Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003834.1 Hibiscus syriacus cultivar Beakdansim tig00008220_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: 70912
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:4498 original size:72 final size:72
Alignment explanation
Indices: 4381--4524 Score: 261
Period size: 72 Copynumber: 2.0 Consensus size: 72
4371 GGTCCAACTA
* *
4381 CCAGAGGTGGTCCTAACGTATCCTCGTCTTCTTCGAGGAATTACGATCTTGACTATATCTTGTTG
1 CCAGAGGTGGTCCTAACGTATCCTCGTCGTCTTCGAGGAATTACGATATTGACTATATCTTGTTG
4446 AAGCTGC
66 AAGCTGC
*
4453 CCAGAGGTGGTCCTAACGTATCCTTGTCGTCTTCGAGGAATTACGATATTGACTATATCTTGTTG
1 CCAGAGGTGGTCCTAACGTATCCTCGTCGTCTTCGAGGAATTACGATATTGACTATATCTTGTTG
4518 AAGCTGC
66 AAGCTGC
4525 AGCTACAGCT
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 69 1.00
ACGTcount: A:0.22, C:0.22, G:0.23, T:0.33
Consensus pattern (72 bp):
CCAGAGGTGGTCCTAACGTATCCTCGTCGTCTTCGAGGAATTACGATATTGACTATATCTTGTTG
AAGCTGC
Found at i:5221 original size:2 final size:2
Alignment explanation
Indices: 5208--5243 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
5198 AATGTTGCAA
*
5208 AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5244 TGTTGCAAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:7013 original size:4 final size:4
Alignment explanation
Indices: 6999--7037 Score: 53
Period size: 4 Copynumber: 9.5 Consensus size: 4
6989 CGAGATAAAG
6999 ATAA GATAA ATAA ATAA ATAA ATAA ATTAA A-AA ATAA AT
1 ATAA -ATAA ATAA ATAA ATAA ATAA A-TAA ATAA ATAA AT
7038 TGAGATGAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
3 3 0.09
4 21 0.66
5 8 0.25
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:7985 original size:23 final size:23
Alignment explanation
Indices: 7967--8027 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
7957 CTCATATAAA
*
7967 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGTAGTGCCACATAGAAT
* *
7990 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACATAGAAT
8013 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
8028 TATAATAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.20
Consensus pattern (23 bp):
TGCACCGTAGTGCCACATAGAAT
Found at i:8215 original size:103 final size:104
Alignment explanation
Indices: 8043--8261 Score: 377
Period size: 103 Copynumber: 2.1 Consensus size: 104
8033 TAATGTCCAT
* *
8043 AAGGACCACATATCATTTCCTTAAAAATCATATACATATACTAGGGATCAAGTATGTGTCTCACC
1 AAGGACCACATATCATTTCCTTAAAAATCATATACATATACCAAGGATCAAGTATGTGTCTCACC
*
8108 AGACTTCACACATGTTCCAAAGAATACATATATGTCTCG
66 AGACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
8147 AAGGACCACATATCA-TTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACC
1 AAGGACCACATATCATTTCCTTAAAAATCATATACATATACCAAGGATCAAGTATGTGTCTCACC
*
8211 AGACTTCATACATGTTCCAAAGAATACATATATGTCCCG
66 AGACTTCACACATGTTCCAAAGAATACATATATGTCCCG
8250 AAGGACCACATA
1 AAGGACCACATA
8262 GACCCTCGAC
Statistics
Matches: 109, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
103 94 0.86
104 15 0.14
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (104 bp):
AAGGACCACATATCATTTCCTTAAAAATCATATACATATACCAAGGATCAAGTATGTGTCTCACC
AGACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:11527 original size:19 final size:19
