Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000043.1 Hibiscus syriacus cultivar Beakdansim tig00000067_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: 70261
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:2133 original size:17 final size:17
Alignment explanation
Indices: 2108--2140 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2098 ATGTTAAAAT
2108 TTTTATATTATATTTTCG
1 TTTTATATTAT-TTTTCG
2126 TTTT-TATTATTTTTC
1 TTTTATATTATTTTTC
2141 ATATATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 6 0.40
18 4 0.27
ACGTcount: A:0.18, C:0.06, G:0.03, T:0.73
Consensus pattern (17 bp):
TTTTATATTATTTTTCG
Found at i:2751 original size:22 final size:22
Alignment explanation
Indices: 2725--2791 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 22
2715 AACAAAATGC
2725 TAATAAATAAAAAATGAATAAAA
1 TAATAAATAAAAAAT-AATAAAA
2748 -AAT--ATAAAAAATAATAATAA
1 TAATAAATAAAAAATAATAA-AA
*
2768 TAATGAAAGAAAGAAATAATAAAA
1 TAAT-AAATAAA-AAATAATAAAA
2792 GGTTAAGTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
19 5 0.14
20 11 0.30
21 3 0.08
22 3 0.08
24 6 0.16
25 9 0.24
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (22 bp):
TAATAAATAAAAAATAATAAAA
Found at i:4072 original size:19 final size:19
Alignment explanation
Indices: 4040--4088 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 19
4030 CCTGGAGAAA
* * *
4040 AAAATATATGAAATTAAAT
1 AAAATAAATAAAATAAAAT
* *
4059 TAAATTAATAAAATAAAAT
1 AAAATAAATAAAATAAAAT
4078 AAAATAAATAA
1 AAAATAAATAA
4089 TATGATATAA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (19 bp):
AAAATAAATAAAATAAAAT
Found at i:4098 original size:19 final size:18
Alignment explanation
Indices: 4076--4115 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
4066 ATAAAATAAA
4076 ATAAAATAAATAATATGAT
1 ATAAAATAAATAATAT-AT
* *
4095 ATAAACTATATAATATAT
1 ATAAAATAAATAATATAT
4113 ATA
1 ATA
4116 TTTCAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.35
Consensus pattern (18 bp):
ATAAAATAAATAATATAT
Found at i:4276 original size:38 final size:38
Alignment explanation
Indices: 4097--4405 Score: 158
Period size: 38 Copynumber: 8.5 Consensus size: 38
4087 AATATGATAT
* *
4097 AAACTATATAATATATATATTTCA-AAAATATGTTTTAGA
1 AAACTATATATTATATA-ATTTCACAAAAAATGTTTTA-A
* * **
4136 AAACTATATA-T-TAT-ACTT-A-AAAAAAAGTTTCCA
1 AAACTATATATTATATAATTTCACAAAAAATGTTTTAA
* * * *
4169 AAACTATATATTACATAGTTT-TC--AAAACGTTTTAA
1 AAACTATATATTATATAATTTCACAAAAAATGTTTTAA
* *
4204 AAA-TAT-TA-TATA-AGTTTTTCA-AAAAAATGTTTTTA
1 AAACTATATATTATATA--ATTTCACAAAAAATGTTTTAA
*
4239 AAACTATATATTATATAATTTCACAAAAAATGTTTTTA
1 AAACTATATATTATATAATTTCACAAAAAATGTTTTAA
* ** *
4277 AAACTATATACTATAT-ATGTTTTC--AAAATGGTTTAA
1 AAACTATATATTATATAAT-TTCACAAAAAATGTTTTAA
* * * *
4313 AAACTATATAATATATAAACGTTT-TC--AATATGTTTTCA
1 AAACTATATATTATAT-AA--TTTCACAAAAAATGTTTTAA
* * *
4351 AAACTATATATTATATATATTTTA-AAAATAT-TTTCAA
1 AAACTATATATTATATA-ATTTCACAAAAAATGTTTTAA
*
4388 AAACTATATAATATATAA
1 AAACTATATATTATATAA
