Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006610.1 Hibiscus syriacus cultivar Beakdansim tig00016222_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: 53800
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:9408 original size:3 final size:3
Alignment explanation
Indices: 9400--9470 Score: 53
Period size: 3 Copynumber: 25.0 Consensus size: 3
9390 TGTAAAAATG
* * *
9400 TAA TAA TAA TAA TTA T-T TAT TTAA TAA TAA T-A TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
* *
9443 TAA TAT TAA -AA CAA -AA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
9471 ATAAAACAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
2 9 0.16
3 46 0.81
4 2 0.04
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:9481 original size:22 final size:22
Alignment explanation
Indices: 9421--9480 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
9411 ATTATTTATT
* * *
9421 TAATAATAATATAATATAATAA
1 TAATAATAAAACAAAATAATAA
*
9443 TAATATTAAAACAAAATAATAA
1 TAATAATAAAACAAAATAATAA
9465 TAATAAATAAAACAAA
1 TAAT-AATAAAACAAA
9481 TGAAATAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 22 0.69
23 10 0.31
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.28
Consensus pattern (22 bp):
TAATAATAAAACAAAATAATAA
Found at i:16353 original size:43 final size:39
Alignment explanation
Indices: 16305--16415 Score: 163
Period size: 38 Copynumber: 2.8 Consensus size: 39
16295 TTCTATCTCG
*
16305 TTCGTTGGACTTTACAAAATTGAATTATTTACTCACTCAATTA
1 TTCGTTTGACTTTAC-AAATTG-A--ATTTACTCACTCAATTA
16348 TTCGTTTGACTTTACAAATTG-ATTTACTCACTCAATTA
1 TTCGTTTGACTTTACAAATTGAATTTACTCACTCAATTA
16386 TTCGTTTGACTTTACAAATTG-ATTTACTCA
1 TTCGTTTGACTTTACAAATTGAATTTACTCA
16416 ATCGTTCACT
Statistics
Matches: 67, Mismatches: 1, Indels: 5
0.92 0.01 0.07
Matches are distributed among these distances:
38 47 0.70
42 6 0.09
43 14 0.21
ACGTcount: A:0.30, C:0.17, G:0.09, T:0.44
Consensus pattern (39 bp):
TTCGTTTGACTTTACAAATTGAATTTACTCACTCAATTA
Found at i:16376 original size:38 final size:38
Alignment explanation
Indices: 16327--16415 Score: 171
Period size: 38 Copynumber: 2.4 Consensus size: 38
16317 TACAAAATTG
16327 AATT-ATTTACTCACTCAATTATTCGTTTGACTTTACA
1 AATTGATTTACTCACTCAATTATTCGTTTGACTTTACA
16364 AATTGATTTACTCACTCAATTATTCGTTTGACTTTACA
1 AATTGATTTACTCACTCAATTATTCGTTTGACTTTACA
16402 AATTGATTTACTCA
1 AATTGATTTACTCA
16416 ATCGTTCACT
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
37 4 0.08
38 47 0.92
ACGTcount: A:0.30, C:0.18, G:0.07, T:0.45
Consensus pattern (38 bp):
AATTGATTTACTCACTCAATTATTCGTTTGACTTTACA
Found at i:16553 original size:11 final size:11
Alignment explanation
Indices: 16509--16560 Score: 52
Period size: 11 Copynumber: 4.5 Consensus size: 11
16499 TGGTTTTTTT
16509 TTATTAATATA
1 TTATTAATATA
*