Alignment explanation
Indices: 11492--11529 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
11482 AATTAAATAT
*
11492 AAAAAATTAATCATTTAAA
1 AAAAAATTAAACATTTAAA
*
11511 AAAAAATTAAACCTTTAAA
1 AAAAAATTAAACATTTAAA
11530 CCACCAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAAAATTAAACATTTAAA
Found at i:14845 original size:31 final size:31
Alignment explanation
Indices: 14810--14875 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
14800 AAAACATAAT
14810 ATATGATCACTTTCGGTTTTATTTAATTAAG
1 ATATGATCACTTTCGGTTTTATTTAATTAAG
* *
14841 ATATGATCACTTTTGTTTTTATTTAATTAAG
1 ATATGATCACTTTCGGTTTTATTTAATTAAG
14872 ATAT
1 ATAT
14876 AGTAACCACG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.30, C:0.08, G:0.11, T:0.52
Consensus pattern (31 bp):
ATATGATCACTTTCGGTTTTATTTAATTAAG
Found at i:15038 original size:2 final size:2
Alignment explanation
Indices: 15031--15062 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
15021 ACATGGCATA
15031 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15063 TTAACTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15098 original size:26 final size:27
Alignment explanation
Indices: 15064--15136 Score: 69
Period size: 29 Copynumber: 2.6 Consensus size: 27
15054 TATATATATT
*
15064 TAACTTTAAAAATATTTTTTTATATAA-A
1 TAAC-TTAAAAATATTTTATTAT-TAATA
15092 T-ACTTAAAATTATAATTTTATTATTAATA
1 TAACTTAAAA--AT-ATTTTATTATTAATA
*
15121 TAATTTAAAAATATTT
1 TAACTTAAAAATATTT
15137 AATTTTATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
26 6 0.16
27 6 0.16
28 8 0.21
29 11 0.29
30 7 0.18
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.51
Consensus pattern (27 bp):
TAACTTAAAAATATTTTATTATTAATA
Found at i:15141 original size:32 final size:30
Alignment explanation
Indices: 15068--15210 Score: 111
Period size: 32 Copynumber: 4.8 Consensus size: 30
15058 TATATTTAAC
*
15068 TTTAAAAATATTTTTTTA-TA-TAA-AT-A
1 TTTAAAAATATTATTTTATTATTAATATAA
* * *
15094 CTTAAAATTATAATTTTATTATTAATATAA
1 TTTAAAAATATTATTTTATTATTAATATAA
*
15124 TTTAAAAATATTTAATTTTATT-TTAATTTTAA
1 TTTAAAAATA-TT-ATTTTATTATTAA-TATAA
* * *
15156 ATTAAAAAT-TATATTTTATTATTATCTAAAA
1 TTTAAAAATAT-TATTTTATTATTA-ATATAA
15187 TTTTAAAAATA-TATTTTATTATTA
1 -TTTAAAAATATTATTTTATTATTA
15211 TGTCATGTGG
Statistics
Matches: 92, Mismatches: 13, Indels: 19
0.74 0.10 0.15
Matches are distributed among these distances:
26 14 0.15
27 2 0.02
28 3 0.03
29 2 0.02
30 18 0.20
31 25 0.27
32 28 0.30
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (30 bp):
TTTAAAAATATTATTTTATTATTAATATAA
Found at i:16733 original size:2 final size:2
Alignment explanation
Indices: 16721--16768 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
16711 ATTCACAAGT
16721 TA TA T- 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
16762 TA TA TA T
1 TA TA TA T
16769 GTTTTTATCT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16852 original size:24 final size:23
Alignment explanation
Indices: 16807--16857 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
16797 TTACTTTTTT
16807 TTTATTTCTTGTTATTTAATTTA
1 TTTATTTCTTGTTATTTAATTTA
*
16830 TTTATTT-TTGTCGTATTTTATTTA
1 TTTATTTCTTGT--TATTTAATTTA
16854 TTTA
1 TTTA