4406 ATTTTTGAAA
Statistics
Matches: 215, Mismatches: 32, Indels: 49
0.73 0.11 0.17
Matches are distributed among these distances:
31 1 0.00
32 3 0.01
33 16 0.07
34 14 0.07
35 30 0.14
36 34 0.16
37 33 0.15
38 70 0.33
39 13 0.06
40 1 0.00
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.41
Consensus pattern (38 bp):
AAACTATATATTATATAATTTCACAAAAAATGTTTTAA
Found at i:4316 original size:74 final size:72
Alignment explanation
Indices: 4226--4405 Score: 209
Period size: 74 Copynumber: 2.4 Consensus size: 72
4216 AGTTTTTCAA
* * *
4226 AAAAATGTTTTTAAAACTATATATTATATAA-TTTCACAAAAAATGTTTTTAAAACTATATACTA
1 AAAAATGTTTTAAAAACTATATAATATATAACTTT-AC--AAAATGTTTTCAAAACTATATACTA
*
4290 TATATGTTTT
63 TATATATTTT
* * * * *
4300 CAAAATGGTTTAAAAACTATATAATATATAAACGTTTTCAATATGTTTTCAAAACTATATATTAT
1 AAAAATGTTTTAAAAACTATATAATATAT-AAC-TTTACAAAATGTTTTCAAAACTATATACTAT
4365 ATATATTTT
64 ATATATTTT
*
4374 AAAAATATTTTCAAAAACTATATAATATATAA
1 AAAAATGTTTT-AAAAACTATATAATATATAA
4406 ATTTTTGAAA
Statistics
Matches: 90, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
74 66 0.73
75 20 0.22
76 1 0.01
77 3 0.03
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42
Consensus pattern (72 bp):
AAAAATGTTTTAAAAACTATATAATATATAACTTTACAAAATGTTTTCAAAACTATATACTATAT
ATATTTT
Found at i:4417 original size:38 final size:38
Alignment explanation
Indices: 4210--4443 Score: 156
Period size: 38 Copynumber: 6.1 Consensus size: 38
4200 TTAAAAATAT
* * ** *
4210 TATATAAGTTTTTCAAAAAAATGTTTTTAAAACTATATAT
1 TATATAAATTTTTC-AAAATAT-TTTCAAAAACTATATAA
** * ** *
4250 TATAT-AATTTCACAAAAAATGTTTTTAAAACTATATAC
1 TATATAAATTTTTCAAAATAT-TTTCAAAAACTATATAA
**
4288 TATAT--ATGTTTTCAAAATGGTTT-AAAAACTATATAA
1 TATATAAAT-TTTTCAAAATATTTTCAAAAACTATATAA
* * * *
4324 TATATAAACGTTTTCAATATGTTTTC-AAAACTATATAT
1 TATATAAA-TTTTTCAAAATATTTTCAAAAACTATATAA
* *
4362 TATATATA-TTTTAAAAATATTTTCAAAAACTATATAA
1 TATATAAATTTTTCAAAATATTTTCAAAAACTATATAA
* * * *
4399 TATATAAATTTTTGAAAATCATTTTCTGAAAATTATATAT
1 TATATAAATTTTTCAAAAT-ATTTTC-AAAAACTATATAA
4439 TATAT
1 TATAT
4444 TTTGTCAAAA
Statistics
Matches: 160, Mismatches: 25, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
36 29 0.18
37 23 0.14
38 77 0.48
39 11 0.07
40 20 0.12
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (38 bp):
TATATAAATTTTTCAAAATATTTTCAAAAACTATATAA
Found at i:4424 original size:75 final size:74
Alignment explanation
Indices: 4265--4443 Score: 207
Period size: 74 Copynumber: 2.4 Consensus size: 74
4255 AATTTCACAA
* * * * * *
4265 AAAATGTTTTTAAAACTATATACTATATATGTTTTCAAAATGGTTTAAAAACTATATAATATATA
1 AAAATATTTTCAAAACTATATATTATATATATTTTAAAAATAGTTTAAAAACTATATAATATATA
4330 AACGTTTTC
66 AACGTTTTC
* * *
4339 AATATGTTTTCAAAACTATATATTATATATATTTTAAAAATATTTTCAAAAACTATATAATATAT
1 AAAATATTTTCAAAACTATATATTATATATATTTTAAAAATAGTTT-AAAAACTATATAATATAT
* *
4404 AAA-TTTTTG
65 AAACGTTTTC
*
4413 AAAATCATTTTCTGAAAATTATATATTATAT
1 AAAAT-ATTTTC--AAAACTATATATTATAT
4444 TTTGTCAAAA
Statistics
