Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006938.1 Hibiscus syriacus cultivar Beakdansim tig00017820_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: 77682
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Found at i:62 original size:26 final size:27
Alignment explanation
Indices: 24--77 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
14 CTTAATAATT
* *
24 TTAAATTCGTAAATTTTTTAAATTAAA
1 TTAAATTCGTAAACTTTTTAAATCAAA
*
51 TTAAATT-TTAAACTTTTTAAATCAAA
1 TTAAATTCGTAAACTTTTTAAATCAAA
77 T
1 T
78 CGAACTCATC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 17 0.71
27 7 0.29
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (27 bp):
TTAAATTCGTAAACTTTTTAAATCAAA
Found at i:583 original size:2 final size:2
Alignment explanation
Indices: 578--627 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
568 ATATATATAT
*
578 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG CG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
620 AG AG AG AG
1 AG AG AG AG
628 TTTGTACTCT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.48, C:0.02, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3257 original size:23 final size:23
Alignment explanation
Indices: 3224--3268 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
3214 AATGATTCAG
*
3224 TGCTGACTGATTCAGCAAAACAA
1 TGCTGAATGATTCAGCAAAACAA
3247 TGCTGAATGATTCAGCAAAACA
1 TGCTGAATGATTCAGCAAAACA
3269 GTACATTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.40, C:0.20, G:0.18, T:0.22
Consensus pattern (23 bp):
TGCTGAATGATTCAGCAAAACAA
Found at i:3346 original size:15 final size:15
Alignment explanation
Indices: 3308--3346 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
3298 CAGCATGTCA
*
3308 CATTCAGAACCAAAT
1 CATTCAGAGCCAAAT
*
3323 CATTCAGAGCCAACT
1 CATTCAGAGCCAAAT
3338 CATTCAGAG
1 CATTCAGAG
3347 TCTCTGAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.38, C:0.28, G:0.13, T:0.21
Consensus pattern (15 bp):
CATTCAGAGCCAAAT
Found at i:7053 original size:23 final size:22
Alignment explanation
Indices: 7027--7106 Score: 72
Period size: 23 Copynumber: 3.5 Consensus size: 22
7017 GGTTCTACGC
7027 GGTCCTTCGGAACAATTCTATGT
1 GGTCCTTCGG-ACAATTCTATGT
* *
7050 GGTCCTTCGGGACAAATTCTACGC
1 GGTCCTTC-GGAC-AATTCTATGT
* *
7074 AGTCCTTCAGGACAAGTCTATGT
1 GGTCCTTC-GGACAATTCTATGT
7097 GG-CACTTCGG
1 GGTC-CTTCGG
7107 TATATATTCT
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
22 3 0.07
23 22 0.48
24 21 0.46
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.29
Consensus pattern (22 bp):
GGTCCTTCGGACAATTCTATGT
Found at i:7078 original size:24 final size:24
Alignment explanation
Indices: 7019--7088 Score: 88
Period size: 24 Copynumber: 3.0 Consensus size: 24
7009 GAGTCGAGGG
*
7019 TTCTACGCGGTCCTTCGGAAC-AA
1 TTCTACGCGGTCCTTCGGGACAAA
* *
7042 TTCTATGTGGTCCTTCGGGACAAA
1 TTCTACGCGGTCCTTCGGGACAAA
* *
7066 TTCTACGCAGTCCTTCAGGACAA
1 TTCTACGCGGTCCTTCGGGACAA
7089 GTCTATGTGG
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 18 0.46
24 21 0.54
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (24 bp):
TTCTACGCGGTCCTTCGGGACAAA
Found at i:7122 original size:23 final size:23
Alignment explanation
Indices: 7096--7140 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
7086 CAAGTCTATG
*
7096 TGGCACTTCGGTATATATTCTAC
1 TGGCACTTCGGTATAAATTCTAC
*
7119 TGGCACTTCGGTGTAAATTCTA
1 TGGCACTTCGGTATAAATTCTA
7141 AGCGGCAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (23 bp):
TGGCACTTCGGTATAAATTCTAC