16520 TAATATAATA-A
1 TTAT-TAATATA
16531 TTATATACATATA
1 TTAT-TA-ATATA
16544 TTATTAATATA
1 TTATTAATATA
*
16555 TAATTA
1 TTATTA
16561 TGACATATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
11 20 0.57
12 10 0.29
13 5 0.14
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (11 bp):
TTATTAATATA
Found at i:16554 original size:19 final size:18
Alignment explanation
Indices: 16509--16558 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 18
16499 TGGTTTTTTT
16509 TTATTAATATATAATATA
1 TTATTAATATATAATATA
16527 --A-TAATTATATACATATA
1 TTATTAA-TATATA-ATATA
16544 TTATTAATATATAAT
1 TTATTAATATATAAT
16559 TATGACATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
15 3 0.11
16 7 0.26
17 5 0.19
18 2 0.07
19 7 0.26
20 3 0.11
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (18 bp):
TTATTAATATATAATATA
Found at i:16566 original size:26 final size:28
Alignment explanation
Indices: 16513--16574 Score: 83
Period size: 26 Copynumber: 2.2 Consensus size: 28
16503 TTTTTTTTAT
*
16513 TAATATATAATATAATAATTATATACATA
1 TAATAT-TAATATAATAATTATAGACATA
*
16542 TATTATTAATAT-ATAATTAT-GACATA
1 TAATATTAATATAATAATTATAGACATA
16568 TAATATT
1 TAATATT
16575 TAAAAATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
26 11 0.37
27 8 0.27
28 6 0.20
29 5 0.17
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (28 bp):
TAATATTAATATAATAATTATAGACATA
Found at i:16583 original size:26 final size:27
Alignment explanation
Indices: 16513--16583 Score: 74
Period size: 26 Copynumber: 2.6 Consensus size: 27
16503 TTTTTTTTAT
*
16513 TAATATATAATATAATAATTATATACATA
1 TAATAT-TAATA-AATAATTATAGACATA
* *
16542 TATTATTAATATATAATTAT-GACATA
1 TAATATTAATAAATAATTATAGACATA
16568 TAATATTTAA-AAATAA
1 TAATA-TTAATAAATAA
16584 AATAAAAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
26 14 0.39
27 12 0.33
28 5 0.14
29 5 0.14
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (27 bp):
TAATATTAATAAATAATTATAGACATA
Found at i:17848 original size:15 final size:16
Alignment explanation
Indices: 17814--17852 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
17804 AAAAATGAAA
17814 AAAAT-TAAAAAAAGTC
1 AAAATATAAAAAAAG-C
17830 AAAATATAAAAAAAG-
1 AAAATATAAAAAAAGC
17845 AAAATATA
1 AAAATATA
17853 TTTTTAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.36
16 5 0.23
17 9 0.41
ACGTcount: A:0.74, C:0.03, G:0.05, T:0.18
Consensus pattern (16 bp):
AAAATATAAAAAAAGC
Found at i:18175 original size:26 final size:27
Alignment explanation
Indices: 18124--18176 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
18114 ATATTTTATA
* *
18124 TTTTAAATTTAAATAACATCATATTTT
1 TTTTAAAATTAAATAACATCAAATTTT
*
18151 TTTTAAAATTAAATAA-GTCAAATTTT
1 TTTTAAAATTAAATAACATCAAATTTT
18177 CTAAAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 8 0.35
27 15 0.65
