATAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
24 20 0.69
26 9 0.31
ACGTcount: A:0.36, C:0.03, G:0.08, T:0.52
Consensus pattern (24 bp):
GAAAATTTAATGTTTTCTTAATTT
Found at i:53394 original size:3 final size:3
Alignment explanation
Indices: 53386--53410 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
53376 ATCGTCATCC
53386 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
53411 CTCCTGCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:55132 original size:21 final size:21
Alignment explanation
Indices: 55106--55155 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
55096 AGTTGAGTTA
55106 AACTCAACACTAATCGAATTC
1 AACTCAACACTAATCGAATTC
* *
55127 AACTCAACTCTAGTCGAATTC
1 AACTCAACACTAATCGAATTC
55148 AACTCAAC
1 AACTCAAC
55156 CCATTTAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.40, C:0.30, G:0.06, T:0.24
Consensus pattern (21 bp):
AACTCAACACTAATCGAATTC
Found at i:55367 original size:20 final size:20
Alignment explanation
Indices: 55342--55406 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 20
55332 GGCAGCAGAC
55342 AGATCTATGTAAACCAGATA
1 AGATCTATGTAAACCAGATA
** * **
55362 AGATCT-TCCAACAGCAG-CC
1 AGATCTATGTAA-ACCAGATA
55381 AGATCTATGTAAACCAGATA
1 AGATCTATGTAAACCAGATA
55401 AGATCT
1 AGATCT
55407 TCCAATCATT
Statistics
Matches: 32, Mismatches: 10, Indels: 6
0.67 0.21 0.12
Matches are distributed among these distances:
19 13 0.41
20 19 0.59
ACGTcount: A:0.40, C:0.22, G:0.15, T:0.23
Consensus pattern (20 bp):
AGATCTATGTAAACCAGATA
Found at i:55388 original size:39 final size:39
Alignment explanation
Indices: 55334--55411 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
55324 GAAAAAGAGG
55334 CAGCAGACAGATCTATGTAAACCAGATAAGATCTTCCAA
1 CAGCAGACAGATCTATGTAAACCAGATAAGATCTTCCAA
*
55373 CAGCAGCCAGATCTATGTAAACCAGATAAGATCTTCCAA
1 CAGCAGACAGATCTATGTAAACCAGATAAGATCTTCCAA
55412 TCATTTGAGA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.40, C:0.24, G:0.15, T:0.21
Consensus pattern (39 bp):
CAGCAGACAGATCTATGTAAACCAGATAAGATCTTCCAA
Found at i:71646 original size:21 final size:20
Alignment explanation
Indices: 71609--71752 Score: 116
Period size: 19 Copynumber: 7.2 Consensus size: 20
71599 AAATTTACGT
*
71609 TAGTCCAAATT-CGTTGCGA
1 TAGTCCAAGTTCCGTTGCGA
*
71628 TAGTCGAAGTTCGCGTTGCGA
1 TAGTCCAAGTTC-CGTTGCGA
** *
71649 TTTTCCAAATT-CGTTGCGA
1 TAGTCCAAGTTCCGTTGCGA
*
71668 TAGTCCAAGTTCACGTTGCGT
1 TAGTCCAAGTTC-CGTTGCGA
** *
71689 TTTTCCAAATT-CGTTGCGA
1 TAGTCCAAGTTCCGTTGCGA
*
71708 TAGTCCAAGTTCACGTTGCGT
1 TAGTCCAAGTTC-CGTTGCGA
** *
71729 TTTTCCAAATT-CGTTGCGA
1 TAGTCCAAGTTCCGTTGCGA
71748 TAGTC
1 TAGTC
71753 AAAGACACGT
Statistics
Matches: 95, Mismatches: 24, Indels: 12
0.73 0.18 0.09
Matches are distributed among these distances:
19 50 0.53
21 45 0.47
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.36
Consensus pattern (20 bp):
TAGTCCAAGTTCCGTTGCGA
Found at i:71667 original size:40 final size:40
Alignment explanation
Indices: 71612--71752 Score: 255
Period size: 40 Copynumber: 3.5 Consensus size: 40
71602 TTTACGTTAG
* * *
71612 TCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTT
1 TCCAAATTCGTTGCGATAGTCCAAGTTCACGTTGCGTTTT
71652 TCCAAATTCGTTGCGATAGTCCAAGTTCACGTTGCGTTTT
1 TCCAAATTCGTTGCGATAGTCCAAGTTCACGTTGCGTTTT
71692 TCCAAATTCGTTGCGATAGTCCAAGTTCACGTTGCGTTTT
1 TCCAAATTCGTTGCGATAGTCCAAGTTCACGTTGCGTTTT
71732 TCCAAATTCGTTGCGATAGTC
1 TCCAAATTCGTTGCGATAGTC
71753 AAAGACACGT
Statistics
Matches: 98, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 98 1.00
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.36
Consensus pattern (40 bp):
TCCAAATTCGTTGCGATAGTCCAAGTTCACGTTGCGTTTT
Found at i:72123 original size:22 final size:22
Alignment explanation
Indices: 72098--72154 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 22
72088 ACTATCGCAA
*
72098 CAACACATTTTTCAAACTCTCG
1 CAACACATTTTTCAAACTATCG
72120 CAACACA-TTTT--AACTATCG
1 CAACACATTTTTCAAACTATCG
72139 CAACACATTTTTCAAA
1 CAACACATTTTTCAAA
72155 ATCGCGTTGC
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
19 14 0.45
20 4 0.13
21 4 0.13
22 9 0.29
ACGTcount: A:0.37, C:0.28, G:0.04, T:0.32
Consensus pattern (22 bp):
CAACACATTTTTCAAACTATCG
Found at i:72204 original size:21 final size:21
Alignment explanation
Indices: 72156--72209 Score: 76
Period size: 20 Copynumber: 2.6 Consensus size: 21
72146 TTTTTCAAAA
*
72156 TCGCGTTGCGAATCTTATAAT
1 TCGCGTTGCGAATCTGATAAT
72177 T-GCGTTGCGAATCTGGAT-AT
1 TCGCGTTGCGAATCT-GATAAT
72197 TCGCGTTGCGAAT
1 TCGCGTTGCGAAT
72210 TTGAAAACTG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (21 bp):
TCGCGTTGCGAATCTGATAAT
Found at i:100264 original size:13 final size:14
Alignment explanation
Indices: 100235--100265 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
100225 AACTATGCAA
100235 GTGATATGAACTAT
1 GTGATATGAACTAT
100249 GTGATATGAA-TAT
1 GTGATATGAACTAT
100262 GTGA
1 GTGA
100266 AATATGATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.35
Consensus pattern (14 bp):
GTGATATGAACTAT
Found at i:103346 original size:21 final size:21
Alignment explanation
Indices: 103320--103360 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
103310 CCTAAAATCG
*
103320 AAATATTATCTTAT-TTCAACT
1 AAATA-TAACTTATATTCAACT
103341 AAATATAACTTATATTCAAC
1 AAATATAACTTATATTCAAC
103361 CACCATAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (21 bp):
AAATATAACTTATATTCAACT
Done.