Found at i:9673 original size:3 final size:3
Alignment explanation
Indices: 9665--9716 Score: 65
Period size: 3 Copynumber: 17.7 Consensus size: 3
9655 ACCTATAAAA
9665 AAT AAT AAT AAT AAT AAT AAT AAT AAAT AAAT AAT -AT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT -AAT AAT AAT AAT AAT AAT
9710 -AT AAT AA
1 AAT AAT AA
9717 AATGTTTTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
2 6 0.13
3 32 0.71
4 7 0.16
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:9684 original size:22 final size:21
Alignment explanation
Indices: 9659--9716 Score: 55
Period size: 22 Copynumber: 2.7 Consensus size: 21
9649 CATGGGACCT
9659 ATAAAAAATAATAATAATAATA
1 ATAAAAAATAATAATAAT-ATA
*
9681 AT-AATAATAAATAAATAATATA
1 ATAAAAAAT-AAT-AATAATATA
* *
9703 ATATAATATAATAA
1 ATAAAAAATAATAA
9717 AATGTTTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
21 7 0.24
22 13 0.45
23 9 0.31
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAAAAAATAATAATAATATA
Found at i:10082 original size:84 final size:84
Alignment explanation
Indices: 9964--10127 Score: 238
Period size: 84 Copynumber: 2.0 Consensus size: 84
9954 CTCTTCAGTT
* * * * * * *
9964 TTTTGGTGGCAGATAGCTCTTCTCGATTTAAGCTATGTTGCAAATGATGTGCCTTTGAGCTGAGT
1 TTTTGGTGGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
10029 GTAATCGAACTCGAAGGGC
66 GTAATCGAACTCGAAGGGC
* *
10048 TTTTGGTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
1 TTTTGGTGGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
*
10113 GTAGTCGAACTCGAA
66 GTAATCGAACTCGAA
10128 TGTTTGGTGT
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
84 70 1.00
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (84 bp):
TTTTGGTGGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
GTAATCGAACTCGAAGGGC
Found at i:10255 original size:73 final size:72
Alignment explanation
Indices: 10167--10493 Score: 393
Period size: 73 Copynumber: 4.6 Consensus size: 72
10157 AAGGTTTTTT
10167 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAG
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACTGTCTCAAGAG
*
10232 AGATAAAA
65 AGACAAAA
* *
10240 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTAAAGAGAAACTGTCTCAAGAGA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGA
10305 GACAAAA
66 GACAAAA
* * * * * ** *
10312 CTTAGTTCCAAAAGAAACTATCTCAAGGGAGACGGAATTTGTTTCAA-GGAAGAC-GTATTC-A-
1 -TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAA-ACTGT-CTCAAG
*
10373 A-AG----AT
63 AGAGACAAAA
* * * *
10378 TTTGCTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAATGTCTCAAGATA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGA
10443 GACAAAA
66 GACAAAA
*
10450 TTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTT
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTGTTT
10494 TGAGTAAATT
Statistics
Matches: 212, Mismatches: 29, Indels: 26
0.79 0.11 0.10
Matches are distributed among these distances:
65 40 0.19
66 8 0.04
67 1 0.00
68 2 0.01
70 2 0.01
71 1 0.00
72 73 0.34
73 85 0.40
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.27
Consensus pattern (72 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGA
GACAAAA
Found at i:10256 original size:36 final size:36
Alignment explanation
Indices: 10167--10493 Score: 384
Period size: 36 Copynumber: 9.2 Consensus size: 36
10157 AAGGTTTTTT
10167 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* *
10203 CTTTGTTTCAAGGGAAACTGTCTCAAGAGAGATAAAA
1 -TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