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (27 bp):
TTTTAAAATTAAATAACATCAAATTTT
Found at i:21668 original size:17 final size:17
Alignment explanation
Indices: 21648--21690 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
21638 AGGGAAGTAG
21648 TTCATTAAACTAGTTCA
1 TTCATTAAACTAGTTCA
* *
21665 TTCATCAAACTAGTTCG
1 TTCATTAAACTAGTTCA
*
21682 TTTATTAAA
1 TTCATTAAA
21691 TTAACTCTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.35, C:0.16, G:0.07, T:0.42
Consensus pattern (17 bp):
TTCATTAAACTAGTTCA
Found at i:24471 original size:17 final size:17
Alignment explanation
Indices: 24449--24510 Score: 70
Period size: 17 Copynumber: 3.6 Consensus size: 17
24439 AATTAAGATA
*
24449 AATGAACTAGTTTGATG
1 AATGAACTAGTTTAATG
*
24466 AATGAACTAGTTTAATT
1 AATGAACTAGTTTAATG
* * *
24483 AATGAACTAACTTTATTC
1 AATGAACT-AGTTTAATG
24501 AATGAACTAG
1 AATGAACTAG
24511 ATGCATGAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
17 24 0.63
18 14 0.37
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (17 bp):
AATGAACTAGTTTAATG
Found at i:24504 original size:18 final size:18
Alignment explanation
Indices: 24466--24509 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
24456 TAGTTTGATG
*
24466 AATGAACT-AGTTTAATT
1 AATGAACTAACTTTAATT
24483 AATGAACTAACTTT-ATT
1 AATGAACTAACTTTAATT
24500 CAATGAACTA
1 -AATGAACTA
24510 GATGCATGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.36
Consensus pattern (18 bp):
AATGAACTAACTTTAATT
Found at i:25716 original size:25 final size:26
Alignment explanation
Indices: 25677--25729 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
25667 CTCTTTTTTG
25677 TTTCAAAAATATCCTCTTTC-CC-CTC
1 TTTCAAAAATATCCT-TTTCTCCACTC
25702 TTTCACAAAAT-TCCTTTTCTCCACTC
1 TTTCA-AAAATATCCTTTTCTCCACTC
25728 TT
1 TT
25730 AATGTCTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
24 4 0.16
25 11 0.44
26 10 0.40
ACGTcount: A:0.23, C:0.34, G:0.00, T:0.43
Consensus pattern (26 bp):
TTTCAAAAATATCCTTTTCTCCACTC
Found at i:28201 original size:17 final size:17
Alignment explanation
Indices: 28161--28225 Score: 67
Period size: 17 Copynumber: 3.8 Consensus size: 17
28151 AACAATTAAG
*
28161 ATAAATGAACTAGTTTG
1 ATAAATGAACTAGTTTA
**
28178 ACGAATGAACTAGTTTA
1 ATAAATGAACTAGTTTA
*
28195 ATAAATGAACTAACTTTA
1 ATAAATGAACT-AGTTTA
* *
28213 TTCAATGAACTAG
1 ATAAATGAACTAG
28226 ATGCTTGAAT
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
17 24 0.63
18 14 0.37
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (17 bp):
ATAAATGAACTAGTTTA
Found at i:29725 original size:8 final size:8
Alignment explanation
Indices: 29712--29736 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
29702 TTCATCTTTA
29712 TATTCAAT
1 TATTCAAT
29720 TATTCAAT
1 TATTCAAT
29728 TATTCAAT
1 TATTCAAT
29736 T