16858 CATTTGTTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 4 0.16
23 7 0.28
24 14 0.56
ACGTcount: A:0.20, C:0.04, G:0.06, T:0.71
Consensus pattern (23 bp):
TTTATTTCTTGTTATTTAATTTA
Found at i:16863 original size:24 final size:24
Alignment explanation
Indices: 16819--16864 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
16809 TATTTCTTGT
**
16819 TATTTAATTTATTTATTTTTGTCG
1 TATTTAATTTATTTACATTTGTCG
*
16843 TATTTTATTTATTTACATTTGT
1 TATTTAATTTATTTACATTTGT
16865 TCCTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.22, C:0.04, G:0.07, T:0.67
Consensus pattern (24 bp):
TATTTAATTTATTTACATTTGTCG
Found at i:28277 original size:105 final size:105
Alignment explanation
Indices: 28095--28761 Score: 1163
Period size: 105 Copynumber: 6.3 Consensus size: 105
28085 AGGTTTTACC
*
28095 CAGAGCCAATTTCAACTTCACAACAAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
28160 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
28200 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
28265 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
28305 CAGAGCCAATTTCAACTTCACAACGAAGGATATTAGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
28370 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAACT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
28410 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
28475 ACGAAGGGACCGCTGGTTGTCAACAAATATTTTTCAAACT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
28515 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
28580 ACGAAGGGACCACTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
** * *
28620 CAGAGCCAATTTCAACTTCACGGCGAAGGATATTGGACTCCAAACAACGCAAGTTTAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
28685 ACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAAATT
* * * *
28726 CGGAGCCAATTTCAACTTCATAGCGAAAGATATTGG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
28762 CCTCGAAACA
Statistics
Matches: 538, Mismatches: 23, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
105 496 0.92
106 42 0.08
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
Found at i:30497 original size:2 final size:2
Alignment explanation
Indices: 30490--30518 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
30480 AGTTATATTT
30490 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
30519 GTTTTTATCT
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:30595 original size:24 final size:23
Alignment explanation
Indices: 30556--30606 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
30546 TTTACTTTTT
30556 TTTATTTCTTGTTATTTAATTTA
1 TTTATTTCTTGTTATTTAATTTA
*
30579 TTTATTT-TTGTCGTATTTTATTTA
1 TTTATTTCTTGT--TATTTAATTTA
30603 TTTA
1 TTTA
30607 CATTTGTTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 4 0.16
23 7 0.28
24 14 0.56
ACGTcount: A:0.20, C:0.04, G:0.06, T:0.71
Consensus pattern (23 bp):
TTTATTTCTTGTTATTTAATTTA
Found at i:30612 original size:24 final size:24
Alignment explanation
Indices: 30568--30613 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
30558 TATTTCTTGT
**
30568 TATTTAATTTATTTATTTTTGTCG
1 TATTTAATTTATTTACATTTGTCG
*
30592 TATTTTATTTATTTACATTTGT
1 TATTTAATTTATTTACATTTGT
30614 TCCTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.22, C:0.04, G:0.07, T:0.67