10240 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
*
10276 TTTGTTTAAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * * * **
10312 CTTAGTTCCAAAAGAAACTATCTCAAGGGAGACGGAA
1 -TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* *
10349 TTTGTTTCAAG-GAAGAC-GTATTC-A-A-AG----AT
1 TTTGTTTCAAGAGAA-ACTGT-CTCAAGAGAGACAAAA
* *
10378 TTTGCTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * *
10414 TTTGTTTCAAGGGAAAATGTCTCAAGATAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
*
10450 TTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
10486 CTTTGTTT
1 -TTTGTTT
10494 TGAGTAAATT
Statistics
Matches: 246, Mismatches: 31, Indels: 26
0.81 0.10 0.09
Matches are distributed among these distances:
29 15 0.06
30 6 0.02
31 1 0.00
32 2 0.01
33 2 0.01
35 5 0.02
36 147 0.60
37 68 0.28
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.27
Consensus pattern (36 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:10512 original size:37 final size:34
Alignment explanation
Indices: 10390--10518 Score: 123
Period size: 36 Copynumber: 3.6 Consensus size: 34
10380 TGCTTCAAGG
* *
10390 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGG
1 GAAAATGTCTCAAGAGAGACAAAATTTGTTT--AGA
* *
10426 GAAAATGTCTCAAGATAGACAAAATTTATTTCAAGA
1 GAAAATGTCTCAAGAGAGACAAAATTTGTTT--AGA
* *
10462 GAAACTGTCTCAAGAGAGACAAAACTTTGTTTTGA
1 GAAAATGTCTCAAGAGAGACAAAA-TTTGTTTAGA
* *
10497 GTAAATTAGTCTCAAGCGAGAC
1 G-AAAAT-GTCTCAAGAGAGAC
10519 GACCCCTTGT
Statistics
Matches: 80, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
35 3 0.04
36 58 0.73
37 19 0.24
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.26
Consensus pattern (34 bp):
GAAAATGTCTCAAGAGAGACAAAATTTGTTTAGA
Found at i:10796 original size:124 final size:123
Alignment explanation
Indices: 10576--10816 Score: 385
Period size: 124 Copynumber: 1.9 Consensus size: 123
10566 CTTGTTCTTG
* * *
10576 AAGATGAATGTTGCTGGTGGATACGATTCCCTTTGTCGTGAAGTTGAAACTGCGGATGACCCATT
1 AAGATGAATGTTGCTGGTGGATAC-ATTCCCTTCGTCGTGAAGTTAAAACCGCGGATGACCCATT
*
10641 CGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCATCGTGAAGTTAAAATCAAATCTA
65 CGTTGTGAAGTTGAGCCTTGAATTAGATATCCTTCATCGTGAAGTTAAAATCAAATCTA
*
10700 AAGATGAATGTTGCTGGTGAGCATA-ATTCCCTTCGTCGTGAAGTTAAAACCGTGGATGACCCAT
1 AAGATGAATGTTGCTGGTG-G-ATACATTCCCTTCGTCGTGAAGTTAAAACCGCGGATGACCCAT
* *
10764 TCGTTGTGAAGTTGAGCCTTGAATTAGATATCCTTCATTGTGAAGTTGAAATC
64 TCGTTGTGAAGTTGAGCCTTGAATTAGATATCCTTCATCGTGAAGTTAAAATC
10817 CAATGTAAGT
Statistics
Matches: 108, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
124 104 0.96
125 1 0.01
126 3 0.03
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.32
Consensus pattern (123 bp):
AAGATGAATGTTGCTGGTGGATACATTCCCTTCGTCGTGAAGTTAAAACCGCGGATGACCCATTC
GTTGTGAAGTTGAGCCTTGAATTAGATATCCTTCATCGTGAAGTTAAAATCAAATCTA
Found at i:11519 original size:110 final size:110
Alignment explanation
Indices: 11336--11651 Score: 496
Period size: 110 Copynumber: 2.9 Consensus size: 110
11326 TTGTGTCGTT
* *
11336 TCGAGTCTAATATCCTTCACTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
1 TCGAGTCTAATATCCTTCGCTATGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
*
11401 TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTATC
66 TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTATTATC
* *
11446 TCGAGTCTAATATCCTTCGCTATGAAGTTGAAATTGACTCTGAATGAAACTAAAAAGTTATTTGT
1 TCGAGTCTAATATCCTTCGCTATGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
* * *
11511 TGACAGTCAGTCGCCTCTTCGCTGTGAAGTTGATCTTGTATTGTC