Matches: 89, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
74 47 0.53
75 26 0.29
77 16 0.18
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (74 bp):
AAAATATTTTCAAAACTATATATTATATATATTTTAAAAATAGTTTAAAAACTATATAATATATA
AACGTTTTC
Found at i:6799 original size:26 final size:24
Alignment explanation
Indices: 6770--6879 Score: 104
Period size: 23 Copynumber: 4.7 Consensus size: 24
6760 AAGAGACTGG
6770 GTTTATGGAAGAGGAAGAAGAAATGA
1 GTTTATGGAA-A-GAAGAAGAAATGA
* *
6796 GTTTAT-GAAAGAA-AAGGAATGT
1 GTTTATGGAAAGAAGAAGAAATGA
* *
6818 GTTTATGG-AAGAAGAAAAAATAA
1 GTTTATGGAAAGAAGAAGAAATGA
* * *
6841 GTTTATTG-AAGAAGAAGCAACGA
1 GTTTATGGAAAGAAGAAGAAATGA
6864 GTTTATGG-AAGAAGAA
1 GTTTATGGAAAGAAGAA
6880 TGATAAATGA
Statistics
Matches: 70, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
22 18 0.26
23 42 0.60
24 1 0.01
25 3 0.04
26 6 0.09
ACGTcount: A:0.47, C:0.02, G:0.28, T:0.23
Consensus pattern (24 bp):
GTTTATGGAAAGAAGAAGAAATGA
Found at i:6878 original size:46 final size:45
Alignment explanation
Indices: 6783--6879 Score: 124
Period size: 46 Copynumber: 2.1 Consensus size: 45
6773 TATGGAAGAG
* * * * *
6783 GAAGAAGAAATGAGTTTATGAAAGAAAAGGAATGTGTTTATGGAA
1 GAAGAAAAAATAAGTTTATGAAAGAAAAGCAACGAGTTTATGGAA
6828 GAAGAAAAAATAAGTTTATTG-AAGAAGAAGCAACGAGTTTATGGAA
1 GAAGAAAAAATAAGTTTA-TGAAAGAA-AAGCAACGAGTTTATGGAA
6874 GAAGAA
1 GAAGAA
6880 TGATAAATGA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
45 21 0.47
46 24 0.53
ACGTcount: A:0.49, C:0.02, G:0.27, T:0.22
Consensus pattern (45 bp):
GAAGAAAAAATAAGTTTATGAAAGAAAAGCAACGAGTTTATGGAA
Found at i:7759 original size:40 final size:40
Alignment explanation
Indices: 7699--7792 Score: 161
Period size: 40 Copynumber: 2.4 Consensus size: 40
7689 TTTAATTCAC
* *
7699 GGAATGTAAGATTATTAGTGAGAATATAAGATTATCAGTG
1 GGAATGTAAGATTATCAGTGAGAATATAAGATTACCAGTG
7739 GGAATGTAAGATTATCAGTGAGAATATAAGATTACCAGTG
1 GGAATGTAAGATTATCAGTGAGAATATAAGATTACCAGTG
*
7779 GGAATATAAGATTA
1 GGAATGTAAGATTA
7793 CCAGGGAATA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.41, C:0.04, G:0.24, T:0.30
Consensus pattern (40 bp):
GGAATGTAAGATTATCAGTGAGAATATAAGATTACCAGTG
Found at i:7796 original size:20 final size:20
Alignment explanation
Indices: 7699--7792 Score: 134
Period size: 20 Copynumber: 4.7 Consensus size: 20
7689 TTTAATTCAC
* *
7699 GGAATGTAAGATTATTAGTG
1 GGAATATAAGATTATCAGTG
*
7719 AGAATATAAGATTATCAGTG
1 GGAATATAAGATTATCAGTG
*
7739 GGAATGTAAGATTATCAGTG
1 GGAATATAAGATTATCAGTG
* *
7759 AGAATATAAGATTACCAGTG
1 GGAATATAAGATTATCAGTG
7779 GGAATATAAGATTA
1 GGAATATAAGATTA
7793 CCAGGGAATA
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 65 1.00
ACGTcount: A:0.41, C:0.04, G:0.24, T:0.30
Consensus pattern (20 bp):
GGAATATAAGATTATCAGTG
Found at i:7809 original size:16 final size:19
Alignment explanation
Indices: 7720--7802 Score: 96
Period size: 20 Copynumber: 4.3 Consensus size: 19
7710 TTATTAGTGA
*
7720 GAATATAAGATTATCAGTGG
1 GAATATAAGATTACCAG-GG
* * *
7740 GAATGTAAGATTATCAGTGA