Consensus pattern (24 bp):
TATTTAATTTATTTACATTTGTCG
Found at i:40392 original size:19 final size:20
Alignment explanation
Indices: 40368--40408 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
40358 TCATTCGAGC
40368 ATTTAATA-CG-TTAGAAATA
1 ATTTAATATCGTTTA-AAATA
40387 ATTTAATATCGTTTAAAATA
1 ATTTAATATCGTTTAAAATA
40407 AT
1 AT
40409 AATTATTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 8 0.40
20 9 0.45
21 3 0.15
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.41
Consensus pattern (20 bp):
ATTTAATATCGTTTAAAATA
Found at i:43095 original size:3 final size:3
Alignment explanation
Indices: 43087--43130 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
43077 TTTGTTTTAT
*
43087 TTA TTA TTA TTA TT- TTG TT- TTA TTA TTA -TA TTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
43131 AATAATTAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
2 8 0.22
3 29 0.78
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:43111 original size:16 final size:16
Alignment explanation
Indices: 43084--43130 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
43074 TCATTTGTTT
43084 TATT-TATTATTATTA
1 TATTATATTATTATTA
* * *
43099 TTTTGTTTTATTATTA
1 TATTATATTATTATTA
43115 TATTATATTATTATTA
1 TATTATATTATTATTA
43131 AATAATTAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
15 3 0.12
16 23 0.88
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (16 bp):
TATTATATTATTATTA
Found at i:43123 original size:23 final size:23
Alignment explanation
Indices: 43077--43120 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
43067 TTTTATTTCA
43077 TTTGTTTTATTTATTATTATTAT
1 TTTGTTTTATTTATTATTATTAT
43100 TTTGTTTTA-TTATTA-TATTAT
1 TTTGTTTTATTTATTATTATTAT
43121 ATTATTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 6 0.29
22 6 0.29
23 9 0.43
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.73
Consensus pattern (23 bp):
TTTGTTTTATTTATTATTATTAT
Found at i:43602 original size:23 final size:22
Alignment explanation
Indices: 43572--43615 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
43562 GGAGACAGCC
**
43572 ACGGAGAGTCAAACAGAGAGCT
1 ACGGAGAGAAAAACAGAGAGCT
43594 ACGGCAGAGAAAAACAGAGAGC
1 ACGG-AGAGAAAAACAGAGAGC
43616 AACCACCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.45, C:0.18, G:0.32, T:0.05
Consensus pattern (22 bp):
ACGGAGAGAAAAACAGAGAGCT
Found at i:44440 original size:12 final size:11
Alignment explanation
Indices: 44423--44462 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
44413 GTAATTCCTT
44423 TTATTTTAATAA
1 TTATTTTAAT-A
44435 TTATTTTCAATA
1 TTATTTT-AATA
*
44447 TTATTTTATTA
1 TTATTTTAATA
44458 TTATT
1 TTATT
44463 ATTATTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 8 0.31
12 15 0.58
13 3 0.12
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (11 bp):
TTATTTTAATA
Found at i:44451 original size:3 final size:3
Alignment explanation
Indices: 44445--44535 Score: 54
Period size: 3 Copynumber: 32.3 Consensus size: 3
44435 TTATTTTCAA
* *
44445 TAT TAT T-T TAT TAT TAT TAT TAT T-T T-T TAT TGCT T-T AAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT
* * * *
44487 TAT T-T T-T TAT TGCT T-T AAT TAT TAT T-T CAT TAT TAT TAT TTT