1 T
29737 TTGTTACCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.12, G:0.00, T:0.52
Consensus pattern (8 bp):
TATTCAAT
Found at i:34921 original size:27 final size:27
Alignment explanation
Indices: 34867--34921 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
34857 TAAAATTTTT
**
34867 AAAATACCCTTATGTGGTAAAATTACA
1 AAAATACCCTTATGTGGTAAAAAGACA
*
34894 AAAATACCCTTATGTTGTAAAAAGACA
1 AAAATACCCTTATGTGGTAAAAAGACA
34921 A
1 A
34922 GAATTATCCC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.47, C:0.15, G:0.11, T:0.27
Consensus pattern (27 bp):
AAAATACCCTTATGTGGTAAAAAGACA
Found at i:35822 original size:19 final size:19
Alignment explanation
Indices: 35773--35822 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
35763 GAAATATAGG
*
35773 TTGATCTCTGATTTATGTT
1 TTGATCTCTGATATATGTT
* * * *
35792 CTAAACTTTGATATATGTT
1 TTGATCTCTGATATATGTT
35811 TTGATCTCTGAT
1 TTGATCTCTGAT
35823 TTCTGATCTG
Statistics
Matches: 22, Mismatches: 9, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.22, C:0.12, G:0.14, T:0.52
Consensus pattern (19 bp):
TTGATCTCTGATATATGTT
Found at i:37129 original size:42 final size:41
Alignment explanation
Indices: 36911--37219 Score: 238
Period size: 42 Copynumber: 7.5 Consensus size: 41
36901 GGGGGTTGCA
* * *
36911 ACTAAGGTGCATGACTATTGCG-A-TATATATATAAAATACC
1 ACTAAGGTGCATGACTATTGCGAAGTTTAT-TAAAAAATGCC
* * ***
36951 ACTAAGGTGCATGACTATTGCGACGTTTATTGCAAAAACAAC
1 ACTAAGGTGCATGACTATTGCGAAGTTTATT-AAAAAATGCC
* * ** * *
36993 ACAAAAGTATATGACTATTGCGACGTTTATTTAAAAACATTGCG
1 ACTAAGGTGCATGACTATTGCGAAGTTTA-TTAAAAA-A-TGCC
* * ** *
37037 A--AA-GTGCATGACTGTTGTGGCGTTTA-TAAAAAACGCC
1 ACTAAGGTGCATGACTATTGCGAAGTTTATTAAAAAATGCC
37074 ACTAAGGTGCATGACTATTGCGAAGTTTATTACAAAAATGCC
1 ACTAAGGTGCATGACTATTGCGAAGTTTATTA-AAAAATGCC
* * * * *
37116 GCTAAGGTACATGATTGTTGAGAAGTTTATTACAAAAATGCC
1 ACTAAGGTGCATGACTATTGCGAAGTTTATTA-AAAAATGCC
* **
37158 ACTAAGGTGCATGACTGTTTTGACA-TTTA-TAAAAAATGCC
1 ACTAAGGTGCATGACTATTGCGA-AGTTTATTAAAAAATGCC
*
37198 GCTAAGGTGCATGACTATTGCG
1 ACTAAGGTGCATGACTATTGCG
37220 GCATTTATTA
Statistics
Matches: 216, Mismatches: 41, Indels: 24
0.77 0.15 0.09
Matches are distributed among these distances:
37 3 0.01
38 1 0.00
39 8 0.04
40 68 0.31
41 23 0.11
42 108 0.50
43 4 0.02
44 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (41 bp):
ACTAAGGTGCATGACTATTGCGAAGTTTATTAAAAAATGCC
Found at i:37144 original size:123 final size:123
Alignment explanation
Indices: 36914--37237 Score: 332
Period size: 123 Copynumber: 2.6 Consensus size: 123
36904 GGTTGCAACT
* * * * * ** *
36914 AAGGTGCATGACTATTGCGATATATATATAAAATACCACTAAGGTGCATGACTATTGCGACGTTT
1 AAGGTGCATGACTGTTGTGACATTTATAAAAAACGCCACTAAGGTGCATGACTATTGCGAAGTTT
* * * * *
36979 ATTGCAAAAACAACACAAAAGTATATGACTATTGCGACGTTTATTTA-AAAACATTGCGA-