1 GAATATAAGATTACCAG-GG
7760 GAATATAAGATTACCAGTGG
1 GAATATAAGATTACCAG-GG
7780 GAATATAAGATTACCA-GG
1 GAATATAAGATTACCAGGG
7798 GAATA
1 GAATA
7803 AGATTACTGA
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
18 7 0.12
20 51 0.88
ACGTcount: A:0.42, C:0.07, G:0.24, T:0.27
Consensus pattern (19 bp):
GAATATAAGATTACCAGGG
Found at i:7996 original size:36 final size:37
Alignment explanation
Indices: 7951--8020 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 37
7941 AATAAGTTAG
*
7951 AAAATATTTATAT-ATTTTTTTAAAAAAATTAAATTC
1 AAAAAATTTATATAATTTTTTTAAAAAAATTAAATTC
* *
7987 AAAAAATTTATATAATTTTTTTTACAAAATTAAA
1 AAAAAATTTATATAATTTTTTTAAAAAAATTAAA
8021 AATATAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
36 12 0.40
37 18 0.60
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (37 bp):
AAAAAATTTATATAATTTTTTTAAAAAAATTAAATTC
Found at i:11549 original size:16 final size:16
Alignment explanation
Indices: 11528--11566 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
11518 AAGAGACAGG
11528 TTGCCACAAATGCCGA
1 TTGCCACAAATGCCGA
11544 TTGCCACAAATGCCGA
1 TTGCCACAAATGCCGA
11560 TTGCCAC
1 TTGCCAC
11567 CTCATATGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.28, C:0.33, G:0.18, T:0.21
Consensus pattern (16 bp):
TTGCCACAAATGCCGA
Found at i:12942 original size:2 final size:2
Alignment explanation
Indices: 12930--12984 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
12920 TTCTTTCTAT
*
12930 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
12972 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
12985 GCACACGAGA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:13052 original size:2 final size:2
Alignment explanation
Indices: 13045--13070 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
13035 CTCTTCAACA
13045 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
13071 TATGAGATTT
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):
AT
Found at i:19065 original size:20 final size:20
Alignment explanation
Indices: 19037--19093 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
19027 TTGGTTCACT
*
19037 GAATGTAAGATTACTAGTGG
1 GAATGTAAGATTACCAGTGG
*
19057 GAGTGTAAGATTACCAGTGG
1 GAATGTAAGATTACCAGTGG
*
19077 GAATATAAGATTACCAG
1 GAATGTAAGATTACCAG
19094 GGAATAAGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.37, C:0.09, G:0.28, T:0.26
Consensus pattern (20 bp):
GAATGTAAGATTACCAGTGG
Found at i:29026 original size:22 final size:22
Alignment explanation
Indices: 28993--29055 Score: 72
Period size: 22 Copynumber: 2.9 Consensus size: 22
28983 ACAGCTGAAT
*
28993 TATAATTTCAGGAGTTATTTGA
1 TATAATTTCAGGAGTTATATGA
* * * *
29015 TTTAATTCCAGGGGTTACATGA
1 TATAATTTCAGGAGTTATATGA
*
29037 TATAATTTCGGGAGTTATA
1 TATAATTTCAGGAGTTATA
29056 ACAGCTGAAT
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.30, C:0.08, G:0.21, T:0.41
Consensus pattern (22 bp):
TATAATTTCAGGAGTTATATGA
Found at i:32633 original size:17 final size:18
Alignment explanation