1 TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
44529 TAT TAT T
1 TAT TAT T
44536 TATATATATA
Statistics
Matches: 70, Mismatches: 10, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
2 13 0.19
3 53 0.76
4 4 0.06
ACGTcount: A:0.25, C:0.03, G:0.02, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:44455 original size:17 final size:17
Alignment explanation
Indices: 44443--44475 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
44433 AATTATTTTC
44443 AATATTATTTTATTATT
1 AATATTATTTTATTATT
*
44460 ATTATTATTTT-TTATT
1 AATATTATTTTATTATT
44476 GCTTTAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
AATATTATTTTATTATT
Found at i:44488 original size:22 final size:22
Alignment explanation
Indices: 44460--44513 Score: 108
Period size: 22 Copynumber: 2.5 Consensus size: 22
44450 TTTTATTATT
44460 ATTATTATTTTTTATTGCTTTA
1 ATTATTATTTTTTATTGCTTTA
44482 ATTATTATTTTTTATTGCTTTA
1 ATTATTATTTTTTATTGCTTTA
44504 ATTATTATTT
1 ATTATTATTT
44514 CATTATTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.69
Consensus pattern (22 bp):
ATTATTATTTTTTATTGCTTTA
Found at i:48504 original size:18 final size:18
Alignment explanation
Indices: 48430--48526 Score: 61
Period size: 18 Copynumber: 5.0 Consensus size: 18
48420 CTTTGAATAC
*
48430 AATTCTATTTATTTATTAATA
1 AATTCAATTTATTT-TT--TA
*
48451 AATTCTAAGTTTAGTTTCTCTA
1 AATTC-AA-TTTA-TTT-TTTA
*
48473 AATTC-ATTTTTTTTTTA
1 AATTCAATTTATTTTTTA
* **
48490 GATTCAATTTATTTTCGA
1 AATTCAATTTATTTTTTA
48508 AATTCAATTTATTATTTTA
1 AATTCAATTTATT-TTTTA
48527 TTTTGTAAAT
Statistics
Matches: 59, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
17 7 0.12
18 24 0.41
19 6 0.10
20 1 0.02
21 5 0.08
22 8 0.14
23 4 0.07
24 4 0.07
ACGTcount: A:0.31, C:0.08, G:0.04, T:0.57
Consensus pattern (18 bp):
AATTCAATTTATTTTTTA
Found at i:50216 original size:75 final size:76
Alignment explanation
Indices: 50055--50228 Score: 181
Period size: 75 Copynumber: 2.3 Consensus size: 76
50045 ACAAGAAGCG
* * * * * *
50055 AATGTTGTGGCATGCTGAAAACCCTTTTCAATCAGAATCAGGAATATTAAAGTATTCTGAATATT
1 AATGTTGGGGCATGCTGAAAGCCCCTTTCAATCAGAATCAGGAATATTAAAGCATTCTGAACACT
50120 TATATCAGCAA
66 TATATCAGCAA
* * * * * * *
50131 AATGCT-GGGCATGTTGAAAGCCCCTTTCAATCAGAATCAGGACTGTTGATGCATTTTGAACACT
1 AATGTTGGGGCATGCTGAAAGCCCCTTTCAATCAGAATCAGGAATATTAAAGCATTCTGAACACT
* * *
50195 TGTATTAGC-C
66 TATATCAGCAA
*
50205 AATGTTGGGGCATGCTGAAGGCCC
1 AATGTTGGGGCATGCTGAAAGCCC
50229 ATATCATCCT
Statistics
Matches: 78, Mismatches: 19, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
74 5 0.06
75 68 0.87
76 5 0.06
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.30
Consensus pattern (76 bp):
AATGTTGGGGCATGCTGAAAGCCCCTTTCAATCAGAATCAGGAATATTAAAGCATTCTGAACACT
TATATCAGCAA
Found at i:51580 original size:22 final size:22
Alignment explanation
Indices: 51554--51632 Score: 122
Period size: 23 Copynumber: 3.5 Consensus size: 22
51544 ATCTATACTC
51554 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
51576 TTCAAAGATGATAGATTCTCTTT
1 TTCAAAGATGATAGATTCTC-TT
* *
51599 TTTAAAGATGATAGATTCTTTTT
1 TTCAAAGATGATAGATTC-TCTT
51622 TTCAAAGATGA
1 TTCAAAGATGA
51633 AAGCTTTATT
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
22 20 0.38
23 31 0.60
24 1 0.02