66 ATTACAAAAACAACACAAAAGTACATGACTATTGAGAAGTTTA-TTACAAAA-A-TGCCAC
* *
37038 AA-GTGCATGACTGTTGTGGCGTTTATAAAAAACGCCACTAAGGTGCATGACTATTGCGAAGTTT
1 AAGGTGCATGACTGTTGTGACATTTATAAAAAACGCCACTAAGGTGCATGACTATTGCGAAGTTT
*** * * * * *
37102 ATTACAAAAATGCCGCTAAGGTACATGATTGTTGAGAAGTTTATTACAAAAATGCCAC
66 ATTACAAAAACAACACAAAAGTACATGACTATTGAGAAGTTTATTACAAAAATGCCAC
* * * *
37160 TAAGGTGCATGACTGTTTTGACATTTATAAAAAATGCCGCTAAGGTGCATGACTATTGCGGCA-T
1 -AAGGTGCATGACTGTTGTGACATTTATAAAAAACGCCACTAAGGTGCATGACTATTGC-GAAGT
37224 TTATTACAAAAACA
64 TTATTACAAAAACA
37238 CCACCTAATA
Statistics
Matches: 164, Mismatches: 31, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
121 4 0.02
122 4 0.02
123 89 0.54
124 65 0.40
125 2 0.01
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.29
Consensus pattern (123 bp):
AAGGTGCATGACTGTTGTGACATTTATAAAAAACGCCACTAAGGTGCATGACTATTGCGAAGTTT
ATTACAAAAACAACACAAAAGTACATGACTATTGAGAAGTTTATTACAAAAATGCCAC
Found at i:37229 original size:82 final size:83
Alignment explanation
Indices: 36911--37241 Score: 254
Period size: 82 Copynumber: 4.0 Consensus size: 83
36901 GGGGGTTGCA
* * * * *
36911 ACTAAGGTGCATGACTATTGCG-A-TATATATA-TAAAATACCACTAAGGTGCATGACTATTGCG
1 ACTAAGGTGCATGACTATTGCGAAGTTTAT-TACAAAAATGCCGCTAAGGTGCATGACTGTTG-G
* * * **
36973 ACGTTTATTGCAAAAACAAC
64 GCATTTATTACAAAAACGCC
* * ** * *
36993 ACAAAAGTATATGACTATTGCGACGTTTATTTA-AAAACATTG-CG--AAAGTGCATGACTGTTG
1 ACTAAGGTGCATGACTATTGCGAAGTTTA-TTACAAAA-A-TGCCGCTAAGGTGCATGACTGTTG
*
37054 TGGCGTTTA-TA-AAAAACGCC
63 -GGCATTTATTACAAAAACGCC
* * * *
37074 ACTAAGGTGCATGACTATTGCGAAGTTTATTACAAAAATGCCGCTAAGGTACATGATTGTTGAGA
1 ACTAAGGTGCATGACTATTGCGAAGTTTATTACAAAAATGCCGCTAAGGTGCATGACTGTTGGGC
*
37139 AGTTTATTACAAAAATGCC
66 A-TTTATTACAAAAACGCC
* ** *
37158 ACTAAGGTGCATGACTGTTTTGACA-TTTA-TA-AAAAATGCCGCTAAGGTGCATGACTATTGCG
1 ACTAAGGTGCATGACTATTGCGA-AGTTTATTACAAAAATGCCGCTAAGGTGCATGACTGTTG-G
*
37220 GCATTTATTACAAAAACACC
64 GCATTTATTACAAAAACGCC
37240 AC
1 AC
37242 CTAATAAGAG
Statistics
Matches: 197, Mismatches: 38, Indels: 28
0.75 0.14 0.11
Matches are distributed among these distances:
79 2 0.01
80 6 0.03
81 36 0.18
82 80 0.41
83 28 0.14
84 40 0.20
85 4 0.02
86 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (83 bp):
ACTAAGGTGCATGACTATTGCGAAGTTTATTACAAAAATGCCGCTAAGGTGCATGACTGTTGGGC
ATTTATTACAAAAACGCC
Found at i:41429 original size:3 final size:3
Alignment explanation
Indices: 41421--41501 Score: 74
Period size: 3 Copynumber: 26.0 Consensus size: 3
41411 CCGGTCTTAC
* * * *
41421 TTA TTA TTA TTA TTA TTA TATA TATA TAA TTA CATA TTA -TA CTA CTA
1 TTA TTA TTA TTA TTA TTA T-TA T-TA TTA TTA -TTA TTA TTA TTA TTA
*
41468 TTA TTA TATA TTA TTA TTA ATA TTA TTA TTA TTA
1 TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA
41502 AATAATATTA
Statistics
Matches: 67, Mismatches: 7, Indels: 8
0.82 0.09 0.10
Matches are distributed among these distances:
2 2 0.03
3 53 0.79
4 12 0.18
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:45908 original size:13 final size:13
Alignment explanation
Indices: 45890--45936 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
45880 TGTGTCATAA
*
45890 ATTTATGATGCAC
1 ATTTATGATACAC
*
45903 ATTTATGACACAC
1 ATTTATGATACAC
* *
45916 ATTTATGTTACGC
1 ATTTATGATACAC
45929 ATTTATGA
1 ATTTATGA
45937 CGCGCATTGC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (13 bp):
ATTTATGATACAC
Found at i:46021 original size:85 final size:84
Alignment explanation
Indices: 45916--46081 Score: 251
Period size: 85 Copynumber: 2.0 Consensus size: 84
45906 TATGACACAC
** * * *
45916 ATTTATGTTACGCATTTATGACGCGCATTGCGTGTCATTGAAGCCCTTGTCATAAATGAAGATGA
1 ATTTATGACACGCATGTATGACGCACATTGCGTGTCATTGAAGCCCTCGTCATAAATGAAGATGA
45981 CACACATTTCTGTGTCATAA
66 CACACA-TTCTGTGTCATAA
**
46001 ATTTATGACACGCATGTATGACTTACATTGCGTGTCATTGAAGCCCTCGTCATAAATGAAGATGA
1 ATTTATGACACGCATGTATGACGCACATTGCGTGTCATTGAAGCCCTCGTCATAAATGAAGATGA
*
46066 CACACATTGTGTGTCA
66 CACACATTCTGTGTCA
46082 GAGAGTATAT
Statistics
Matches: 73, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
84 9 0.12
85 64 0.88
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (84 bp):
ATTTATGACACGCATGTATGACGCACATTGCGTGTCATTGAAGCCCTCGTCATAAATGAAGATGA
CACACATTCTGTGTCATAA
Found at i:46073 original size:44 final size:43
Alignment explanation
Indices: 45941--46081 Score: 108
Period size: 44 Copynumber: 3.3 Consensus size: 43
45931 TTATGACGCG
45941 CATTGCGTGTCATTGAAGCCCTTGTCATAAATGAAGATGACACA
1 CATTGCGTGTCATTGAAGCCC-TGTCATAAATGAAGATGACACA
* * **** * *** * **
45985 CATTTCTGTGTCA-TAAATTTATGACACGCATG--TATGACTTA
1 CATTGC-GTGTCATTGAAGCCCTGTCATAAATGAAGATGACACA
46026 CATTGCGTGTCATTGAAGCCCTCGTCATAAATGAAGATGACACA
1 CATTGCGTGTCATTGAAGCCCT-GTCATAAATGAAGATGACACA
*
46070 CATTGTGTGTCA
1 CATTGCGTGTCA
46082 GAGAGTATAT
Statistics
Matches: 65, Mismatches: 27, Indels: 10
0.64 0.26 0.10
Matches are distributed among these distances:
40 6 0.09
41 15 0.23
42 6 0.09
43 7 0.11
44 25 0.38
45 6 0.09
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (43 bp):
CATTGCGTGTCATTGAAGCCCTGTCATAAATGAAGATGACACA
Found at i:49740 original size:6 final size:6
Alignment explanation
Indices: 49731--49786 Score: 103
Period size: 6 Copynumber: 9.3 Consensus size: 6
49721 ATTTCCATCA
*
49731 TCATCT TCATAT TCATAT TCATAT TCATAT TCATAT TCATAT TCATAT
1 TCATAT TCATAT TCATAT TCATAT TCATAT TCATAT TCATAT TCATAT
49779 TCATAT TC
1 TCATAT TC
49787 TCCATCATCT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 49 1.00
ACGTcount: A:0.30, C:0.20, G:0.00, T:0.50
Consensus pattern (6 bp):
TCATAT
Done.