Indices: 32594--32641 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
32584 TATTTATGAG
*
32594 GGAATTGGAATCTGTTAA
1 GGAATTAGAATCTGTTAA
32612 GGAATTAGAATCTGTT-A
1 GGAATTAGAATCTGTTAA
32629 GGAATTAGAATCT
1 GGAATTAGAATCT
32642 AATTTCATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
17 14 0.48
18 15 0.52
ACGTcount: A:0.35, C:0.06, G:0.25, T:0.33
Consensus pattern (18 bp):
GGAATTAGAATCTGTTAA
Found at i:33417 original size:253 final size:247
Alignment explanation
Indices: 33000--33600 Score: 815
Period size: 261 Copynumber: 2.4 Consensus size: 247
32990 TCCAAGACCC
* **
33000 GACTCAACCAAAATAAAGTTTCACCCGACCTAACCCGAATATATGAATTAGAAACCGACCCGACC
1 GACTCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCGACCCGACC
* *
33065 CGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAAATGAAATATATATATATA
66 CGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAATGACTTAAATGAAATATATATATAGA
* * * *
33130 GGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATAT-TTTTTGGGTTGGGTCG
131 GGGGTATTATTATAATTATTCCTAAATATATAAGGTAAAACTATATATATATTT---TCGGGTCG
*
33194 GGTATTTTTCACCCT-AA-ACCCGACCCGAATATCACACTTAAAAAAAACCAACCC
193 GGTATTTTTCACCCTAAACACCCGACCCGAATATCACACTT-AAAAAAACCAACCA
*
33248 GAC-CAGATCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAATCCGACCCGA
1 GACTC-GACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAA-CCGACCCGA
* *
33312 CCCGAAATAATAAAAAAATTTATTTTTATTCAATAAAAATAATGACTTAATTGAAAAATATTATA
64 CCCGAAATAATAAAAAAA-TTATTTTTATTCAATAAAAACAATGACTTAAATG--AAATA-TATA
33377 TATAGAGGGGTATTATTATAATTATTCCTAAATATATAAGGTAAAACTATATATATATTTTCGGG
125 TATAGAGGGGTATTATTATAATTATTCCTAAATATATAAGGTAAAACTATATATATATTTTCGGG
* *
33442 TCGTGTATTTTTCACCCTAAACCCGAACTCGACCCGACCCGAATATCACACTTAAAAAAACCGAC
190 TCGGGTATTTTTCACCCT--A----AA--C-ACCCGACCCGAATATCACACTTAAAAAAACCAAC
33507 CA
246 CA
* *
33509 GACTCGACCAAAATAAAGTTTCACCCCACCCGACCCAAATATATGAATTAG-AA---ACCCGACC
1 GACTCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCGACCCGACC
33570 CGAAATAATAAAAAAA-TATTTTTATTCAATA
66 CGAAATAATAAAAAAATTATTTTTATTCAATA
33601 TATGAATAAG
Statistics
Matches: 316, Mismatches: 18, Indels: 32
0.86 0.05 0.09
Matches are distributed among these distances:
247 1 0.00
248 48 0.15
249 27 0.09
250 31 0.10
251 21 0.07
252 5 0.02
253 55 0.17
254 19 0.06
256 24 0.08
258 2 0.01
260 2 0.01
261 58 0.18
262 23 0.07
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.28
Consensus pattern (247 bp):
GACTCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCGACCCGACC
CGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAATGACTTAAATGAAATATATATATAGA
GGGGTATTATTATAATTATTCCTAAATATATAAGGTAAAACTATATATATATTTTCGGGTCGGGT
ATTTTTCACCCTAAACACCCGACCCGAATATCACACTTAAAAAAACCAACCA
Found at i:47962 original size:465 final size:465
Alignment explanation
Indices: 47091--48020 Score: 1851
Period size: 465 Copynumber: 2.0 Consensus size: 465
47081 GGGACAAGTT
47091 ATTTGCGTATTTTTTGTAAGGCCACTACTGTTACCTGTGTCTTTCATCTATTTATTTTGTCGGTC