66 TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTATTATC
* * *
11556 ACGAGTCTAATATCCTTTGCTATGAAGTTAAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
1 TCGAGTCTAATATCCTTCGCTATGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
*
11621 TG--A--CAGTCGCCCCTTCGCTGTGAATTTGAGC
66 TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGC
11652 AACTACCATC
Statistics
Matches: 190, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
106 25 0.13
108 1 0.01
110 164 0.86
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (110 bp):
TCGAGTCTAATATCCTTCGCTATGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTATTATC
Found at i:20619 original size:3 final size:3
Alignment explanation
Indices: 20594--20654 Score: 63
Period size: 3 Copynumber: 20.3 Consensus size: 3
20584 ACCTACAAAA
* * *
20594 AAT AAA AAT AAA AAT ATT AAT AAT AAT AAT AAT AAT AAT AAAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT -AAT
20641 AAT -AT AAT AA- AAT A
1 AAT AAT AAT AAT AAT A
20655 TTTTTTAGAC
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
2 4 0.08
3 38 0.78
4 7 0.14
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:23291 original size:49 final size:49
Alignment explanation
Indices: 23229--23358 Score: 172
Period size: 49 Copynumber: 2.6 Consensus size: 49
23219 GTACTTGTAT
* ** *
23229 ATTCTACGAGGCACTTTGTGTGCACTTCTA-TAAGGTACTTTGTGTGCAT
1 ATTCTACGAGGCACTTTGTGTGCAATTCTACT-AGACACTTTGTGTGCAA
* * *
23278 TTTCTATGGGGCACTTTGTGTGCAATTCTACTAGACACTTTGTGTGCAA
1 ATTCTACGAGGCACTTTGTGTGCAATTCTACTAGACACTTTGTGTGCAA
23327 ATTCTACGAGGCACTTTGTGTGCATATTCTAC
1 ATTCTACGAGGCACTTTGTGTGCA-ATTCTAC
23359 ATGGCACATT
Statistics
Matches: 69, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
49 61 0.88
50 8 0.12
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (49 bp):
ATTCTACGAGGCACTTTGTGTGCAATTCTACTAGACACTTTGTGTGCAA
Found at i:23358 original size:25 final size:25
Alignment explanation
Indices: 23227--23358 Score: 160
Period size: 25 Copynumber: 5.4 Consensus size: 25
23217 CAGTACTTGT
23227 ATATTCTACGAGGCACTTTGTGTGC
1 ATATTCTACGAGGCACTTTGTGTGC
* ** *
23252 A-CTTCTATAAGGTACTTTGTGTGC
1 ATATTCTACGAGGCACTTTGTGTGC
* * *
23276 ATTTTCTATGGGGCACTTTGTGTGC
1 ATATTCTACGAGGCACTTTGTGTGC
* *
23301 A-ATTCTACTAGACACTTTGTGTGC
1 ATATTCTACGAGGCACTTTGTGTGC
*
23325 AAATTCTACGAGGCACTTTGTGTGC
1 ATATTCTACGAGGCACTTTGTGTGC
23350 ATATTCTAC
1 ATATTCTAC
23359 ATGGCACATT
Statistics
Matches: 89, Mismatches: 16, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
24 39 0.44
25 50 0.56
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (25 bp):
ATATTCTACGAGGCACTTTGTGTGC
Found at i:23772 original size:3 final size:3
Alignment explanation
Indices: 23764--23796 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
23754 TTTATATTTA
*
23764 TAT TAT TAT TAT TAT TAC TAT TAT TAT T-T TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
23797 TACGTTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:23773 original size:18 final size:18
Alignment explanation
Indices: 23744--23798 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
23734 TTCTATTAAT
23744 TTTAT-TTA-TATTTATA
1 TTTATATTATTATTTATA
23760 TTTATATTATTA-TTAT-
1 TTTATATTATTATTTATA
23776 TATTACTATTATTATTT-TA
1 T-TTA-TATTATTATTTATA
23795 TTTA
1 TTTA
23799 CGTTATTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
16 6 0.18
17 10 0.30
18 14 0.42
19 3 0.09
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTATATTATTATTTATA
Found at i:23799 original size:18 final size:18
Alignment explanation
Indices: 23752--23799 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
23742 ATTTTATTTA
23752 TATTTATATTTA-TATTAT
1 TATTT-TATTTACTATTAT
23770 TATTATTA-TTACTATTAT
1 TATT-TTATTTACTATTAT
23788 TATTTTATTTAC
1 TATTTTATTTAC
23800 GTTATTAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
17 6 0.22
18 20 0.74
19 1 0.04
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (18 bp):
TATTTTATTTACTATTAT
Found at i:24353 original size:17 final size:18
Alignment explanation
Indices: 24325--24358 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
24315 AAATATACAA
24325 ATTTATTTAAAATTAATC
1 ATTTATTTAAAATTAATC
24343 ATTTA-TTAAAATTAAT
1 ATTTATTTAAAATTAAT
24359 TATAATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTTATTTAAAATTAATC
Found at i:25405 original size:22 final size:23
Alignment explanation
Indices: 25374--25434 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 23
25364 TATTTAAAAT
*
25374 TAATCATTTATTAAAATTTAATTA
1 TAAT-ATTTATTAAAATTAAATTA
* *
25398 TAAT-TTTAATATAATTAAATTA
1 TAATATTTATTAAAATTAAATTA
25420 TAATATTT-TTAAAAT
1 TAATATTTATTAAAAT
25435 AATAATTAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
22 24 0.77
23 3 0.10
24 4 0.13
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (23 bp):
TAATATTTATTAAAATTAAATTA
Found at i:26203 original size:18 final size:18
Alignment explanation
Indices: 26182--26216 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
26172 TAAGATTATA
26182 ATTAAATTTAAATAAATG
1 ATTAAATTTAAATAAATG
*
26200 ATTAATTTTAAATAAAT
1 ATTAAATTTAAATAAAT
26217 CCTTATACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (18 bp):
ATTAAATTTAAATAAATG
Found at i:32305 original size:45 final size:45
Alignment explanation
Indices: 32168--32289 Score: 235
Period size: 45 Copynumber: 2.7 Consensus size: 45
32158 CTTAGTTAAT
*
32168 TTTTTCATGCAAGTACAAAACATATAGAAATAAAAGAGGATTCTG
1 TTTTTCATGCAAGGACAAAACATATAGAAATAAAAGAGGATTCTG
32213 TTTTTCATGCAAGGACAAAACATATAGAAATAAAAGAGGATTCTG
1 TTTTTCATGCAAGGACAAAACATATAGAAATAAAAGAGGATTCTG
32258 TTTTTCATGCAAGGACAAAACATATAGAAATA
1 TTTTTCATGCAAGGACAAAACATATAGAAATA
32290 CACTATCACT
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
45 76 1.00
ACGTcount: A:0.45, C:0.11, G:0.16, T:0.28
Consensus pattern (45 bp):
TTTTTCATGCAAGGACAAAACATATAGAAATAAAAGAGGATTCTG
Found at i:32954 original size:23 final size:23
Alignment explanation
Indices: 32894--32955 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
32884 TAGTGTTTGT
* *
32894 GAACATATTCATTTAATATTTAC
1 GAACATATTCATTTAACATTCAC
* * *
32917 GAATATGTTCGTTTAACATTCAC
1 GAACATATTCATTTAACATTCAC
*
32940 GAACATATTTATTTAA
1 GAACATATTCATTTAA
32956 TATATATATA
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.42
Consensus pattern (23 bp):
GAACATATTCATTTAACATTCAC
Found at i:36098 original size:17 final size:17
Alignment explanation
Indices: 36068--36101 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
36058 GGCATTGAAT
36068 TAAATGTAAAAAAAGAG
1 TAAATGTAAAAAAAGAG
36085 TAAAT-TAAACAAAAGAG
1 TAAATGTAAA-AAAAGAG
36102 AAAGGAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.65, C:0.03, G:0.15, T:0.18
Consensus pattern (17 bp):
TAAATGTAAAAAAAGAG
Found at i:36511 original size:15 final size:14
Alignment explanation
Indices: 36490--36518 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
36480 AGTCTCTAAA
36490 TTATA-AAAAGATT
1 TTATATAAAAGATT
36503 TTATATAAAAGATT
1 TTATATAAAAGATT
36517 TT
1 TT