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:52469 original size:165 final size:166
Alignment explanation
Indices: 52150--52475 Score: 485
Period size: 165 Copynumber: 2.0 Consensus size: 166
52140 AGAATGAACA
52150 TTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTTCCAAAAAAATAATAATGAGAAA
1 TTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTT---AAAAAATAATAATGAGAAA
***
52215 ACGATTTCCATAGCTTCTCATTTTATCTTTTCTAAAATGAAATTGTTAAAAAGTAAGAAAACGAT
63 ACGATTTCCATAGCTTCTCATACAATCTTTTCTAAAATGAAATTGTTAAAAAGTAAGAAAACGAT
* *
52280 TTCCTTAGTTTTTTACTTAGTAAACTATTTCCAACAGCC
128 TTCCATAGTTTCTTACTTAGTAAACTATTTCCAACAGCC
**
52319 TTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTT-TGAAA-AATAATGAGAAAACG
1 TTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTTAAAAAATAATAATGAGAAAACG
* * * *
52382 ATTTTCATAGTTTCTCATACAATCTTTTCTAAAAATGAAATTGTTGAATAGTAAGAAAACGATTT
66 ATTTCCATAGCTTCTCATACAATCTTTTCT-AAAATGAAATTGTTAAAAAGTAAGAAAACGATTT
* *
52447 TCATAGTTTCTTACTTAGTAAACTTTTTC
130 CCATAGTTTCTTACTTAGTAAACTATTTC
52476 TCACATCTGT
Statistics
Matches: 143, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
164 40 0.28
165 60 0.42
169 43 0.30
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (166 bp):
TTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTTAAAAAATAATAATGAGAAAACG
ATTTCCATAGCTTCTCATACAATCTTTTCTAAAATGAAATTGTTAAAAAGTAAGAAAACGATTTC
CATAGTTTCTTACTTAGTAAACTATTTCCAACAGCC
Found at i:52689 original size:17 final size:17
Alignment explanation
Indices: 52667--52707 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
52657 TGAAGAAGGA
52667 AGAAGAAGTTCATAATG
1 AGAAGAAGTTCATAATG
52684 AGAAGAAGTTCATAATG
1 AGAAGAAGTTCATAATG
52701 AGAAGAA
1 AGAAGAA
52708 CTTGTTTAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.51, C:0.05, G:0.24, T:0.20
Consensus pattern (17 bp):
AGAAGAAGTTCATAATG
Found at i:52809 original size:113 final size:112
Alignment explanation
Indices: 52684--53055 Score: 579
Period size: 113 Copynumber: 3.3 Consensus size: 112
52674 GTTCATAATG
* *
52684 AGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTTGAATTCATCATTCGATGGATCA
1 AGAAGAAGTTCATAATGAGAAGAACTTATTCAACCTTTTGCTTGAATTCATCATTCGATGGATCA
*
52749 GCATTACCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
66 GCATTACCAGGTAGAGTTCATAATAAGAAGAACTCATCTG-AGAAGGA
*
52797 AGAAGAAGTTCATAATGAGAAGAACTTATTCAACCTTTCGCTTGAATTCATCATTCGATGGATCA
1 AGAAGAAGTTCATAATGAGAAGAACTTATTCAACCTTTTGCTTGAATTCATCATTCGATGGATCA
*
52862 GCATTACCAGGTAGAGTTCATAATAAGAAGAACTCATCTGAGGA-GA
66 GCATTACCAGGTAGAGTTCATAATAAGAAGAACTCATCTGAGAAGGA
* * * *
52908 AGAAGAAGTTCATAATGAGAAGAATTTATTCAACTTTTTGCTCGATTTCATCATTCGATGGATCA
1 AGAAGAAGTTCATAATGAGAAGAACTTATTCAACCTTTTGCTTGAATTCATCATTCGATGGATCA
* * *
52973 GTATTGCCAGGAAGAGTTCATAATAAGAAGAACTCATCT--GAAGGA
66 GCATTACCAGGTAGAGTTCATAATAAGAAGAACTCATCTGAGAAGGA
* * *
53018 AGAAGAAATTCATAATGAGAAGAGCTTGTTCAACCTTT
1 AGAAGAAGTTCATAATGAGAAGAACTTATTCAACCTTT
53056 GTTTGATGCT
Statistics
Matches: 239, Mismatches: 19, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
109 2 0.01
110 35 0.15
111 98 0.41
112 3 0.01
113 101 0.42
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (112 bp):
AGAAGAAGTTCATAATGAGAAGAACTTATTCAACCTTTTGCTTGAATTCATCATTCGATGGATCA