1 ATTTGCGTATTTTTTGTAAGGCCACTACTGTTACCTGTGTCTTTCATCTATTTATTTTGTCGGTC
47156 AAACAACGAAAACAACATCGATTGTGCATGTAGGAACTACCTTTTACTGAACTGTGTCTTTCATC
66 AAACAACGAAAACAACATCGATTGTGCATGTAGGAACTACCTTTTACTGAACTGTGTCTTTCATC
47221 TATTCACCATGTCATACTTGCTGTATTTTCTGCTTTGCTTTTCTAATCTAATTAACTCAAAAGGT
131 TATTCACCATGTCATACTTGCTGTATTTTCTGCTTTGCTTTTCTAATCTAATTAACTCAAAAGGT
47286 TAAAGGATCTCCTTTTGTTTATGCTTTCTGGTGTGCAGCTAGTGGTCGTAGGCCAACGCTTAATC
196 TAAAGGATCTCCTTTTGTTTATGCTTTCTGGTGTGCAGCTAGTGGTCGTAGGCCAACGCTTAATC
47351 TTGAAAGACGTTTAGATCATGATGGGCATCCTCTTGCTATCGCTGCAGCTGATGCAGTTGCAGCC
261 TTGAAAGACGTTTAGATCATGATGGGCATCCTCTTGCTATCGCTGCAGCTGATGCAGTTGCAGCC
47416 AATGGAGTTCCTCCTTGGAGTTGGAGAGGGACATCCGGAAATGGTAAATTCTGTTAGAATTTTTG
326 AATGGAGTTCCTCCTTGGAGTTGGAGAGGGACATCCGGAAATGGTAAATTCTGTTAGAATTTTTG
47481 CTGAACCAATTTTAAATATGACGGTTTTGCAGAGTCTTTTGTTGGTAAGACACGGGCACGGTTTC
391 CTGAACCAATTTTAAATATGACGGTTTTGCAGAGTCTTTTGTTGGTAAGACACGGGCACGGTTTC
47546 TTCGAACTTG
456 TTCGAACTTG
47556 ATTTGCGTATTTTTTGTAAGGCCACTACTGTTACCTGTGTCTTTCATCTATTTATTTTGTCGGTC
1 ATTTGCGTATTTTTTGTAAGGCCACTACTGTTACCTGTGTCTTTCATCTATTTATTTTGTCGGTC
47621 AAACAACGAAAACAACATCGATTGTGCATGTAGGAACTACCTTTTACTGAACTGTGTCTTTCATC
66 AAACAACGAAAACAACATCGATTGTGCATGTAGGAACTACCTTTTACTGAACTGTGTCTTTCATC
47686 TATTCACCATGTCATACTTGCTGTATTTTCTGCTTTGCTTTTCTAATCTAATTAACTCAAAAGGT
131 TATTCACCATGTCATACTTGCTGTATTTTCTGCTTTGCTTTTCTAATCTAATTAACTCAAAAGGT
47751 TAAAGGATCTCCTTTTGTTTATGCTTTCTGGTGTGCAGCTAGTGGTCGTAGGCCAACGCTTAATC
196 TAAAGGATCTCCTTTTGTTTATGCTTTCTGGTGTGCAGCTAGTGGTCGTAGGCCAACGCTTAATC
47816 TTGAAAGACGTTTAGATCATGATGGGCATCCTCTTGCTATCGCTGCAGCTGATGCAGTTGCAGCC
261 TTGAAAGACGTTTAGATCATGATGGGCATCCTCTTGCTATCGCTGCAGCTGATGCAGTTGCAGCC
*
47881 AATGGAGTTCCTCCTTGGAGTTGGAGAGGGACATCCGGAAATGGTAAATTCTGTTGGAATTTTTG
326 AATGGAGTTCCTCCTTGGAGTTGGAGAGGGACATCCGGAAATGGTAAATTCTGTTAGAATTTTTG
47946 CTGAACCAATTTTAAATATGACGGTTTTGCAGAGTCTTTTGTTGGTAAGACACGGGCACGGTTTC
391 CTGAACCAATTTTAAATATGACGGTTTTGCAGAGTCTTTTGTTGGTAAGACACGGGCACGGTTTC
48011 TTCGAACTTG
456 TTCGAACTTG
48021 CTCAACTGAA
Statistics
Matches: 464, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
465 464 1.00
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Consensus pattern (465 bp):
ATTTGCGTATTTTTTGTAAGGCCACTACTGTTACCTGTGTCTTTCATCTATTTATTTTGTCGGTC
AAACAACGAAAACAACATCGATTGTGCATGTAGGAACTACCTTTTACTGAACTGTGTCTTTCATC
TATTCACCATGTCATACTTGCTGTATTTTCTGCTTTGCTTTTCTAATCTAATTAACTCAAAAGGT
TAAAGGATCTCCTTTTGTTTATGCTTTCTGGTGTGCAGCTAGTGGTCGTAGGCCAACGCTTAATC
TTGAAAGACGTTTAGATCATGATGGGCATCCTCTTGCTATCGCTGCAGCTGATGCAGTTGCAGCC
AATGGAGTTCCTCCTTGGAGTTGGAGAGGGACATCCGGAAATGGTAAATTCTGTTAGAATTTTTG
CTGAACCAATTTTAAATATGACGGTTTTGCAGAGTCTTTTGTTGGTAAGACACGGGCACGGTTTC
TTCGAACTTG
Found at i:63989 original size:2 final size:2
Alignment explanation
Indices: 63982--64010 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
63972 TTAAGATGTA
63982 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
64011 CACATTCAAG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.