36519 TTTATTAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (14 bp):
TTATATAAAAGATT
Found at i:36792 original size:60 final size:60
Alignment explanation
Indices: 36704--36850 Score: 145
Period size: 60 Copynumber: 2.4 Consensus size: 60
36694 TATTTTGGAT
* * * * *
36704 AAATTATACAAATAGTCTCTCGATTATAGAATGTTATTTTATTGAATCTTCTAATTATCAA
1 AAATTATA-AAATAGTATCTCGACTATAGAATATTATTTTATTGAATCATCTAACTATCAA
** * * *
36765 AAATTATAAAATAGTTATC-CGACTATAGCGTATTTTTTTATTGAGTCATCTAACTATTAA
1 AAATTATAAAATAG-TATCTCGACTATAGAATATTATTTTATTGAATCATCTAACTATCAA
* *
36825 AATTTATAAAATAATCAT-TCGACTAT
1 AAATTATAAAATAGT-ATCTCGACTAT
36851 TCATAAGTTC
Statistics
Matches: 71, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
59 1 0.01
60 59 0.83
61 11 0.15
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (60 bp):
AAATTATAAAATAGTATCTCGACTATAGAATATTATTTTATTGAATCATCTAACTATCAA
Found at i:37472 original size:2 final size:2
Alignment explanation
Indices: 37465--37493 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
37455 TAAACTTTAG
37465 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
37494 TCAGAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:46533 original size:19 final size:19
Alignment explanation
Indices: 46479--46543 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
46469 CTCTATATAT
* * *
46479 TATTTTTTAATTAAACTCA
1 TATTTTTTAATAAAAATAA
46498 TATTTTTATTGAATAAAAATAA
1 TA-TTTT-TT-AATAAAAATAA
* *
46520 TATTTTTTAATAAATATAT
1 TATTTTTTAATAAAAATAA
46539 TATTT
1 TATTT
46544 CAGATCAGAT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
19 16 0.42
20 6 0.16
21 6 0.16
22 10 0.26
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.54
Consensus pattern (19 bp):
TATTTTTTAATAAAAATAA
Found at i:47843 original size:27 final size:29
Alignment explanation
Indices: 47776--47843 Score: 79
Period size: 27 Copynumber: 2.4 Consensus size: 29
47766 TGTTTAAGGT
* *
47776 ATATTTTA-TTATATTTAGCATTTTGTTA
1 ATATTTTATTTAAATTTAGAATTTTGTTA
* *
47804 GTAATTTATTTAAATTTA-AATTTT-TTA
1 ATATTTTATTTAAATTTAGAATTTTGTTA
47831 ATATTTTATTTAA
1 ATATTTTATTTAA
47844 TTATTTTTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
27 14 0.42
28 11 0.33
29 8 0.24
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.60
Consensus pattern (29 bp):
ATATTTTATTTAAATTTAGAATTTTGTTA
Found at i:55694 original size:28 final size:28
Alignment explanation
Indices: 55653--55717 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 28
55643 AAGAGTCGAG
55653 GGTTCTACGTGGTCCTAAGGGACATA-T
1 GGTTCTACGTGGTCCTAAGGGACATAGT
* **
55680 GTGTTCTATGTGGTCCTTCGGGACATAGT
1 G-GTTCTACGTGGTCCTAAGGGACATAGT
55709 GGTTCTACG
1 GGTTCTACG
55718 GGACAAATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
27 1 0.03
28 29 0.91
29 2 0.06
ACGTcount: A:0.17, C:0.18, G:0.31, T:0.34
Consensus pattern (28 bp):
GGTTCTACGTGGTCCTAAGGGACATAGT
Found at i:57530 original size:21 final size:21
Alignment explanation
Indices: 57462--57561 Score: 103
Period size: 21 Copynumber: 4.7 Consensus size: 21
57452 TCGAAATGGA
*
57462 GTGCATGGATGCACTACA-TG
1 GTGCATGGATGCACTACAGGG
* **
57482 GTGCATCGATGCACTATTGGCAG
1 GTGCATGGATGCACTACAGG--G
**
57505 GTGCATGGATGCACTGTAGGG
1 GTGCATGGATGCACTACAGGG
*
57526 GTGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTACAGGG
*
57547 GTACATGGATGCACT
1 GTGCATGGATGCACT
57562 TTGACACCCT
Statistics
Matches: 68, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
20 15 0.22
21 35 0.51
23 18 0.26
ACGTcount: A:0.22, C:0.19, G:0.35, T:0.24