GCATTACCAGGTAGAGTTCATAATAAGAAGAACTCATCTGAGAAGGA
Found at i:52989 original size:111 final size:111
Alignment explanation
Indices: 52684--53055 Score: 575
Period size: 111 Copynumber: 3.3 Consensus size: 111
52674 GTTCATAATG
* *
52684 AGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTTGAATTCATCATTCGATGGATCA
1 AGAAGAAGTTCATAATGAGAAGAACTTATTCAACCTTTTGCTTGAATTCATCATTCGATGGATCA
* *
52749 GCATTACCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
66 GCATTACCAGGTAGAGTTCATAATAAGAAGAACTCATCTG-AGGA-GA
*
52797 AGAAGAAGTTCATAATGAGAAGAACTTATTCAACCTTTCGCTTGAATTCATCATTCGATGGATCA
1 AGAAGAAGTTCATAATGAGAAGAACTTATTCAACCTTTTGCTTGAATTCATCATTCGATGGATCA
52862 GCATTACCAGGTAGAGTTCATAATAAGAAGAACTCATCTGAGGAGA
66 GCATTACCAGGTAGAGTTCATAATAAGAAGAACTCATCTGAGGAGA
* * * *
52908 AGAAGAAGTTCATAATGAGAAGAATTTATTCAACTTTTTGCTCGATTTCATCATTCGATGGATCA
1 AGAAGAAGTTCATAATGAGAAGAACTTATTCAACCTTTTGCTTGAATTCATCATTCGATGGATCA
* * * *
52973 GTATTGCCAGGAAGAGTTCATAATAAGAAGAACTCATCTGAAG-GA
66 GCATTACCAGGTAGAGTTCATAATAAGAAGAACTCATCTGAGGAGA
* * *
53018 AGAAGAAATTCATAATGAGAAGAGCTTGTTCAACCTTT
1 AGAAGAAGTTCATAATGAGAAGAACTTATTCAACCTTT
53056 GTTTGATGCT
Statistics
Matches: 240, Mismatches: 19, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
110 35 0.15
111 101 0.42
112 3 0.01
113 101 0.42
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (111 bp):
AGAAGAAGTTCATAATGAGAAGAACTTATTCAACCTTTTGCTTGAATTCATCATTCGATGGATCA
GCATTACCAGGTAGAGTTCATAATAAGAAGAACTCATCTGAGGAGA
Found at i:53388 original size:13 final size:12
Alignment explanation
Indices: 53370--53431 Score: 58
Period size: 13 Copynumber: 5.2 Consensus size: 12
53360 AGACACTAGT
53370 TTTTATTTCATTA
1 TTTTATTT-ATTA
53383 TTTTATTTATTA
1 TTTTATTTATTA
*
53395 TTATTA-TT-TTG
1 TT-TTATTTATTA
53406 TTTTA-TTATTA
1 TTTTATTTATTA
*
53417 TATTATATTATTA
1 TTTTAT-TTATTA
53430 TT
1 TT
53432 AAATAATTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
10 5 0.12
11 10 0.24
12 8 0.20
13 18 0.44
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.71
Consensus pattern (12 bp):
TTTTATTTATTA
Found at i:53397 original size:3 final size:3
Alignment explanation
Indices: 53379--53432 Score: 55
Period size: 3 Copynumber: 19.3 Consensus size: 3
53369 TTTTTATTTC
*
53379 ATT ATT -TT ATTT ATT ATT ATT ATT -TT GTT -TT ATT ATT A-T ATT
1 ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
53421 A-T ATT ATT ATT A
1 ATT ATT ATT ATT A
53433 AATAATTAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
2 10 0.22
3 32 0.71
4 3 0.07
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.69
Consensus pattern (3 bp):
ATT
Found at i:53412 original size:19 final size:18
Alignment explanation
Indices: 53369--53417 Score: 64
Period size: 19 Copynumber: 2.7 Consensus size: 18
53359 AAGACACTAG
*
53369 TTTTTATT-TCATTATTT
1 TTTTTATTATTATTATTT
*
53386 TATTTATTATTATTATTT
1 TTTTTATTATTATTATTT
53404 TGTTTTATTATTAT
1 T-TTTTATTATTAT
53418 ATTATATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 7 0.26
18 9 0.33
19 11 0.41
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (18 bp):
TTTTTATTATTATTATTT
Found at i:53413 original size:16 final size:16
Alignment explanation