Consensus pattern (21 bp):
GTGCATGGATGCACTACAGGG
Found at i:57808 original size:21 final size:21
Alignment explanation
Indices: 57785--57823 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
57775 TGTTTAATGA
57785 AAAAT-ATACCAATTGTTAAC
1 AAAATGATACCAATTGTTAAC
*
57805 AAAATGATATCAATTGTTA
1 AAAATGATACCAATTGTTA
57824 CCAATTGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.49, C:0.10, G:0.08, T:0.33
Consensus pattern (21 bp):
AAAATGATACCAATTGTTAAC
Found at i:60499 original size:21 final size:21
Alignment explanation
Indices: 60400--60491 Score: 157
Period size: 21 Copynumber: 4.4 Consensus size: 21
60390 ACTAGTGGCA
*
60400 GGTGCATGGATGCACTGCCGG
1 GGTGCATGGATGCACTGCAGG
*
60421 GGTGCATGGATGCACTGCCGG
1 GGTGCATGGATGCACTGCAGG
60442 GGTGCATGGATGCACTGCAGG
1 GGTGCATGGATGCACTGCAGG
60463 GGTGCATGGATGCACTGCAGG
1 GGTGCATGGATGCACTGCAGG
*
60484 GGTACATG
1 GGTGCATG
60492 TATACACTTT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 69 1.00
ACGTcount: A:0.17, C:0.21, G:0.42, T:0.20
Consensus pattern (21 bp):
GGTGCATGGATGCACTGCAGG
Found at i:60911 original size:80 final size:80
Alignment explanation
Indices: 60821--60971 Score: 205
Period size: 80 Copynumber: 1.9 Consensus size: 80
60811 TTTTGTTATT
* * * *
60821 ATTTTTTTAACATTTCTGGTAAAAAATTACCTAAAACATTATTATTTATAC-TGATTTTGTTATT
1 ATTTTGTTAACATATATGGTAAAAAACTACCTAAAACATTATTATTTATACTTG-TTTTGTTATT
60885 ATTGGACGTTTTTCCG
65 ATTGGACGTTTTTCCG
** * * *
60901 ATTTTGTTAACATATATGGTAAAATGCTACCTAAAATATTATTTTTTCTACTTGTTTTGTTATTA
1 ATTTTGTTAACATATATGGTAAAAAACTACCTAAAACATTATTATTTATACTTGTTTTGTTATTA
60966 TTGGAC
66 TTGGAC
60972 ACTTTACCGG
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
80 59 0.97
81 2 0.03
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.49
Consensus pattern (80 bp):
ATTTTGTTAACATATATGGTAAAAAACTACCTAAAACATTATTATTTATACTTGTTTTGTTATTA
TTGGACGTTTTTCCG
Found at i:65643 original size:68 final size:68
Alignment explanation
Indices: 65534--65671 Score: 276
Period size: 68 Copynumber: 2.0 Consensus size: 68
65524 TTTCCGACTG
65534 TGTGGTTGATTCTCCTTGCTGTTTAGTGACTGGTGAGTATGGTTGGACTGCCAACATGGAGAGGA
1 TGTGGTTGATTCTCCTTGCTGTTTAGTGACTGGTGAGTATGGTTGGACTGCCAACATGGAGAGGA
65599 TCA
66 TCA
65602 TGTGGTTGATTCTCCTTGCTGTTTAGTGACTGGTGAGTATGGTTGGACTGCCAACATGGAGAGGA
1 TGTGGTTGATTCTCCTTGCTGTTTAGTGACTGGTGAGTATGGTTGGACTGCCAACATGGAGAGGA
65667 TCA
66 TCA
65670 TG
1 TG
65672 AAGGCACAAG
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 70 1.00
ACGTcount: A:0.19, C:0.14, G:0.33, T:0.34
Consensus pattern (68 bp):
TGTGGTTGATTCTCCTTGCTGTTTAGTGACTGGTGAGTATGGTTGGACTGCCAACATGGAGAGGA
TCA
Found at i:67253 original size:18 final size:16
Alignment explanation
Indices: 67230--67277 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 16
67220 CTTGACCCAA
67230 ACCGTTGACTTTGATATG
1 ACCGTTGACTTTG-T-TG
*
67248 ACCGTTGACATGTCGTTG
1 ACCGTTGAC-T-TTGTTG
67266 ACCGTTGACTTT
1 ACCGTTGACTTT
67278 AACTAGTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
16 1 0.04
17 1 0.04
18 20 0.77
19 2 0.08
20 2 0.08
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.38
Consensus pattern (16 bp):
ACCGTTGACTTTGTTG
Found at i:72561 original size:7 final size:8
Alignment explanation
Indices: 72544--72570 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
72534 TGGTAAGTAG
72544 TTTTAATT
1 TTTTAATT
72552 TTTTAATT
1 TTTTAATT
72560 TTTTAATT
1 TTTTAATT
72568 TTT
1 TTT
72571 GCTTCTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTAATT
Done.