Indices: 53379--53432 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
53369 TTTTTATTTC
*
53379 ATTATTTTATT-TATT
1 ATTATTATATTATATT
* * *
53394 ATTATTATTTTGTTTT
1 ATTATTATATTATATT
53410 ATTATTATATTATATT
1 ATTATTATATTATATT
53426 ATTATTA
1 ATTATTA
53433 AATAATTAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
15 9 0.28
16 23 0.72
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.69
Consensus pattern (16 bp):
ATTATTATATTATATT
Found at i:55699 original size:20 final size:19
Alignment explanation
Indices: 55674--55715 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
55664 ATATTTTATA
55674 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
55694 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
55713 AAT
1 AAT
55716 ATCAAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:56629 original size:22 final size:22
Alignment explanation
Indices: 56598--56641 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
56588 TTTATACATC
* *
56598 TATTTTAAAAAGATTAAAGACG
1 TATTTCAAAAAAATTAAAGACG
56620 TATTTCAAAAAAATTAAAGACG
1 TATTTCAAAAAAATTAAAGACG
56642 CACTATACTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.52, C:0.07, G:0.11, T:0.30
Consensus pattern (22 bp):
TATTTCAAAAAAATTAAAGACG
Found at i:60859 original size:19 final size:18
Alignment explanation
Indices: 60835--60870 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
60825 TAATAAAATT
60835 AATTTAATAATCATAATAA
1 AATTTAATAATC-TAATAA
*
60854 AATTTATTAATCTAATA
1 AATTTAATAATCTAATA
60871 GTTATAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (18 bp):
AATTTAATAATCTAATAA
Found at i:60864 original size:27 final size:28
Alignment explanation
Indices: 60832--60894 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 28
60822 ATTTAATAAA
*
60832 ATTAATTTAATAATCATAA-TAAAATTT
1 ATTAATCTAATAATCATAATTAAAATTT
* *
60859 ATTAATCTAATAGTTATAATTAAAATTT
1 ATTAATCTAATAATCATAATTAAAATTT
*
60887 -TCAATCTA
1 ATTAATCTA
60895 GAGCATAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 23 0.74
28 8 0.26
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (28 bp):
ATTAATCTAATAATCATAATTAAAATTT
Found at i:61766 original size:2 final size:2
Alignment explanation
Indices: 61759--61784 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
61749 ATGGATATTT
61759 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
61785 CTCCAATGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:63597 original size:43 final size:43
Alignment explanation
Indices: 63536--63621 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
63526 TATAAGAAAG
*
63536 GGAGGCCTCGTTAAAACCCCTTTCATAACCGTCAAAAACACTA
1 GGAGGCCTCGTTAAAACCCCCTTCATAACCGTCAAAAACACTA
63579 GGAGGCCTCGTTAAAACCCCCTTCATAACCGTCAAAAACACTA
1 GGAGGCCTCGTTAAAACCCCCTTCATAACCGTCAAAAACACTA
63622 AGGTATCTTG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.35, C:0.31, G:0.14, T:0.20
Consensus pattern (43 bp):
GGAGGCCTCGTTAAAACCCCCTTCATAACCGTCAAAAACACTA
Found at i:64677 original size:2 final size:2
Alignment explanation
Indices: 64670--64697 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
64660 AAATATTTAA
64670 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
64698 TTAAAAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.